==== Front Stud MycolStud. MycolStudies in Mycology0166-06161872-9797CBS Fungal Biodiversity Centre S0166-0616(18)30030-710.1016/j.simyco.2018.06.003Research PaperPhylogeny and genetic diversity of the banana Fusarium wilt pathogen Fusarium oxysporum f. sp. cubense in the Indonesian centre of origin Maryani N. nani.maryanimartawi@wur.nl123∗Lombard L. 4Poerba Y.S. 5Subandiyah S. 6Crous P.W. 24Kema G.H.J. gert.kema@wur.nl12∗1 Wageningen University and Research, Wageningen Plant Research, The Netherlands2 Wageningen University and Research, Laboratory of Phytopathology, Wageningen, The Netherlands3 Biology Education, Universitas Sultan Ageng Tirtayasa (UNTIRTA), Banten, Indonesia4 Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands5 Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia6 Entomology and Phytopathology Department, Gajah Mada University, Yogyakarta, Indonesia∗ Correspondence: N. Maryani; G.H.J. Kema nani.maryanimartawi@wur.nlgert.kema@wur.nl05 7 2018 3 2019 05 7 2018 92 155 194 © 2018 Westerdijk Fungal Biodiversity Institute. Production and hosting by ELSEVIER B.V.2018Westerdijk Fungal Biodiversity InstituteThis is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).Fusarium oxysporum f. sp. cubense (Foc), the causal agent of Fusarium wilt or Panama disease on banana, is one of the major constraints in banana production worldwide. Indonesia is the centre of origin for wild and cultivated bananas, which likely co-evolved with Foc. This study explored the widest possible genetic diversity of Foc by sampling across Indonesia at 34 geographically and environmentally different locations in 15 provinces at six islands. This resulted in a comprehensive collection of ∼200 isolates from 40 different local banana varieties. Isolates were identified and assessed using sequence analysis of the translation elongation factor-1alpha (tef1), the RNA polymerase II largest subunit (rpb1), and the RNA polymerase II second largest subunit (rpb2). Phylogenetic analyses of these genes allowed the identification of 180 isolates of Fusarium oxysporum f. sp. cubense (Foc), and 20 isolates of the Fusarium fujikuroi species complex (FFSC), the Fusarium incarnatum-equiseti species complex (FIESC), and the Fusarium sambucinum species complex (FSSC). Further analyses, incorporating a worldwide collection of Foc strains, revealed nine independent genetic lineages for Foc, and one novel clade in the Fusarium oxysporum species complex (FOSC). Selected isolates from each lineage were tested on the banana varieties Gros Michel and Cavendish to characterise their pathogenicity profiles. More than 65 % of the isolates were diagnosed as Tropical Race 4 (Foc-TR4) due to their pathogenicity to Cavendish banana, which supports the hypothesis that Foc-TR4 is of Indonesian origin. Nine independent genetic lineages for Foc are formally described in this study. This biodiversity has not been studied since the initial description of Foc in 1919. This study provides a detailed overview of the complexity of Fusarium wilt on banana and its diversity and distribution across Indonesia. Key words MorphologyNew speciesPanama diseasePathogenicityTropical Race 411 New taxaTaxonomic novelties: New species Fusarium cugenangense N. Maryani, L. Lombard, Kema & CrousF. duoseptatum N. Maryani, L. Lombard, Kema & CrousF. grosmichelii N. Maryani, L. Lombard, Kema & CrousF. hexaseptatum N. Maryani, L. Lombard, Kema & CrousF. kalimantanense N. Maryani, L. Lombard, Kema & CrousF. odoratissimum N. Maryani, L. Lombard, Kema & CrousF. phialophorum N. Maryani, L. Lombard, Kema & CrousF. purpurascens N. Maryani, L. Lombard, Kema & CrousF. sangayamense N. Maryani, L. Lombard, Kema & CrousF. tardichlamydosporum N. Maryani, L. Lombard, Kema & CrousF. tardicrescens N. Maryani, L. Lombard, Kema & Crous ==== Body Introduction Indonesia is one of the main centres of origin for banana in South-East Asia (Valmayor et al. 1999). Edible banana cultivars are descendants from two ancestral wild Musa species, Musa acuminata Colla (AA, 2n = 22) and Musa balbisiana Colla (BB, 2n = 22) (Simmonds 1962). These diversified into various edible varieties comprising diploids (AA, BB), triploids (AAA, AAB, ABB) and tetraploids (ABBB). Indonesia is the main contact area between species and subspecies of wild banana in sub-centres of diversity (Perrier et al. 2011) and, therefore, represents the primary gene centre for banana, resulting in a huge phenotypic and genotypic diversity. Indonesia is among the top 10 banana producing countries (FAOSTAT 2017) with over 200 varieties that are presently grown in almost every region of the Indonesian archipelago (Nasution 1993). The actual number of identified cultivated banana varieties could easily surpass 500. Banana is one of Indonesia's primary fruit commodities (BPS 2017), with most production supplying the domestic market. Despite this great diversity and high popularity of bananas, there are some constraints on production. The most important of these is fungal diseases, including Fusarium wilt, also known as Panama disease (Stover 1962a). Fusarium wilt is caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc), which first appeared in the 1900s in a banana plantation on Java (Stover 1962a) and thereafter disseminated to other banana production areas in Indonesia and beyond. This devastating agent of wilt on banana was first reported in the literature from samples collected in a Cuban banana plantation, and it subsequently gained notoriety as Fusarium cubense (Smith 1910). The history of Fusarium wilt on banana goes back to the 20th century when this disease eliminated thousands of hectares of the favoured Gros Michel banana in Central America. The outbreak evolved into one of the worst plant epidemics of all times. The discovery of resistant Cavendish bananas eventually quenched the epidemic and the variety was so successful that it was disseminated around the world until it attained its current predominance in the global banana trade. The resistance of Cavendish bananas to the so-called Foc-Race1 strains, which caused the epidemic in Gros Michel is unique and durable. The risk of global monocultures is evident and problems surfaced again once other pathogenic Fusarium oxysporum strains appeared that were able to cause Fusarium wilt in Cavendish plantations. A harmful strain was initially reported from Taiwan, from whence it spread further into South-East Asia, and recently to the Indian subcontinent, the Middle East and Africa (Ordonez et al. 2015). The ongoing epidemic in Cavendish bananas is caused by a unique genotype, Vegetative Compatibility Group (VCG) 01213, of Foc and is called Tropical Race 4 (TR4). It has caused significant losses in commercial and subsistence production areas of Taiwan, Malaysia, and the northern territories of Australia (Su et al., 1986, Gerlach et al., 2000, Hermanto et al., 2009). In Indonesia, Nasir et al. (1999) reported that Fusarium wilt occurred from the Aceh province of Sumatra in the far west, to the far eastern Papua province. Losses in export Cavendish plantations in southern Sumatra have exceeded 70 %. In Northern Sumatra over 1 000 ha of plantations were destroyed within 3 yr after the appearance of the disease in this area (Nasir et al. 1999). Not only was Cavendish affected, but also many local popular varieties named in Bahasa Indonesia with ‘Pisang’ (=‘banana’) variety names, such as Pisang Raja Bulu, P. Raja Sereh, P. Ambon, P. Mas and P. Barangan, were damaged. The affected varieties are very important for the local markets (Hermanto et al. 2009). To date, no control method has yet been identified or successfully implemented to effectively manage TR4. This is further complicated by the soil-borne nature of Foc and its ability to produce persistent chlamydospores that contaminate soils for decades (Booth 1971). Essentially, there are presently no control methods, except prevention by using pathogen-free tissue culture plants planted in non-infested soil (Ploetz 1994), and the adoption of quarantine strategies. However, these practices are mostly applied in large commercial plantations, but not in smallholder settings. Evidently, the development of new resistant banana cultivars would be the most effective control strategy to follow, and therefore research on the diversity of this pathogen is essential, particularly since it has been shown to be polyphyletic (O'Donnell et al., 1998, O'Donnell et al., 2009). It is therefore essential to acquire a better understanding of the differences between the genetic lineages for developing control strategies, and for effective resistance breeding. In Fusarium systematics, Foc belongs to the Fusarium oxysporum species complex (FOSC). Four clades of FOSC have been identified using translation elongation factor 1-alpha (tef1) and mitochondrial subunit rDNA (mtssu), with Foc isolates clustering as basal lineage (O'Donnell et al. 2004). The incorporation of Foc isolates from native host populations, especially those from indigenous ecosystems, will be of great importance for diversity studies of this complex species. Diversity studies on Foc isolates were conducted by using various physiological and molecular methods, which included VCGs (Moore et al. 1993), random amplified polymorphic DNA markers (RAPDs; Bentley et al. 1995), restriction fragment length polymorphisms (RFLPs; Koenig et al. 1997), amplified fragment length polymorphism (AFLP; Groenewald et al. 2006) and DNA sequence analyses (O'Donnell et al. 1998). These studies showed that the South-East Asian population of this fungus exhibits a high degree of variation, suggesting that Foc lineages co-evolved with their hosts in South-East Asia (Ploetz & Pegg 1997). However, these studies used Foc isolates from various disconnected geographical areas and lacked evidence on genetic diversity from the genetic centre of banana diversity, which is likely also the origin of the co-evolving Foc (Buddenhagen 2007). It has alternatively been suggested that Foc has multiple independent evolutionary origins, both within and outside the Musa genetic centre (Bentley et al. 1998). Using the phylogenetic genealogical approach, O'Donnell et al. (1998) identified five independent genetic lineages of Foc in a global population. Using a similar approach and additional data, Fourie et al. (2009) found three additional lineages. However, neither of these studies included Indonesian populations, and hence only limited information is available on the diversity of Foc at the centre of origin of banana. Here, we explore the genetic diversity among Indonesian Foc strains that were isolated from local banana varieties in various different ecosystems across the country. This overview of the complexity of Fusarium wilt of banana enables us to greatly improve our knowledge of the taxonomic and phylogenetic position of Foc in the FOSC. Materials and methods Isolates A comprehensive survey of Fusarium wilt of banana was undertaken in Indonesia. In total, 34 locations in 15 provinces were visited, representing the main banana-producing regions in Java, Sumatra, Kalimantan, Sulawesi, Papua, and Nusa Tenggara (Table 1, Fig. 1). Sampling expeditions to the former three islands were undertaken in 2014, whereas the other islands were sampled in 2015. Sampling locations were identified in two to three different regions in each province. Diagnostic specimen were collected from diseased banana plants displaying typical Fusarium wilt symptoms: yellowing of older leaf margins, collapsed leaves at the petioles, and pseudostem discolouration and splitting. The pseudostems of the diseased plants were cut and discoloured vascular strands were sampled and placed on sterile filter paper to dry, and were eventually packed in a paper envelope. Global positioning coordinates were recorded and ecological parameters, including soil pH, light intensity and vegetation of the sampling area were collected at each site. For each banana plant sampled, the youngest (cigar) leaf was taken for ploidy identification of the germplasm by flow-cytometry analyses and morphological characterisation following Valmayor et al. (1999) and Simmonds & Shepherd (1955), as well as in-situ comparisons with local banana varieties in the Musa collection at the Indonesian Institute of Sciences (LIPI) Cibinong, Bogor, Indonesia.Fig. 1 Map of sampling collection in 2014–2015 in the island of Java, Sumatra, Kalimantan, Sulawesi, Papua, and Flores. Fig. 1Table 1 Names and geographical details of 34 sampling locations in Indonesia for establishing the Indonesian Fusarium oxysporum f. sp. cubense collection. Table 1Province District GPS Long. Lat. Alt. (m) East Kalimantan Kutai Timur 117.62 0.68 57 Benajam 116.77 −1.62 21 Central Kalimantan Kapuas Timur 114.48 −3.10 16 Katingan 113.42 −1.71 35 Palangkaraya 114.02 −2.43 18 South Kalimantan Kota Baru 116.22 −2.58 118 Tanah Bumbu 115.74 −3.63 13 Banjar 115.03 −3.41 34 West Borneo Kubu Raya 109.29 −0.06 8 Pontianak 109.34 −0.04 17 West Java Bogor 107.10 −6.68 657 Cianjur 107.10 −7.02 875 Sukabumi 106.79 −7.01 263 Central Java Kendal 110.35 −7.20 794 Semarang 110.59 −7.00 9 Demak 110.74 −7.06 21 East Java Lumajang 113.11 −8.08 637 Bondowoso 113.94 −8.09 379 Purwodadi 112.75 −7.82 491 Jember 113.68 −8.24 39 Aceh Jantho Aceh Besar 95.63 5.35 133 North Sumatra Karo 98.25 3 NA Brastagi 98.51 3.19 NA West Sumatra Bukittinggi 100.38 −0.29 NA Padang 100.35 −0.94 NA South Sumatra Ogan Ilir 104.70 −3.29 27 Palembang 104.75 −2.99 NA Lampung Way Jepara 105.54 −5.56 NA Papua Sentani Jayapura 140.83 −2.65 NA South Sulawesi Barru 119.62 −4.08 8 Bone 120.02 −4.62 101 Maros 119.63 −5.10 48 Sidreng Rappang 119.69 −3.93 165 East Nusa Tenggara Sikka Flores 122.37 −8.61 20 Isolation The dried pseudostem samples were cut into pieces of 2 × 3 cm and plated on Komada medium (Komada 1975). After approximately 2 d, fungal colonies resembling Fusarium were transferred to potato dextrose agar (PDA) plates (Leslie & Summerell 2006). Axenic cultures were derived by streaking a small amount of conidia, collected with the tip of an inoculation needle, on water agar (WA) plates, which allowed conidia to separate. After 24 h of incubation, plates were observed under a dissection microscope at 50× magnification and single germinating conidia were collected and transferred to PDA. Monospore isolates were either maintained on PDA or in 20 % (v/v) glycerol at −80 °C. All isolates were deposited in the Indonesian Culture Collection (InaCC) Cibinong, Indonesia. Twenty-four Foc isolates, representing the known VCG's (Ordonez et al. 2015) in the global Foc collection were included for phylogenetic analyses. DNA isolation, amplification and analyses Total genomic DNA was extracted from axenic isolates grown for 7 d on PDA, using the DNA Wizard Magnetic DNA Purification System for Food kit (Promega, USA) following the protocols provided by the manufacturer. Partial gene sequences were determined for the RNA polymerase largest subunit gene (rpb1) using primers RPB1-Fa & RPB1-G2R (O'Donnell et al. 2010), the RNA polymerase second largest subunit gene (rpb2) using primers RPB2-5f2 & RPB2-7cr (O'Donnell et al. 2010), and the translation elongation factor 1-alpha gene (tef1) using primers EF1 & EF2 (O'Donnell et al. 1998). Amplicons were sequenced in both directions using the same primer pairs as were used for amplification to ensure integrity of the sequences. Consensus sequences were determined and assembled using MEGA v. 6 (Tamura et al. 2013) and compared to representative sequences from previous studies (O'Donnell et al., 1998, Fourie et al., 2009, Ordonez et al., 2015). Subsequent alignments for each individual locus were generated using MAFFT v. 7.110 (Katoh & Standley 2013) and manually corrected if necessary. The individual sequences generated in this study were compared with those maintained in the Fusarium MLST database (http://www.westerdijkinstitute.nl/fusarium/) and the NCBI's GenBank, and relevant sequences were included in the subsequent phylogenetic inference. Phylogenetic congruencies of the three loci were tested using a 70 % reciprocal bootstrap criterion (Mason-Gamer & Kellogg 1996). Phylogenetic inference in this study was based on Maximum Likelihood (ML) and Bayesian Inference (BI). The ML analysis was performed using RAxML v. 8. (randomised accelerated (sic) maximum likelihood for high performance computing) (Stamatakis 2014) through RAxML BlackBox (http://embnet.vital-it.ch/raxml-bb/index.php). Bootstrap support (BS) was determined automatically by the software to assess the robustness of the analyses. The BI analysis was performed using MrBayes v. 3.2 (Ronquist et al. 2012). A Markov Chain Monte Carlo (MCMC) algorithm of four chains was initiated in parallel from a random tree topology with a heating parameter set at 0.3. The MCMC analyses lasted until the average standard deviations of split frequencies were below 0.01 with phylogenies saved every 1 000 generations. The first 25 % of saved phylogenies were discarded as the “burn-in” phase and posterior probabilities (PP) were determined from the remaining phylogenies. All the sequences generated in this study were deposited in the European Nucleotide Archive (ENA) and the alignments in TreeBASE. Morphology All Foc isolates were grown on carnation leaf agar (CLA; Fisher et al. 1982), synthetic low-nutrient agar (SNA; Nirenberg 1981) and PDA to induce sporulation under continuous light (Osram L18W/840 Cool White) for 7 d at 25 °C. Growth rates of all isolates were determined after 7 d incubation at 25 °C in the dark on PDA. Colony colours were determined using the mycological colour charts of Rayner (1970). Gross morphological characters, including microconidia, macroconidia, chlamydospores and conidiophores, were examined (50×) after mounting fungal structures in sterile water and observed using light microscopy at 1 000× magnification. For each taxonomically informative structure, the extremes are provided, but for conidia we calculated the 95 % confidence intervals and provide extremes in parentheses. All descriptions, illustrations and nomenclatural data were deposited in MycoBank (Crous et al. 2004). Pathogenicity assays Isolates of Foc clustering in different clades based on the MLST analyses were selected for pathogenicity assays. The Foc-TR4 reference strain FocII5-NRRL 54006 (Ordonez et al. 2015) was included as a positive control, and negative controls were treated with water. For all assays, we followed the inoculum production, inoculation and diseases assessment protocols developed by Garcia-Bastidas et al. (2018, in submission) using 2–3-mo-old Cavendish and Gros Michel plants. Prior and post-inoculation greenhouse conditions were adjusted to a constant day temperature of 25 °C (ambient light until max. 16 h), a night temperature of 23 °C, and a relative humidity of ≥ 75 %. After 7 wk, disease severities were evaluated by scoring external foliage and internal corm symptoms. Results Isolates Symptoms characteristic of Fusarium wilt were observed in most of the sampling locations on a diverse suite of banana varieties in typical backyards and in a Cavendish industrial plantation (Fig. 2). In total, 40 local banana varieties showed Fusarium wilt symptoms and were sampled (Table 2, Fig. 3). However, wild banana species, including Musa acuminata var. bantamensis in West Java, M. acuminata var. rutilifes in the forest of East Java, and M. acuminata var. microcarpa and M. bornensis in Kalimantan, and the Musa-related species, Ensete glaucum in Flores, were consistently free of external Fusarium wilt symptoms. In total, 203 isolates were obtained from the symptomatic banana plants (Table 3).Fig. 2 Symptoms of Fusarium wilt on banana. A. External wilting symptom on leaves in a monoculture plantation in Lampung, Sumatra. B. External wilting symptom in a backyard home plantation in Cianjur, West Java. C. Splitting of the pseudostem. D. Internal symptoms, discoloration of the pseudostem. E. Discoloration of the corm. Fig. 2Fig. 3 Local Indonesian banana varieties. A. Pisang Raja Bulu (AAB). B. Pisang Awak (ABB). C. Pisang Ambon Hijau (AAA). D. Pisang Udang (ABB). E. Left, Pisang Raja Manten (AAB), right, Pisang Barangan (AAA). F. Pisang Mas Lampung (AA). G. Pisang Tanduk (AAB). H. Pisang Susu (AAB). I. Pisang Kepok (ABB). J. Pisang Jarum (AA). Fig. 3Table 2 List of 40 susceptible local banana varieties at six Indonesian islands from which samples were taken to isolate Fusarium oxysporum f. sp. cubense strains. Table 2Islands Banana varieties Scientific name1 Genome1 Local name Popular name International name Sumatra Pisang Ayam Pisang Barangan Lakatan Musa acuminata AAA P. Wak P. Awak Awak Musa sp. ABB P. Abe P. Kepok Saba Musa sp. ABB P. Talon P. Raja Raja Musa sp. AAB P. Barangan P. Barangan Lakatan Musa acuminata AAA P. Tanduk Bawen P. Tanduk Horn Musa sp. AAB P. Mas P. Mas Sucrier Musa acuminata AA Kalimantan P. Sanggar/Manurun/Nipah P. Kepok Saba Musa sp. ABB P. Awak/Pulau Pinang P. Awak Awak Musa sp. ABB P. Ambon P. Ambon Hijau Cavendish Musa acuminata AAA P. Susu P. Raja Sereh Silk Musa sp. AAB P. Hawa P. Awak Awak Musa sp. ABB P. Gelobok P. Awak Awak Musa sp. ABB P. Talas P. Talas NA Musa acuminata AA P. Selendang NA NA Musa acuminata AAA Dwarf Cavendish P. Kapal Dwarf Cavendish Musa acuminata AAA P. Raja P. Raja Bulu Raja Musa sp. AAB P. Kepok P. Kepok Saba Musa sp. ABB Java P. Mas Kirana P. Mas Kirana Sucrier Musa acuminata AA P. Embuk NA NA Musa sp. AAB P. Kongkong NA NA Musa acuminata AAA P. Susu P. Raja Sereh Silk Musa sp. AAB P. Glintung NA NA − NA P. Ambon P. Ambon Kuning Gros Michel Musa acuminata AAA P. Ambon Lumut P. Ambon Hijau Cavendish Musa acuminata AAA Cau Langadai P. Siem NA Musa sp. ABB Cau Apu P. Siem NA Musa sp. ABBB P. Jimbluk P. Siem Jumbo NA Musa sp. ABBB P. Uli P. Uli NA Musa acuminata AA P. Raja Nangka P. Nangka Laknau Musa acuminata AAA P. Cavendish P. Ambon Hijau Cavendish Musa acuminata AAA P. Kepok Pipik P. Kepok Putih NA Musa sp. ABB P. Raja P. Raja Bulu Raja Musa sp. AAB Papua P. Tanduk P. Tanduk Horn Musa sp. AAB P. Raja P. Raja Bulu Raja Musa sp. AAB Sulawesi P. Kepok P. Kepok Saba Musa sp. ABB P. Ambon P. Ambon Hijau Cavendish Musa acuminata AAA P. Cere NA NA Musa acuminata AAA East Nusa Tenggara P. Kepok P. Kepok Saba Musa sp. ABB P. Barangan P. Barangan Lakatan Musa acuminata AAA 1 https://www.crop-diversity.org/mgis/taxonomy. Table 3 Details of strains included in the phylogenetic analyses. Table 3Species name Accession number1 Identification2 f. sp Country Host GenBank/ENA accession3 rpb1 rpb2 tef1 Fusarium cugenangense 9InaCC F983 7 cubense Indonesia Musa sp. var. Pisang Kepok LS479559 LS479307 LS479756 InaCC F984 7 cubense Indonesia Musa sp. var. Pisang Kepok LS479560 LS479308 LS479757 NRLL 36118 7 cubense Thailand Musa sp. var. Pisang Kepok LS479477 LS479221 LS479669 NRRL 25433 7 vasinvectum Gossypium sp. LS479462 LS479202 LS479648 F. dimerum NRRL 36140 Citrus sp. HM347203 HM347218 HM347133 F. duoseptatum 4,5FocMal43 5 cubense Malaysia Musa sp. var. Pisang Rastali – LS479207 LS479653 InaCC F828 5 cubense Indonesia Musa sp. var. Pisang Rastali LS479520 LS479266 LS479715 InaCC F829 5 cubense Indonesia Musa sp. var. Pisang Rastali LS479528 LS479274 LS479723 InaCC F831 5 cubense Indonesia Musa sp. var. Pisang Rastali LS479538 LS479285 LS479734 InaCC F835 5 cubense Indonesia M. acuminata var. Dwarf Cavendish LS479567 LS479315 LS479764 InaCC F911 5 cubense Indonesia M. acuminata var. Pisang Ambon – LS479234 LS479683 InaCC F915 5 cubense Indonesia Musa sp. Pisang Raja LS479494 LS479238 LS479687 8InaCC F916 5 cubense Indonesia Musa sp. var. Pisang Kepok LS479495 LS479239 LS479688 InaCC F920 5 cubense Indonesia Musa sp. var. Pisang Hawa LS479499 LS479244 LS479693 InaCC F921 5 cubense Indonesia Musa sp. var. Pisang Hawa LS479500 LS479245 LS479694 InaCC F975 5 cubense Indonesia Musa sp. var. Pisang Awak LS479549 LS479296 LS479745 InaCC F976 5 cubense Indonesia Musa sp. var. Pisang Awak LS479550 LS479297 LS479746 InaCC F977 5 cubense Indonesia Musa sp. var. Pisang Susu LS479551 LS479298 LS479747 InaCC F978 5 cubense Indonesia Musa sp. var. Pisang Susu LS479552 LS479299 LS479748 8InaCC F979 5 cubense Indonesia Musa sp. var. Pisang Susu LS479553 LS479300 LS479749 InaCC F980 5 cubense Indonesia Musa sp. var. Pisang Susu LS479554 LS479301 LS479750 Indo80 5 cubense Indonesia Musa sp. var. Pisang Hawa LS479619 LS479387 LS479829 NRRL 36115 5 cubense Malaysia M. acuminata var. Pisang Ambon LS479475 LS479218 LS479666 NRRL 36116 5 cubense Malaysia Musa sp. var. Pisang Keling – LS479219 LS479667 F. grosmichelii 8InaCC F820 4 cubense Indonesia M. acuminata var. Pisang Ambon – LS479364 LS479810 InaCC F832 4 cubense Indonesia Musa sp. var. Pisang Awak LS479542 LS479289 LS479738 8InaCC F833 4 cubense Indonesia Musa sp. var. Pisang Awak LS479548 LS479295 LS479744 8InaCC F848 4 cubense Indonesia M. acuminata var. Pisang Ambon LS479588 LS479338 LS479786 InaCC F849 4 cubense Indonesia M. acuminata var. Pisang Ambon LS479589 LS479339 LS479787 InaCC F850 4 cubense Indonesia M. acuminata var. Pisang Ambon – LS479340 LS479788 8InaCC F851 4 cubense Indonesia M. acuminata var. Pisang Ambon – LS479341 LS479789 8InaCC F852 4 cubense Indonesia M. acuminata var. Pisang Ambon Lumut – LS479342 LS479790 InaCC F853 4 cubense Indonesia M. acuminata var. Pisang Ambon Lumut – LS479343 LS479791 InaCC F854 4 cubense Indonesia M. acuminata var. Pisang Ambon Lumut LS479591 LS479345 LS479793 InaCC F855 4 cubense Indonesia M. acuminata var. Pisang Ambon Lumut LS479592 LS479346 LS479794 InaCC F859 4 cubense Indonesia M. acuminata var. Cavendish LS479596 LS479350 LS479796 InaCC F861 4 cubense Indonesia M. acuminata var. Cavendish LS479597 LS479351 LS479797 InaCC F862 4 cubense Indonesia M. acuminata var. Cavendish LS479598 LS479352 LS479798 InaCC F863 4 cubense Indonesia Musa sp. var. Pisang Siem Jumbo LS479599 LS479353 LS479799 InaCC F867 4 cubense Indonesia M. acuminata var. Pisang Ambon Kuning – LS479360 LS479806 InaCC F868 4 cubense Indonesia M. acuminata var. Pisang Ambon Kuning – LS479361 LS479807 InaCC F884 4 cubense Indonesia M. acuminata var. Pisang Ambon LS479616 LS479382 LS479824 InaCC F887 4 cubense Indonesia Musa sp. var. Pisang Siem Jumbo LS479620 LS479388 LS479830 InaCC F888 4 cubense Indonesia Musa sp. var. Pisang Siem Jumbo LS479621 LS479389 LS479831 Indo83 4 cubense Indonesia Musa sp. var. Pisang Kepok – LS479390 – NRRL 36120 4 cubense Thailand LS479478 LS479222 LS479670 F. fujikuroi CBS 221.76 FFSC Oryza sativa – – JN695747 F. hexaseptatum 8InaCC F866 8 cubense Indonesia M. acuminata var. Pisang Ambon Kuning – LS479359 LS479805 F. incarnatum-equiseti NRRL 45997 FIESC Poaceae – GQ505850 GQ505672 F. kalimantanense 9InaCC F917 FOSC Clade 5 Nov. cubense Indonesia M. acuminata var. Pisang Ambon LS479497 LS479241 LS479690 InaCC F918 FOSC Clade 5 Nov. cubense Indonesia M. acuminata var. Pisang Ambon – LS479242 LS479691 InaCC F922 FOSC Clade 5 Nov. cubense Indonesia M. acuminata var. Pisang Ambon – LS479246 LS479695 F. longipes NRRL 20695 FSSC – GQ915493 GQ915509 F. mangiferae UMA F0924 FFSC Mangifera indica KP753435 KP753442 KP753402 F. odoratissimum 7FocII5-NRRL 54006 1 cubense Indonesia M. acuminata var. Pisang Manurung LS479459 LS479198 LS479644 InaCC F816 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479485 LS479228 LS479677 7InaCC F817 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479556 LS479304 LS479753 InaCC F818 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479584 LS479333 LS479782 InaCC F819 1 cubense Indonesia M. acuminata var. Pisang Ambon LS479600 LS479354 LS479800 InaCC F821 1 cubense Indonesia Musa sp. var. Pisang Raja LS479609 LS479374 LS479818 7InaCC F822 1 cubense Indonesia Musa sp. var. Pisang Raja LS479618 LS479386 LS479828 7InaCC F824 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479486 LS479229 LS479678 InaCC F825 1 cubense Indonesia Musa sp. var. Pisang Raja LS479496 LS479240 LS479689 7InaCC F836 1 cubense Indonesia M. acuminata var. Pisang Mas Kirana LS479577 LS479325 LS479774 InaCC F837 1 cubense Indonesia M. acuminata var. Pisang Mas Kirana LS479578 LS479326 LS479775 InaCC F838 1 cubense Indonesia M. acuminata var. Pisang Mas Kirana LS479579 LS479327 LS479776 InaCC F839 1 cubense Indonesia M. acuminata var. Pisang Mas Kirana LS479580 LS479328 LS479777 InaCC F840 1 cubense Indonesia Musa sp. var. Pisang Embuk – LS479329 LS479778 InaCC F841 1 cubense Indonesia Musa sp. var. Pisang Embuk LS479581 LS479330 LS479779 7InaCC F846 1 cubense Indonesia Musa sp. var. Pisang Susu – LS479336 LS479785 InaCC F847 1 cubense Indonesia Musa sp. var. Pisang Susu LS479587 LS479337 – 7InaCC F856 1 cubense Indonesia Musa sp. var. Pisang Siem LS479593 LS479347 – InaCC F857 1 cubense Indonesia Musa sp. var. Pisang Siem LS479594 LS479348 LS479795 InaCC F858 1 cubense Indonesia Musa sp. var. Pisang Siem LS479595 LS479349 – InaCC F864 1 cubense Indonesia Musa sp. var. Pisang Siem – LS479356 LS479802 InaCC F865 1 cubense Indonesia Musa sp. var. Pisang Siem – LS479358 LS479804 InaCC F870 1 cubense Indonesia Musa sp. var. Pisang Susu LS479602 LS479363 LS479809 InaCC F871 1 cubense Indonesia Musa sp. var. Pisang Susu – LS479365 LS479811 InaCC F873 1 cubense Indonesia Musa sp. var. Pisang Susu LS479604 LS479369 LS479814 InaCC F874 1 cubense Indonesia Musa sp. var. Pisang Susu LS479606 LS479371 – InaCC F875 1 cubense Indonesia M. acuminata var. Cavendish LS479607 LS479372 LS479816 InaCC F876 1 cubense Indonesia M. acuminata var. Cavendish LS479608 LS479373 LS479817 InaCC F877 1 cubense Indonesia Musa sp. var. Pisang Susu LS479610 LS479375 LS479819 InaCC F878 1 cubense Indonesia Musa sp. var. Pisang Susu LS479611 LS479376 – InaCC F879 1 cubense Indonesia Musa sp. var. Pisang Susu LS479612 LS479377 LS479820 InaCC F880 1 cubense Indonesia M. acuminata var. Pisang Ambon – LS479378 LS479821 InaCC F881 1 cubense Indonesia M. acuminata var. Pisang Ambon LS479613 LS479379 – InaCC F882 1 cubense Indonesia M. acuminata var. Pisang Ambon LS479614 LS479380 LS479822 InaCC F883 1 cubense Indonesia M. acuminata var. Pisang Ambon LS479615 LS479381 LS479823 InaCC F885 1 cubense Indonesia Musa sp. var. Pisang Raja – LS479384 LS479826 InaCC F890 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479623 LS479392 – 7InaCC F891 1 cubense Indonesia Musa sp. var. Pisang Glitung – LS479393 LS479833 InaCC F892 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479624 LS479394 LS479834 InaCC F893 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479625 LS479395 LS479835 InaCC F894 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479626 LS479396 LS479836 InaCC F896 1 cubense Indonesia Musa sp. var. Pisang Wak LS479629 LS479399 LS479839 InaCC F897 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479630 LS479400 LS479840 InaCC F898 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479631 LS479401 LS479841 7InaCC F899 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479632 LS479402 LS479842 InaCC F900 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479633 LS479403 LS479843 InaCC F901 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479634 LS479404 LS479844 InaCC F902 1 cubense Indonesia Musa sp. var. Pisang Talon LS479635 LS479405 LS479845 InaCC F903 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479636 LS479406 LS479846 InaCC F904 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479637 LS479407 LS479847 InaCC F905 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479638 LS479408 LS479848 InaCC F906 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479639 LS479409 LS479849 InaCC F907 1 cubense Indonesia Musa sp. var. Pisang Tanduk LS479487 LS479230 LS479679 7InaCC F908 1 cubense Indonesia Musa sp. var. Pisang Tanduk LS479488 LS479231 LS479680 7InaCC F909 1 cubense Indonesia M. acuminata var. Pisang Mas LS479489 LS479232 LS479681 InaCC F910 1 cubense Indonesia M. acuminata var. Pisang Mas LS479490 LS479233 LS479682 InaCC F912 1 cubense Indonesia M. acuminata var. Pisang Ambon LS479491 LS479235 LS479684 InaCC F919 1 cubense Indonesia Musa sp. var. Pisang Awak LS479498 LS479243 LS479692 InaCC F923 1 cubense Indonesia Musa sp. var. Pisang Raja LS479501 LS479247 LS479696 InaCC F924 1 cubense Indonesia Musa sp. var. Pisang Raja LS479502 LS479248 LS479697 InaCC F925 1 cubense Indonesia Musa sp. var. Pisang Raja LS479503 LS479249 LS479698 InaCC F926 1 cubense Indonesia Musa sp. var. Pisang Raja LS479504 LS479250 LS479699 7InaCC F927 1 cubense Indonesia Musa sp. var. Pisang Raja LS479506 LS479252 LS479701 InaCC F928 1 cubense Indonesia Musa sp. var. Pisang Raja LS479507 LS479253 LS479702 InaCC F929 1 cubense Indonesia Musa sp. var. Pisang Tanduk LS479508 LS479254 LS479703 InaCC F930 1 cubense Indonesia Musa sp. var. Pisang Tanduk LS479509 LS479255 LS479704 7InaCC F931 1 cubense Indonesia Musa sp. var. Pisang Tanduk LS479510 LS479256 LS479705 InaCC F932 1 cubense Indonesia Musa sp. var. Pisang Tanduk LS479511 LS479257 LS479706 InaCC F933 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479512 LS479258 LS479707 InaCC F934 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479514 LS479260 LS479709 InaCC F935 1 cubense Indonesia M. acuminata var. Pisang Ambon LS479515 LS479261 LS479710 7InaCC F936 1 cubense Indonesia M. acuminata var. Pisang Ambon LS479516 LS479262 LS479711 InaCC F937 1 cubense Indonesia M. acuminata var. Pisang Ambon LS479517 LS479263 LS479712 InaCC F938 1 cubense Indonesia M. acuminata var. Pisang Ambon LS479518 LS479264 LS479713 InaCC F939 1 cubense Indonesia M. acuminata var. Pisang Ambon LS479519 LS479265 LS479714 InaCC F942 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479521 LS479267 LS479716 InaCC F943 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479522 LS479268 LS479717 InaCC F944 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479523 LS479269 LS479718 InaCC F945 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479524 LS479270 LS479719 InaCC F946 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479525 LS479271 LS479720 InaCC F947 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479526 LS479272 LS479721 InaCC F948 1 cubense Indonesia M. acuminata var. Pisang Barangan LS479527 LS479273 LS479722 InaCC F953 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479529 LS479275 LS479724 InaCC F954 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479530 LS479276 LS479725 InaCC F955 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479531 LS479277 LS479726 InaCC F973 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479547 LS479294 LS479743 InaCC F985 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479562 LS479310 LS479759 InaCC F986 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479563 LS479311 LS479760 7InaCC F988 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479565 LS479313 LS479762 InaCC F989 1 cubense Indonesia Musa sp. var. Pisang Kepok LS479566 LS479314 LS479763 InaCC F990 1 cubense Indonesia Musa sp. var. Pisang Kepok Pipik LS479568 LS479316 LS479765 InaCC F994 1 cubense Indonesia M. acuminata var. Pisang Mas Kirana LS479569 LS479317 LS479766 7InaCC F997 1 cubense Indonesia M. acuminata var. Cavendish LS479572 LS479320 LS479769 7InaCC F998 1 cubense Indonesia M. acuminata var. Cavendish LS479573 LS479321 LS479770 InaCC F999 1 cubense Indonesia M. acuminata var. Cavendish LS479574 LS479322 LS479771 InaCC F1000 1 cubense Indonesia M. acuminata var. Cavendish LS479575 LS479323 LS479772 Indo4 1 cubense Indonesia M. acuminata var. Pisang Ambon LS479590 LS479344 LS479792 Indo51 1 cubense Indonesia Musa sp. var. Pisang Siem LS479601 LS479355 LS479801 Indo53 1 cubense Indonesia Musa sp. var. Pisang Siem – LS479357 LS479803 Indo61 1 cubense Indonesia Musa sp. var. Pisang Susu – LS479366 LS479812 Indo62 1 cubense Indonesia Musa sp. var. Pisang Susu – LS479367 – Indo66 1 cubense Indonesia Musa sp. var. Pisang Susu LS479605 LS479370 LS479815 Indo77 1 cubense Indonesia Musa sp. var. Pisang Kepok Pipik LS479617 LS479383 LS479825 Indo89 1 cubense Indonesia Musa sp. var. Pisang Wak LS479627 LS479397 LS479837 Indo204 1 cubense Indonesia Musa sp. var. Pisang Uli LS479561 LS479309 LS479758 Indo222 1 cubense Indonesia M. acuminata var. Cavendish LS479576 LS479324 LS479773 4JV11 1 cubense Jordan M. acuminata var. Cavendish LS479465 LS479205 LS479651 4Leb1.2C 1 cubense Lebanon M. acuminata var. Cavendish LS479466 LS479206 LS479652 NRRL 36102 1 cubense China M. acuminata var. Cavendish LS479468 LS479209 LS479655 4Pak1.1A 1 cubense Pakistan M. acuminata var. Cavendish LS479479 LS479223 LS479671 4Phi2.6C 1 cubense Philippines M. acuminata var. GCTCV218 LS479480 LS479224 LS479672 F. oxysporum CAV794 FOSC Clade 1 cubense Indonesia Musa sp. var. Pisang Rubus – – FJ664922 CAV300 FOSC Clade 1 cubense Indonesia M. acuminata var. Valery – – FJ664932 CAV1107 FOSC Clade 1 cubense Vietnam Musa sp. var. Cuoi Xiem – – FJ664950 CAV299 FOSC Clade 1 cubense Nigeria M. acuminata var. Gros Michel – – FJ664946 CAV602 FOSC Clade 2 cubense Australia M. acuminata var. Lady Finger – – FJ664957 CAV189 FOSC Clade 2 cubense Malawi Musa sp. var. Harare – – FJ664956 CAV194 FOSC Clade 2 cubense Indonesia Musa sp. var. Pisang Siem – – FJ664955 4,6,8FocCNPMF-R1 FOSC Clade 4 cubense Brazil Musa sp. var. Silk LS479457 LS479196 LS479642 NRRL 34936 FOSC Clade 3 lycopersici Solanum lycopersicum LS479460 LS479200 LS479646 NRRL 26406 FOSC Clade 3 melonis Cucumis melo LS479461 LS479201 LS479647 NRRL 54002 FOSC Clade 3 Soil LS479455 LS479194 LS479640 NRRL 26381 FOSC Clade 3 lycopersici S. lycopersicum LS479456 LS479195 LS479641 NRRL 25603 FOSC Clade 1 cubense M. acuminata – – AF008487 NRRL 22550 FOSC Clade 1 pernicosum Albizia julibrissin – – AF008506 NRRL 25357 FOSC Clade 1 Soil – – AF008481 NRRL 26035 FOSC Clade 1 canariensis Phoenix canariensis – – AF008485 NRRL 20433 FOSC Clade 2 inflexum Viciba faba – – AF008479 NRRL 25607 FOSC Clade 2 cubense M. acuminata x M. balbisiana – – AF008489 NRRL 25609 FOSC Clade 2 cubense M. acuminata x M. balbisiana – – AF008490 NRRL 26022 FOSC Clade 2 cubense M. acuminata x M. balbisiana – – AF008491 NRRL 25598 FOSC Clade 2 glycines Glycine sp. – – AF008496 NRRL 26178 FOSC Clade 2 melonis Cucumis melo – – AF008503 NRRL 25420 FOSC Clade 2 vasinvectum Gossypium hirsutum – – AF008512 NRRL 25369 FOSC Clade 2 Terminalia ivorensis – – AF008482 NRRL 26406 FOSC Clade 3 melonis C. melo – – AF008504 NRRL 26379 FOSC Clade 3 radicis-lycopersici S. esculentum – – AF008508 NRRL 22549 FOSC Clade 3 passiflorae Passiflora edulis – – AF008505 NRRL 26033 FOSC Clade 3 radicis-lycopersici S. esculentum – – AF008507 NRRL 26574 FOSC Clade 3 erythroxily Erythroxylum coca – – AF008495 NRRL 26383 FOSC Clade 3 lycopersici S. esculentum – – AF008502 NRRL 26380 FOSC Clade 3 lycopersici S. esculentum – – AF008509 NRRL 26029 FOSC Clade 3 cubense M. acuminata X M. balbisiana – – AF008493 NRRL 22555 FOSC Clade 3 tuberosi S. tuberosum – – AF008511 NRRL 26203 FOSC Clade 3 lycopersici S. esculentum – – AF008501 NRRL 26374 FOSC Clade 3 Homo sapiens – – AF008483 NRRL 25594 FOSC Clade 4 batatas Ipomoea batatas – – AY337717 NRRL 26360 FOSC Clade 4 – – AY527522 F. phialophorum 4,5FocIndo25 3 cubense Indonesia M. acuminata var. Pisang Ambon LS479464 LS479204 LS479650 4,5FocST4.98 3 cubense Spain M. acuminata var. Dwarf Cavendish LS479484 LS479227 LS479676 InaCC F826 3 cubense Indonesia Musa sp. var. Pisang Wak LS479505 LS479251 LS479700 InaCC F827 3 cubense Indonesia Musa sp. var. Pisang Wak LS479513 LS479259 LS479708 InaCC F830 3 cubense Indonesia Musa sp. var. Pisang Kepok LS479536 LS479282 LS479731 InaCC F834 3 cubense Indonesia M. acuminata var. Pisang Selendang LS479557 LS479305 LS479754 InaCC F842 3 cubense Indonesia Musa sp. var. Pisang Embuk LS479582 LS479331 LS479780 InaCC F843 3 cubense Indonesia Musa sp. var. Pisang Embuk LS479583 LS479332 LS479781 8InaCC F844 3 cubense Indonesia Musa sp. var. Pisang Susu LS479585 LS479334 LS479783 InaCC F845 3 cubense Indonesia Musa sp. var. Pisang Susu LS479586 LS479335 LS479784 InaCC F869 3 cubense Indonesia M. acuminata var. Pisang Ambon Kuning – LS479362 LS479808 InaCC F889 3 cubense Indonesia M. acuminata var. Pisang Ambon Kuning LS479622 LS479391 LS479832 InaCC F969 3 cubense Indonesia Musa sp. var. Pisang Wak LS479543 LS479290 LS479739 InaCC F970 3 cubense Indonesia Musa sp. var. Pisang Wak LS479544 LS479291 LS479740 8InaCC F971 3 cubense Indonesia Musa sp. var. Pisang Wak LS479545 LS479292 LS479741 InaCC F972 3 cubense Indonesia Musa sp. var. Pisang Wak LS479546 LS479293 LS479742 InaCC F980 3 cubense Indonesia Musa sp. var. Pisang Kepok LS479555 LS479302 LS479751 InaCC F981 3 cubense Indonesia Musa sp. var. Pisang Kepok – LS479303 LS479752 InaCC F982 3 cubense Indonesia Musa sp. var. Pisang Kepok LS479558 LS479306 LS479755 InaCC F987 3 cubense Indonesia Musa sp. var. Pisang Kepok LS479564 LS479312 LS479761 InaCC F995 3 cubense Indonesia M. acuminata var. Pisang Kongkong LS479570 LS479318 LS479767 8InaCC F996 3 cubense Indonesia M. acuminata var. Pisang Kongkong LS479571 LS479319 LS479768 Indo64 3 cubense Indonesia Musa sp. var. Pisang Susu LS479603 LS479368 LS479813 NRRL 36101 3 cubense Australia Musa sp. var. Mons Mari LS479467 LS479208 LS479654 NRRL 36103 3 cubense Philippines M. acuminata var. Cavendish LS479469 LS479210 LS479656 NRRL 36109 3 cubense Australia Musa sp. var. SH 3142 LS479471 LS479214 LS479661 NRRL 36110 3 cubense Australia Musa sp. var. Mons – – LS479662 NRRL 36112 3 cubense South Africa M. acuminata var. Cavendish LS479473 LS479216 LS479664 4,6Race1.0124 3 cubense Cuba LS479483 – LS479675 F. proliferatum NRRL 62905 FFSC KU171687 KU171707 KU171727 F. purpurascens ATCC76244 2 cubense USA M. acuminata var. Apple – LS479199 LS479645 InaCC F823 2 cubense Indonesia Musa sp. var. Pisang Kepok LS479628 LS479398 LS479838 8InaCC F886 2 cubense Indonesia Musa sp. var. Pisang Kepok – LS479385 LS479827 InaCC F913 2 cubense Indonesia Musa sp. var. Pisang Kepok LS479492 LS479236 LS479685 InaCC F914 2 cubense Indonesia Musa sp. var. Pisang Kepok LS479493 LS479237 LS479686 8InaCC F966 2 cubense Indonesia Musa sp. var. Pisang Kepok LS479539 LS479286 LS479735 InaCC F967 2 cubense Indonesia Musa sp. var. Pisang Kepok LS479540 LS479287 LS479736 InaCC F968 2 cubense Indonesia Musa sp. var. Pisang Kepok LS479541 LS479288 LS479737 NRRL36107 2 cubense Honduras Musa sp. var. Maqueno – LS479213 LS479659 F. sacchari NRRL 13999 FFSC – – AF160278 F. sangayamense 9InaCC F960 FOSC Clade 5 Nov. cubense Indonesia Musa sp. var. Pisang Kepok LS479537 LS479283 LS479732 InaCC F961 FOSC Clade 5 Nov. cubense Indonesia Musa sp. var. Pisang Kepok – LS479284 LS479733 F. tardichlamydosporum 4,6FocCNPMF-R2 6 cubense Brazil Musa sp. var. Monthan LS479458 LS479197 LS479643 InaCC F956 6 cubense Indonesia M. acuminata var. Pisang Barangan LS479532 LS479278 LS479727 InaCC F957 6 cubense Indonesia M. acuminata var. Pisang Barangan LS479533 LS479279 LS479728 8InaCC F958 6 cubense Indonesia M. acuminata var. Pisang Barangan LS479534 LS479280 LS479729 InaCC F959 6 cubense Indonesia M. acuminata var. Pisang Barangan LS479535 LS479281 LS479730 NRRL 36105 6 cubense Honduras Musa sp. var. Bluggoe LS479470 LS479211 LS479657 NRRL 36106 6 cubense Australia M. acuminata var. Lady finger – LS479212 LS479658 NRRL 36108 6 cubense Tanzania Musa sp. var. Ney Poovan – – LS479660 NRRL 36111 6 cubense Australia Musa sp. var. Bluggoe LS479472 LS479215 LS479663 NRRL 36117 6 cubense Malaysia Musa sp. var. Pisang awak legor LS479476 LS479220 LS479668 F. tardicrescens NRRL 36113 9 cubense Malawi Musa sp. var. Harare LS479474 LS479217 LS479665 NRRL 37622 9 pisi Cicer sp. LS479463 LS479203 LS479649 NRRL 54005 9 raphani Raphanus sp. LS479482 LS479226 LS479674 NRRL 54008 9 conglutinans Raphanus sp. LS479481 LS479225 LS479673 F. verticilloides NRRL 20956 FFSC Zea mays – – FN552074 Fusarium sp. InaCC F872 FFSC Indonesia Musa sp. var. Pisang Raja Nangka – LS479850 LS479441 InaCC F940 FIESC Indonesia M. acuminata var. Pisang Cere – LS479855 LS479443 InaCC F941 FIESC Indonesia M. acuminata var. Pisang Cere – LS479856 LS479444 9InaCC F950 FFSC Indonesia Musa sp. var. Pisang Kepok LS479870 LS479852 – InaCC F951 FFSC Indonesia Musa sp. var. Pisang Kepok LS479871 LS479853 – InaCC F952 FFSC Indonesia Musa sp. var. Pisang Kepok LS479872 LS479854 – InaCC F962 FFSC Indonesia M. acuminata var. Pisang Talas – LS479868 LS479453 InaCC F963 FIESC Indonesia Musa sp. var. Pisang Awak LS479875 LS479859 LS479445 InaCC F964 FIESC Indonesia Musa sp. var. Pisang Awak LS479876 LS479860 LS479446 InaCC F965 FIESC Indonesia M. acuminata var. Pisang Talas LS479877 LS479863 LS479448 9InaCC F974 FSSC Indonesia Musa sp. var. Pisang Awak LS479880 LS479866 LS479451 InaCC F991 FFSC Indonesia Musa sp. var. Pisang Kepok LS479881 LS479867 LS479452 9InaCC F992 FFSC Indonesia M. acuminata var. Pisang Mas Kirana LS479882 LS479869 LS479454 InaCC F993 FFSC Indonesia M. acuminata var. Pisang Mas Kirana – LS479851 LS479442 Indo161 FIESC Indonesia M. acuminata var. Pisang Talas LS479873 LS479857 – Indo167 FIESC Indonesia Musa sp. var. Pisang Kepok LS479874 LS479858 – Indo 174 FIESC Indonesia Musa sp. var. Pisang Awak – LS479861 – Indo175 FIESC Indonesia M. acuminata var. Pisang Talas – LS479862 LS479447 Indo186 FIESC Indonesia Musa sp. var. Pisang Kepok LS479878 LS479864 LS479449 Indo188 FIESC Indonesia Musa sp. var. Pisang Awak LS479879 LS479865 LS479450 1 InaCC: Indonesian Culture Collection, Research Center for Biology, Indonesian Institute of Sciences (LIPI) Cibinong, Indonesia; ATCC: American Type Culture Collection, U.S.A.; CAV: Forestry Agricultural Biotechnology Institutre (FABI), University of Pretoria South Africa; CBS: The Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; Indo: Collection of N. Maryani at Wageningen Plant Research, Wageningen University, The Netherlands; NRRL: Agricultural Research Service Culture Collection, USA; UMAF: Microbiology and Plant Pathology Laboratory Collection, University of Malaga, Spain. 2 Foc lineage/FOSC clade/Fusarium species complex. 3 rbp1: RNA polymerase II largest subunit; rpb2: RNA polymerase II second largest subunit; tef1: translation elongation factor-1alpha. 4 Collection of Wageningen Plant Research, Wageningen University, The Netherlands. 5 Ecosciences Precinct, Brisbane Australia. 6 Embrapa Cassava & Tropical Fruits, Brazil. 7 Pathogenic on Cavendish and Gros Michel (Tropical Race 4). 8 Pathogenic on Gros Michel (Race 1). 9 Non-pathogenic on Cavendish and Gros Michel. Phylogenetic analyses Approximately 632 bp were determined for tef1, 864 bp for rpb2 and 1 444 bp for the rpb1 gene regions. The congruency analyses revealed no conflicts in tree topologies, with only minor differences in branch support. Therefore, the sequences of the three loci were combined in a single dataset for subsequent analyses. For the BI and ML analyses, a GTR+I+G model was selected for all three gene regions and incorporated into the analyses. The ML tree topology confirmed the tree topologies obtained from the BI analyses, and therefore, only the ML tree is presented. The combined tef1, rpb1 and rpb2 sequences dataset included 244 ingroup taxa and F. dimerum (NRRL 36140) as outgroup taxon. This dataset consisted of 2 909 characters, which yielded a single best ML tree with −InL = -9286.260647 (Fig. 4). The BI lasted for 11 M generations, and the consensus tree, with posterior probabilities, was calculated from 8 251 trees left after 2 750 trees were discarded as the “burn-in” phase.Fig. 4 Maximum likelihood tree inferred from the combined rpb1, rpb2 and tef1 genes sequence data set of 244 isolates. The bootstrap support values (BP) and Bayesian posterior probabilities (PP) are given at nodes. Coloured blocks indicate the various Fusarium species complexes included. The tree is rooted to Fusarium dimerum (NRRL 36140). Fig. 4 Phylogenetic inference of the three gene regions placed all isolates recovered from the symptomatic samples in the genus Fusarium (Fig. 4). Of these, 180 isolates clustered in the FOSC clade, one isolate clustered in the Fusarium sambucinum species complex (FSSC) closely related to F. longipes, 11 isolates clustered in the Fusarium incarnatum-equiseti species complex (FIESC), and eight isolates clustered in the Fusarium fujikuroi species complex (FFSC). The highest phylogenetic support was obtained using the tef1 and rpb1 gene regions. The rpb2 gene region displayed less resolution of the isolates, between the various Fusarium species complexes and within each complex. The clades representing FIESC and FSSC resolved in this study were highly supported (BS = 100 %; PP = 1). The FFSC resolved FOSC and other members of the FFSC into two highly supported clades (BP = 100 %; PP = 1 & BP = 97 %; PP = 1, respectively). In the FOSC, using the single gene analyses of tef1, and after incorporation of the dataset of O'Donnell et al. (2004) and Fourie et al. (2009), two clades were resolved as in the previous study (O'Donnell et al. 2004; Fig. 5). None of the Indonesian isolates resided in Clade 3. A single isolate, representing FocCNPMF.R1 (Dita et al. 2010), clustered in the FOSC Clade 4. The phylogeny, however, revealed one new clade in the FOSC (BP = 100 %, PP = 1.0), assigned to FOSC Clade 5, comprising five isolates that were isolated from Pisang Kepok (ABB, 2n = 33) and Pisang Ambon (AAA, 2n = 33) in Central and South Kalimantan.Fig. 5 Maximum likelihood tree inferred from the tef1 gene sequence data set of 183 Indonesian isolates in the FOSC clade. Included are representatives of the studies by O'Donnell et al., 1998, O'Donnell et al., 2004 and Fourie et al. (2009), indicated in bold. The bootstrap support values >70 % (BS) and Bayesian posterior probabilities >0.95 (PP) are given at nodes. The tree is rooted to Fusarium fujikuroi (CBS 221.76). Fig. 5 Further analyses of the Foc phylogeny using the combined tef1, rpb1 and rpb2 dataset included 216 ingroup taxa and F. fujikuroi (CBS 221.76.) as an outgroup taxon (Fig. 6). The majority of Indonesian isolates clustered in Clade 1, including eight previously established Foc lineages (Fig. 6; O'Donnell et al., 1998, Fourie et al., 2009), and the overall phylogeny revealed nine independent clonal lineages (Fig. 6). The Indonesian Foc isolates were equally distributed across the nine lineages except for L9 that did not include any Indonesian isolate. We did not identify significant correlation between the origin of the isolates and host genotypes.Fig. 6 Maximum likelihood tree inferred from the combined rpb1, rpb2 and tef1 genes sequence data sets. The bootstrap support values >70 % (BS) and Bayesian posterior probabilities >0.95 (PP) are given at nodes. Foc lineages are numbered based on the consensus from single and combine gene data sets represented by the coloured blocks. The tree is rooted to Fusarium fujikuroi (CBS 221.76). Fig. 6 Taxonomy Based on phylogenetic inference and morphological observations, several novel Fusarium taxa could be identified in this study, and these are described below. Foc Lineage L1 Fusarium odoratissimum N. Maryani, L. Lombard, Kema & Crous, sp. nov. MycoBank MB826800. Fig. 7, Fig. 8. Fig. 7 Fusarium odoratissimum (InaCC F817). A. Culture grown on PDA. B–C. Sporodochia on carnation leaves. D–E. Sporodochial branched conidiophores with monophialides. F. False head. G. Falcate-shaped macroconidia. H. Microconidia. I. Chlamydospores. J. Polyphialides. Scale bars D–J = 10 µm. Fig. 7Fig. 8 Fusarium odoratissimum (ex-type InaCC F822). A. Culture grown on PDA. B. Sporodochia on carnation leaves. C. Monophialides with initial conidia being formed. D. Falcate-shaped macroconida. E. Branched conidophores. F. Elliptical microconidia. G. Thick-walled chlamydospores. Scale bars C–G = 10 µm. Fig. 8 Etymology: Name refers to the strong odour associated with older cultures. Macroconidia abundant on CLA, less abundant on PDA and SNA, formed on sporodochia on CLA and on aerial conidiophores on SNA and PDA, falcate, (44–)59–75(–79) × 6–8 μm (av. 67 × 7  μm), 0–6-septate, with apical cells papillate, basal cells foot-shaped. Conidiogenous cells mono- or polyphialidic on sporodochia, or formed directly on hyphae (lateral phialides), 12–28 × 4–8 μm. Microconidia abundant on PDA and SNA, less frequent on CLA, oval to ellipsoid, (6–)8–16(–23) × (4–)6(–8) μm (av. 12 × 5 μm), 0–3-septate, arranged in false heads on branched conidiophores carried on hyphae. Aerial conidiophores rare on CLA and SNA but formed abundantly on PDA, branched sparsely or formed laterally. Chlamydospores globose to subglobose, formed intercalarily or terminally, single or in pairs, (7–)9–13(–14) × (7–)8–11(–12) μm, rarely produced on SNA after 7 d, rough-walled. Culture characteristics: Colony on PDA showing optimal growth at 25 °C with an average growth rate of 4.5–5.0 mm/d. Colony reverse, uniformly white and unpigmented. Colony surface dry, cottony, white, with filamentous margin. No exudates observed. Aerial mycelium abundant, cottony, with abundant sporulation. Sporodochia formed abundantly on CLA after 7 d, pale orange. Geography and host: Kutai Timur, East Kalimantan, Musa sp. var. Pisang Kepok (ABB). Pathogenicity: Pathogen on Gros Michel (AAA) and Cavendish (AAA). Material examined: Indonesia, Kampung Salak Martadinata, Kutai Timur, East Kalimantan (117°26′850″E and 0°11′590″N), on infected pseudostem of Musa sp. var. Pisang Kepok (ABB), 16 Jun. 2014, N. Maryani (holotype preserved as metabolically inactive culture, InaCC F822). Notes: Fusarium odoratissimum formed a small cryptic clade within the L1 cluster (Fig. 6), and can be distinguished by the septation of its macroconidia (0–6-septate) and microconidia (0–3-septate), characteristics not common for F. oxysporum (Leslie & Summerell 2006). This species also produces chlamydospores relatively more rapidly than was observed for other Fusarium isolates examined in this study. F. odoratissimum and all isolates in L1 produce a strong peculiarly stale odour in mature cultures, of which the causal volatiles remain to be characterised. Pathogenicity tests showed that F. odoratissimum and all isolates in L1 were able to infect Cavendish and Gros Michel bananas. Isolates in this lineage were thus classified as Foc-TR4. Foc Lineage L2 Fusarium purpurascens N. Maryani, L. Lombard, Kema & Crous, sp. nov. MycoBank MB826801. Fig. 9. Fig. 9 Fusarium purpurascens (ex-type InaCC F886). A. Culture grown on PDA. B–C. Sporodochia grown on carnation leaves. D. Falcate-shaped macroconidia. E. False heads. F. Microconidia. G. Monophialides. Scale bars D–G = 10 µm. Fig. 9 Etymology: Name reflects the purple pigmentation which was observed when cultivated on potato dextrose agar. Macroconidia abundant on CLA, less abundant on PDA and SNA, formed on sporodochia on CLA and on aerial conidiophores on SNA and PDA, falcate (50–)55–63(–67) × (4–)6–7(–9) μm (av. 59 × 7 μm), 3–5-septate, with apical cells papillate, basal cells foot-shaped. Conidiogenous cells mono- or polyphialidic on sporodochia, or formed directly from hyphae (lateral phialides), 5–45 × 3–8 μm. Microconidia abundant on PDA and SNA, less frequent on CLA, ovoid to ellipsoid, (8–)18(–37) × (3–)5(–6) μm (av. 12 × 4 μm), 0–1-septate, arranged in false heads on branched conidiophores carried on hyphae. Aerial conidiophores rare on CLA and SNA, and formed abundantly on PDA, branched sparsely or formed laterally. Chlamydospores not observed. Culture characteristics: Colony on PDA showing optimal growth at 25 °C with an average growth rate of 4.4–4.8 mm/d. Colony reverse, livid purple. Colony surface dry, cottony, white, filamentous in the centre and livid purple towards the margin, forming exudate droplets. Aerial mycelium abundant, cottony, with moderate sporulation. Sporodochia formed abundantly on CLA after 7 d, pale orange. Geography and host: Kutai Timur, East Kalimantan, Musa sp. var. Pisang Kepok (ABB). Pathogenicity: Pathogen on Gros Michel (AAA). Material examined: Indonesia, Kampung Salak Martadinata, Kutai Timur, East Kalimantan (117°26′684″E, 0°26′684″N), on infected pseudostem of Musa sp. var. Pisang Kepok (ABB), 17 Jun. 2014, N. Maryani (holotype preserved as metabolically inactive culture, InaCC F886). Notes: Fusarium pupurascens exhibits the strongest purple colony colour on PDA of all the isolates with purple colonies. It is relatively slow-growing compared to other isolates clustered in lineage L1. No chlamydospores were observed for this species, in contrast to other L1 members, which readily produce chlamydospores in culture. Furthermore, F. purpurascens produces exudate droplets, something not observed among other L1 isolates. Older cultures become pigmented, a distinctive phenomenon rarely seen in L1. F. purpurascens and other isolates in this lineage were able to infect Gros Michel, and were therefore classified as Foc-Race1. Foc Lineage L3 Fusarium phialophorum N. Maryani, L. Lombard, Kema & Crous, sp. nov. MycoBank MB826802. Fig. 10. Fig. 10 Fusarium phialophorum (ex-type InaCC F971) A. Culture grown on PDA. B–C. Sporodochia on carnation leaves. D. Aerial conidiophore on carnation leaves. E–F. Sporodochial phialides. G. Falcate-shaped macroconidia. H. Microconidia. I. False head. J. Lateral monophialides with long collaretes. K. Thick-walled chlamydospores. Scale bars E–K = 10 µm. Fig. 10 Etymology: Name refers to its elongated phialidic collarettes observed in culture. Macroconidia abundant on CLA, less abundant on PDA and SNA, formed on sporodochia on CLA and on aerial conidiophores on SNA and PDA, falcate, (50–)54–60(–62) × (3–)4–5(–7) μm (av. 57 × 7 μm), 2–5-septate, with apical cells papillate, basal cells foot-shaped. Conidiogenous cells monophialidic on sporodochia, or formed directly from hyphae (lateral phialides) with elongated collarettes, 7–41 × 3–7 μm. Microconidia abundant on PDA, less frequent on CLA, ovoid to ellipsoid, (6–)7–16(–24) × (3–)4(–6) μm (av. 12 × 5 μm), 0–1-septate, arranged in false heads on branched or lateral conidiophores carried on hyphae. Aerial conidiophores rare on CLA and SNA and formed abundantly on PDA, branched sparsely or forming short lateral conidiophores. Chlamydospores globose to subglobose, formed terminally, single or in pairs, (8–)9–12(–13) × (9–)10(–11) μm, rarely produced on SNA after 7 d, rough-walled. Culture characteristics: Colony on PDA showing optimal growth at 25 °C with an average growth rate of 4.9–5.2 mm/d. Colony reverse, uniformly white and unpigmented. Colony surface dry, cottony, white, filamentous margin. No exudates observed. Aerial mycelium abundant, cottony, with high sporulation. Sporodochia formed abundantly on CLA after 7 d, pale orange to orange. Geography and host: Tanah Bumbu, South Kalimantan, Musa sp. var. Pisang Awak (ABB). Pathogenicity: Pathogen on Gros Michel (AAA). Materials examined: Indonesia, Kampung Betung, Tanah Bumbu, South Kalimantan (115°37′477″E, 3°37′45″S), on infected pseudostem of Musa sp. var. Pisang Awak (ABB), 20 Jun. 2014, N. Maryani (holotype preserved as metabolically inactive culture, InaCC F971). Notes: Fusarium phialophorum has elongated phialidic collarettes, which are rarely found in other lineages. Polyphialidic conidiophores were not found, and chlamydospores were formed, but were rare. Isolates in this lineage were able to infect Gros Michel but not Cavendish, and were therefore classified as Foc-Race1. Foc Lineage L4 Fusarium grosmichelii N. Maryani, L. Lombard, Kema & Crous, sp. nov. MycoBank MB826803. Fig. 11. Fig. 11 Fusarium grosmichelii (ex-type InaCC F833). A. Culture grown on PDA. B. Sporodochia on carnation leaves. C. Aerial conidiophores from stereo microscope. D. Falcate-shaped macroconidia. E. Microconidia. F. Chlamydospores. G–H. Sporodochial phialides. I. False heads. J. Polyphialides. K. Branched conidiophore. Scale bars D–F, H–K = 10 µm, G = 20 µm. Fig. 11 Etymology: Name reflects its association with the banana variety Gros Michel. Macroconidia abundant on CLA, less abundant on PDA and SNA, formed on sporodochia on CLA and on aerial conidiophores on SNA and PDA, falcate, (47–)51–59(–64) × (5–)6–8(–9) μm (av. 55 × 7 μm), 3–5-septate, with apical cells papillate, basal cells foot-shaped. Conidiogenous cells mono- or polyphialidic on sporodochia, on branched conidiophores, or formed directly from hyphae (lateral phialides), (8–)16–28(–36) × (3–)4–6(–7) μm. Microconidia abundant on PDA and SNA, less frequent on CLA, ovoid to ellipsoid, (4–)9–17(–21) × (3–)4–6(–7) μm (av. 12 × 5 μm), 0–1-septate, arranged in false heads on branched or lateral conidiophores carried on hyphae. Chlamydospores globose to subglobose, formed terminally or intercalarily, single or in clumps, rarely produced on SNA after 7 d, rough-walled. Culture characteristics: Colony on PDA showing optimal growth at 25 °C with an average growth rate of 4.7–5.0 mm/d. Colony reverse in the dark uniformly white and unpigmented. Colony surface dry, cottony white with filamentous margin. No exudates observed. Aerial mycelium abundant, cottony, with abundant sporulation. Sporodochia formed abundantly on CLA after 7 d, pale orange to orange. Geography and host: Bogor, West Java, Musa acuminata var. Pisang Ambon Lumut (AAA). Pathogenicity: Pathogen on Gros Michel (AAA). Materials examined: Indonesia, Suakarya Megamendung, Bogor, West Java (106°54′214″E, 6°41′185″N), on infected pseudostem Musa acuminata var. Pisang Ambon Lumut (AAA), 10 Jul. 2014, N. Maryani, (holotype preserved as metabolically inactive culture InaCC F833). Notes: Fusarium grosmichelii is morphologically very similar to F. phialophorum, but differs in having a higher number of septa in its macroconidia (3–5-septate). F. grosmichelii and others in this lineage are morphologically similar to F. odoratissimum, but F. grosmichelii was not able to infect Cavendish. Most of the isolates in L4 were tested on Gros Michel, and were able to cause disease, and were thus classified as Foc-Race1. Foc Lineage L5 Fusarium duoseptatum N. Maryani, L. Lombard, Kema & Crous, sp. nov. MycoBank MB826804. Fig. 12. Fig. 12 Fusarium duoseptatum (ex-type InaCC F916). A. Culture grown on PDA. B–C. Sporodochia on carnation leaves. D. Falcate-shaped macroconidia. E. Microconidia. F. Polyphialidic conidiogenous cells. G. False heads. H. Chlamydospores. Scale bars D–H = 10 µm. Fig. 12 Etymology: Name reflects the fact that its microconidia are frequently 2-septate. Macroconidia abundant on CLA, less abundant on PDA and SNA, formed on sporodochia on CLA and on aerial conidiophores on SNA and PDA, falcate, (50–)53–63(–68) × (5–)6–8(–9) μm (av. 58 × 7 μm), 3–5-septate, with apical cells papillate, basal cells foot-shaped. Conidiogenous cells mono- or polyphialidic on sporodochia, or on aerial hyphae, or formed directly from hyphae as lateral phialides, (5–)9–25(–38) × (3–)4–7(–9) μm. Microconidia abundant on PDA and SNA, less frequent on CLA, ovoid to ellipsoid, (9–)21(–33) × (2–)3(–6) μm (av. 15 × 5 μm), 0–2-septate, arranged in false heads on branched conidiophores carried on hyphae. Aerial conidiophores rare on CLA and SNA, formed abundantly on PDA, branched sparsely or formed laterally. Chlamydospores globose to subglobose, formed laterally, intercalary or terminally, single or in pairs, (6–)8–10(–11) × (6–)7–9(–11) μm, abundantly produced on SNA after 7 d, rough-walled. Culture characteristics: Colony on PDA showing optimal growth at 25 °C with an average growth rate of 3.8–4.1 mm/d. Colony reverse violet, mycelium becoming purple, and pigmented with age. Colony surface dry, cottony violet in the centre, and white towards the margin. No exudates observed. Aerial mycelium abundant, cottony, with moderate sporulation. Sporodochia formed abundantly on CLA after 7 d, pale orange to orange. Geographic and host: Kapuas, Central Kalimantan, Musa sp. var. Pisang Kepok (ABB). Pathogenicity: Pathogen on Gros Michel (AAA). Material examined: Indonesia, Serapat tengah, Kapuas Timur, Central Kalimantan (114°28′65″E, 3°6′9″S), on infected pseudostem of Musa sp. var. Pisang Kepok (ABB), 22 Jun. 2014, N. Maryani, (holotype preserved as metabolically inactive culture InaCC F916). Notes: Fusarium duoseptatum has distinctive septation in its microconidia, being 0–2-septate, thus differing from F. grosmichelii, which is 0–1-septate. The former is relatively slow-growing compared to members of the most closely related lineage, L4, and forms pigmentation in the centre of colony that is not observed in isolates of L4. F. duoseptatum and most of the members of L5 were able to infect Gros Michel, and were therefore classified as Foc-Race1. Foc Lineage L6 Fusarium tardichlamydosporum N. Maryani, L. Lombard, Kema & Crous, sp. nov. MycoBank MB826805. Fig. 13. Fig. 13 Fusarium tardichlamydosporum (ex-type InaCC F958). A. Culture grown on PDA. B. Sporodochia on carnation leaves. C. Aerial conidiophore. D. Microconidia. E. Falcate-shaped macroconidia. F. Chlamydospores. G. Sporodochial phialides. H. False heads. Scale bars D–H = 10 µm. Fig. 13 Etymology: Name reflects the delayed chlamydospore production observed in this species. Macroconidia abundant on CLA, less abundant on PDA and SNA, formed on sporodochia on CLA and on aerial conidiophores on SNA and PDA, falcate, (36–)37–43(–45) × (4–)5–6(–7) μm (av. 40 × 5 μm), 3–5-septate, with apical cells papillate, basal cells foot-shaped. Conidiogenous cells monophialidic on sporodochia, or on aerial hyphae, or formed directly on hyphae as lateral phialides, (3–)7–14(–19) × (2–)3–5(–8) μm. Microconidia abundant on PDA and SNA, ovoid to ellipsoid, (3–)5–9(–15) × (2–)5(–9) μm (av. 7 × 3 μm), 0–2-septate, arranged in false heads on branched conidiophores carried on hyphae. Aerial conidiophores rare on CLA and SNA and formed abundantly on PDA, branched sparsely or formed laterally. Chlamydospores abundantly produced after 4 wk, globose to subglobose, (6–)7–10(–13) × (4–)6–9(–10) μm, formed terminally or intercalarily, single or in pairs, rough-walled. Culture characteristics: Colony on PDA showing optimal growth at 25 °C with an average growth rate of 4.6–5.6 mm/d. Colony reverse sparsely dark purple in the centre, becoming white towards the margins, and purple slate, pigmented with age. Colony surface dry, cottony, with white filamentous margin, and lacking exudates. Aerial mycelium abundant, cottony, with abundant sporulation. Sporodochia formed abundantly on CLA after 7 d, pale orange to orange. Geography and host: Sikka Flores, Musa acuminata var. Pisang Barangan (AAA). Pathogenicity: Pathogen on Gros Michel (AAA). Materials examined: Indonesia, Desa Kota Uneng Kecamatan Alok, Sikka Flores, East Nusa Tenggara (112°12′16″E, 8°37′11″S), on infected pseudostem of Musa acuminata var. Pisang Barangan (AAA), 21 Aug. 2015, N. Maryani, (holotype preserved as metabolically inactive culture, InaCC F958). Notes: Colonies of Fusarium tardichlamydosporum are relatively fast growing (av. 4.6–5.6 mm/d) compared to those of F. duoseptatum (av. 38–41 mm/d). Polyphialidic conidiophores were not observed in this species/lineage. Chlamydospores were produced, but only after 4 wk. F. tardichlamydosporum was able to infect Gros Michel, and is therefore classified as Foc-Race1. Foc Lineage L7 Fusarium cugenangense N. Maryani, L. Lombard, Kema & Crous, sp. nov. MycoBank MB826807. Fig. 14. Fig. 14 Fusarium cugenangense (ex-type InaCC F984). A. Culture grown on PDA. B–C. Sporodochia on carnation leaves. D. Falcate-shaped macroconidia. E. Microconidia. F. Chlamydospores. G. False heads. H. Monophialidic conidiogenous cells. I–J. Branched conidiophores. Scale bars D–J = 10 µm. Fig. 14 Etymology: Name reflects Cugenang, the location where this species was collected in Indonesia. Macroconidia abundant on CLA, formed on sporodochia, on aerial conidiophores or on lateral phialides, falcate, (44–)47–54(–57) × (5–)6–7(–8) μm (av. 53 × 7 μm), 3–6-septate, with apical cells papillate, basal cells foot-shaped. Conidiogenous cells monophialidic on sporodochia, or on aerial hyphae, or formed directly from hyphae as lateral phialides, (5–)12–31(–45) × (3–)5–7(–8) μm. Microconidia abundant on PDA and SNA, less frequent on CLA, ovoid to ellipsoid, (7–)8–11(–24) × (2–)7(–12) μm (av. 12 × 5 μm), 0–3-septate, arranged in false heads on branched conidiophores carried on hyphae. Aerial conidiophores rare on CLA and SNA, and formed abundantly on PDA, branched sparsely or formed laterally. Chlamydospores rarely produced on SNA after 4 wk, globose to subglobose, (9–)10–14(–16) × (10–)11–14(–16) μm, formed terminally, single or in pairs, rough-walled. Culture characteristics: Colony on PDA showing optimal growth at 25 °C with an average growth rate of 5.2–5.4 mm/d. Colony reverse purple at center to pale viscous grey, white towards the margins, becoming purple slate with age, and pigmented. Colony surface dry, cottony, dark purple to white with filamentous margin, lacking exudates. Aerial mycelium abundant, cottony, with profuse sporulation. Sporodochia formed abundantly on CLA after 7 d, pale orange to orange. Geography and host: Cianjur, West Java, Musa sp. var. Pisang Kepok (ABB). Pathogenicity: Non-pathogenic on Gros Michel (AAA) and Cavendish (AAA). Material examined: Indonesia, Cugenang, Cianjur, West Java (107°4′109″E, 6°47′867″S), on infected pseudostem Musa sp. var. Pisang Kepok (ABB), 10 Jul. 2014, N. Maryani, (holotype preserved as metabolically inactive culture, InaCC F984). Notes: L7, including Fusarium cugenangense and other isolates, represents an Indonesian lineage with isolates that are closely related to other formae speciales (Fig. 6; e.g. NRRL 25433 F. oxysporum f. sp. vasinvectum). Polyphialidic conidiogenous cells were not observed in this species. This species has macroconidia with unique septation (3–6-septate) and microconidia (0–3-septate), which is rather uncommon for F. oxysporum species. This species causes a slight infection on Cavendish and Gros Michel, and testing on other cultivars such as Bluggoe (Pisang Kepok, ABB) are needed to fully classify strains as Foc-Race2. Foc Lineage L8 Fusarium hexaseptatum N. Maryani, L. Lombard, Kema & Crous, sp. nov. MycoBank MB826808. Fig. 15. Fig. 15 Fusarium hexaseptatum (ex-type InaCC F866). A. Culture grown on PDA. B. Sporodochia on carnation leaves. C. Microconidia. D. Falcate-shaped macroconidia. E. Thick-walled chlamydospores. F. False heads. G. Monophialides and polyphialides. Scale bars C–G = 10 µm. Fig. 15 Etymology: Name reflects the six conidial septa observed in its macroconidia. Macroconidia abundant on CLA, less so on PDA and SNA, formed on sporodochia on CLA and on aerial conidiophores on SNA and PDA, falcate, (34–)45–71(–76) × (5–)6–8(–9) μm (av. 58 × 7 μm), 3–6-septate, with apical cells papillate, basal cells foot-shaped. Conidiogenous cells mono- or polyphialidic on sporodochia, or formed directly from on hyphae (lateral phialides), 7–20 × 2–6 μm. Microconidia abundant on PDA and SNA, rare on CLA, ovoid to ellipsoid, (4–)8–23(–29) × (2–)7(–12) μm (av. 16 × 5 μm), 0–1-septate, arranged in false heads on branched conidiophores carried on hyphae. Aerial conidiophores rare on CLA and SNA and formed abundantly on PDA, branched sparsely or formed laterally. Chlamydospores abundantly formed in hyphae, globose to subglobose, (5–)14(–20) × (4–)6–12(–17) μm, formed terminally or intercalarily, single or in pairs. Culture characteristics: Colony on PDA showing optimal growth at 25 °C with an average growth rate of 4.9–5.9 mm/d. Colony reverse, in the dark, white and becoming livid purple in the center of the colony. Colony surface with filamentous margin, dry, cottony, white becoming livid vinaceous in age. No exudates observed. Aerial mycelium abundant, cottony, with high sporulation. Sporodochia formed abundantly on CLA after 7 d, colourless to pale orange. Geography and host: Sukabumi, West Java, Pisang Ambon Kuning (AAA). Pathogenicity: Pathogen on Gros Michel (AAA). Material examined: Indonesia, Parakan Lima, Sukabumi, West Java (107°5′869″E, 6°50′614″S), on infected pseudostem Musa acuminata var. Pisang Ambon Kuning (AAA), 7 Oct. 2014, N. Maryani, (holotype preserved as metabolically inactive culture, InaCC F866). Notes: Fusarium hexaseptatum is the single species in L8. Macroconidia with 6 septa are abundantly observed in this lineage, whereas in L7 and L9, they are very rare. This lineage is distinguished from L7 and L9 by its ability to cause disease on Gros Michel, and therefore it was classified as Foc-Race1. F. hexaseptatum has chlamydospores that are relatively large compared to those in other lineages (av. 9 × 9 μm). Foc Lineage L9 Fusarium tardicrescens N. Maryani, L. Lombard, Kema & Crous, sp. nov. MycoBank MB826809. Fig. 16. Fig. 16 Fusarium tardicrescens (ex-tyoe CBS 102024). A. Culture grown on PDA. B. Sporodochia on carnation leaves. C. Falcate-shaped macroconidia. D. Microconidia. E. Thick-walled chlamydospores. F. Monophialides produce microconidia and macroconidia. G. False head. Scale bars C–G = 10 µm. Fig. 16 Etymology: Name reflects the slow growth rate in culture. Macroconidia abundant on CLA and SNA, less abundant on PDA, formed on sporodochia on CLA and on aerial conidiophore on SNA and PDA, falcate, (52–)56–75(–89) × (5–)6–8(–9) μm (av. 66 × 7 μm), 2–6-septate, with apical cells papillate, basal cells foot-shaped. Conidiogenous cells mono- and polyphialidic on sporodochia formed directly from hyphae (lateral phialides), 7–32 × 2–6 μm. Microconidia abundant on PDA and SNA, less so on CLA, ovoid to ellipsoid, (7–)10–16(–20) × (2)–5(–7) μm (av. 13 × 4 μm), 0–1-septate, arranged in false heads on branched conidiophores carried on hyphae. Chlamydospores globose to subglobose, (5–)7–9(–10) × (5–)6–8(–10) μm, formed intercalarily or terminally, singly or in pairs, produced abundantly on SNA after 7 d, brown, rough-walled. Culture characteristics: Colony on PDA showing optimal growth at 25 °C with an average growth rate of 2.9–3.9 mm/d. Colony reverse, in the dark, dark violet becoming dark livid and pigmented. Colony surface dry, cottony, dark purple becoming dark livid. No exudates observed. Aerial mycelium abundant, cottony, with abundant sporulation. Sporodochia formed abundantly on CLA after 7 d, pale orange to orange. Geography and host: NA. Pathogenicity: NA. Material examined: Malawi, Karonga, Misuku Hills, Musa sapientum cv. Harare, 1989, R.C. Ploetz (holotype preserved as metabolically inactive culture CBS 102024 = NRRL 36113). Notes: Fusarium tardicrescens in L9 represents one of two lineages which clustered with other formae speciales. This lineage does not contain any Indonesian isolates. F. tardicrescens is the slowest growing species (av. 2.9–3.9 mm/d). F. tardicrescens causes moderate infection on both Cavendish and Gros Michel (Ordonez 2018). Novel Clade/Taxa in FOSC Fusarium kalimantanense N. Maryani, L. Lombard, Kema & Crous, sp. nov. MycoBank MB826810. Fig. 17. Fig. 17 Fusarium kalimantanense (ex-type InaCC F917). A. Culture grown on PDA. B–C. Sporodochia on carnation leaves. D–E. Sporodochial phialides. F. Falcate-shaped macroconidia. G. Microconidia. H. Thick-walled chlamydospores. I. Monophialides producing macroconidia. J. Branched conidiophores. K. False heads. Scale bars D–K = 10 µm. Fig. 17 Etymology: Name reflects Kalimantan, the island in Indonesia from where this fungus was collected. Macroconidia abundant on CLA, less abundant on PDA and SNA, formed on sporodochia on CLA and on aerial conidiophores on SNA and PDA, falcate, (52–)56–63(–65) × (5–)6–7(–8) μm (av. 59 × 7 μm), 3–5-septate, with apical cells papillate, basal cells foot-shaped. Conidiogenous cells monophialidic on sporodochia, or on aerial hyphae, or formed directly from hyphae as lateral phialides, (9–)11–15(–16) × (2–)3(–5) μm. Microconidia abundant on PDA and SNA, less frequent on CLA, ovoid to ellipsoid, (6–)8–15(–20) × (2–)3–4(–7) μm (av. 12 × 4 μm), aseptate, arranged in false heads on branched conidiophores borne on hyphae. Aerial conidiophore sparse on CLA and SNA and formed abundantly on PDA, branched sparsely or formed laterally. Chlamydospores rarely produced on SNA after 7 d, globose to subglobose, formed terminally or laterally, single or in pairs, (6–)7–10(–11) × (7–)8–9(–10) μm, rough-walled. Culture characteristics: Colony on PDA showing optimal growth at 25 °C with an average growth rate of 4.8–1.2 mm/d. Colony reverse rosy buff (pinkish) to white towards the margins, becoming fuscous black and pigmented with age. Colony surface dry, cottony, rosy buff (pinkish) to white, becoming purplish grey with age, filamentous margin, and lacking exudates. Aerial mycelium abundant, cottony, with moderate sporulation. Sporodochia formed abundantly on CLA after 7 d, pale orange to orange. Geography and host: Katingan, Central Kalimantan, Musa acuminata var. Pisang Ambon (AAA). Pathogenicity: Non-pathogenic on Gros Michel (AAA) and Cavendish (AAA). Material examined: Indonesia, Pulau Malam, Katingan, Central Kalimantan (113°13′333″E, 1°36′374″S), on infected pseudostem Musa acuminata var. Pisang Ambon (AAA), 23 Jun. 2014, N. Maryani, (holotype preserved as metabolically inactive culture, InaCC F917). Notes: Fusarium kalimantanense represents a new clade (Clade 5) in FOSC, which was previously considered to include only four clades (Fig. 5; sensu O'Donnell et al. 2004). This species has relatively fast-growing colonies compared to those of other members of FOSC in this study, and has a unique character in its aseptate microconidia. F. kalimantanense causes a slight infection on both Cavendish and Gros Michel. Further pathogenicity tests on other cultivars like Bluggoe (syn. Pisang Kepok, AAB) will be required to determine its race. Fusarium sangayamense N. Maryani, L. Lombard, Kema & Crous, sp. nov. MycoBank MB826811. Fig. 18. Fig. 18 Fusarium sangayamense (ex-type InaCC F960). A. Culture grown on PDA. B–C. Sporodochia on carnation leaves. D. Aerial conidiophore. E–F. Sporodochial phialides. G. Falcate-shaped macroconidia. H. Microconidia. I. Short monophialides. J. Thick-walled chlamydospores. Scale bars D–J = 10 µm. Fig. 18Fig. 19 Pathogenicity assays. A. External wilting symptoms. B–C. Left panel Cavendish and right panel Gros Michel, corm symptom caused by Foc-Race1, Fusarium tardichlamydosporum. D–E. Left panel Cavendish and right panel Gros Michel, corm symptom caused by Foc-TR4, Fusarium odoratissimum. Fig. 19 Etymology: Name reflects Sangayam, the location from where this species was collected in Indonesia. Macroconidia abundant on CLA and SNA, rare on PDA, formed on sporodochia on CLA and on aerial conidiophores on SNA and PDA, falcate, (48–)52–60(–65) × (5–)6–7(–8) μm (av. 56 × 7 μm), 2–5-septate, with apical cells papillate, basal cells foot-shaped. Conidiogenous cells monophialidic, similar in sporodochia and on hyphae, polyphialidic, rare, (6–)11–31(–47) × (3–)4–6(–9) μm. Microconidia abundant on PDA and SNA, less frequent on CLA, ovoid to ellipsoid, (8–)9–17(–24) × (3–)4–6(–7) μm (av. 13 × 5 μm), 0–1-septate, arranged in false heads on branched conidiophores borne on hyphae. Aerial conidiophores rare on CLA, and formed abundantly on SNA and PDA, sparsely branched, and formed laterally. Chlamydospores rarely produced on SNA after 7 d, globose to subglobose, formed terminally or intercalarily, single or in pairs, (6–)7–10(–12) × (6–)7(–9) μm, rough-walled. Culture characteristics: Colony on PDA showing optimal growth at 25 °C, with an average growth rate of 3.5–4.2 mm/d. Colony reverse uniformly white and unpigmented. Colony surface dry, cottony, white, with filamentous margin and lacking exudates. Aerial mycelium abundant, cottony, with moderate sporulation. Sporodochia formed abundantly on CLA after 7 d, pale orange. Geography and host: Kota Baru, South Kalimantan, Musa sp. var. Pisang Kepok (ABB). Pathogenicity: Non-pathogenic on Gros Michel (AAA) and Cavendish (AAA). Material examined: Indonesia, Sangayam, Kota Baru, South Kalimantan (115°59′440″E, 2°20′420″S), on infected pseudostem of Musa sp. var. Pisang Kepok (ABB), 19 Jun. 2014, N. Maryani, (holotype preserved as metabolically inactive culture, InaCC F960). Notes: Isolates of Fusarium sangayamense formed a subclade in the new FOSC Clade 5 (Fig. 6) with high support (BP = 100 % and PP = 1.0). F. sangayamense can be distinguished from F. kalimantanense based on the septation of its macroconidia (2–5-septate) and microconidia (0–1-septate). This species has polyphialidic conidiogenous cells, which are absent in F. kalimantanense. F. sangayamense was not able to infect Cavendish or Gros Michel. Pathogenicity assays The pathogenicity assay showed that all collected Foc isolates were able to cause typical Fusarium wilt symptoms on either Cavendish or Gros Michel, or in both varieties (Fig. 19). The positive control isolate FocII5-NRRL 54006 was lethal to both varieties, whereas all negative (water) controls remained free of disease. Isolates affecting Cavendish were classified as Foc-TR4 (Su et al. 1986), while those only infecting Gros Michel were classified as Foc-Race1 (Stover 1962a, Ploetz 1990). No fewer than 65 % of the isolates clustered in L1, which only comprised the strains that caused Fusarium wilt in Cavendish and hence, represented Foc-TR4. The rest of the isolates tested were able to infect Gros Michel and are therefore considered to be Foc-Race1 strains. Strains fitting this pathogenicity profile were equally distributed over all other lineages, except L7 and L9. L7 contains two Indonesian isolates that caused a slight discolouration of the corms of both varieties. Isolates in the new clade within FOSC were not able to cause disease in either tested banana variety. Isolates identified as other Fusarium species in the phylogenetic analyses were negative in all pathogenicity assays. Discussion The Musa gene centre (Perrier et al. 2011), as with the wheat gene centre in the Middle-East (Banke et al. 2004, Stukenbrock et al. 2007) and that of potato in Central Mexico (Grünwald & Flier 2005), contains a myriad of endemic diseases that co-evolved with the host. It is therefore considered a typical hot-spot of pathogen diversity (Stukenbrock & McDonald 2008). The gene centre of Musa has been studied in detail since the previous century. The wild ancestor of edible banana, Musa acuminata, originated in South-East Asia and Melanesia, and Musa balbisiana originated in South Asia (Perrier et al. 2011), where Indonesia is the contact area between these two wild Musa species. Approximately 11–13 Musa acuminata sub-species are of Indonesian origin, found in Sumatra, Kalimantan, Java, and the Lesser Sundas (Daniells, 1995, Simmonds, 1962). Most of the Musa balbisiana sub-species found in Java, Sumatra, and Sulawesi originate from India (Ochse and Bakhuizen van den Brink, 1931, De Langhe, 2009). However, the genetic diversity of Musa pathogens in the centre of origin of Musa has remained virtually unsampled. Although a recent overview of Foc in Asia was published (Mostert et al. 2017), a need remained for a thorough taxonomic analysis of Foc in its centre of origin. Our results present the most comprehensive study of Foc in the Indonesian gene centre of banana to date. Isolates of Foc were recovered from all the samples that were collected in all areas surveyed. The results demonstrated that Fusarium wilt is widely distributed in Indonesia and could be found in every banana producing area surveyed. Past reports showing compatible results have spanned an area from Aceh province in the west to Papua province in the east (Nasir et al., 1999, Wibowo et al., 2011). In 2012, 1 700 of the 21 000 acres of cultivated banana suffered from Fusarium wilt in Indonesia, including large commercial Cavendish plantations (Jumjunidang et al. 2012). Factors making this disease difficult to control include traditional farming practices, limited quarantine restriction on movement of planting material, and limited knowledge on the dissemination of the pathogen(s). As a result, the disease is unwittingly distributed to new areas. Moreover, the abundant diversity of banana varieties in Indonesia allows farmers to easily change the varieties they grow, resulting in epidemiological contact that allows the pathogen to infect new cultivars in different areas. Demographic factors could have played a significant role in the dissemination of this disease in Indonesia. Java is the most populated island and, therefore, banana production and the available cultivated varieties are the most numerous on this island, as is the pathogen. Mass migration of people from this over-populated island to less populated islands such as Kalimantan, Sumatra, and Papua from 1980 to 1990 could account for the dissemination of Fusarium wilt throughout Indonesia, since infected banana planting material was taken along (Nasir et al. 1999). The high number of local banana varieties from which Foc was recovered indicate that co-evolution of this pathogen is occurring along with its host in this region. Nasir et al. (1999) reported that 15 local varieties in Sumatra were susceptible to Fusarium wilt, including the most popular varieties, Pisang Ambon Kuning (AAA, Gros Michel synonym), Barangan (AAA) and Pisang Raja Sereh (AAA). This finding was reconfirmed in this study. An increasing number of infected varieties was also reported by Hermanto et al. (2009) and Jumjunidang et al. (2012). Of the hundreds of banana cultivars identified in Indonesia, many appear to be resistant or partially resistant to Fusarium wilt, a prior finding that was also observed during the present survey. No wild banana or close relative surveyed in this study showed any symptoms of Fusarium wilt. In Africa, Ensete ventricosum, a member of the Musaceae, is susceptible to Foc-Race2 (Ploetz 2006). By contrast, Ensete glaucum growing on the outskirt forest of Flores, Indonesia, was found to be healthy. None of the wild M. acuminata varieties found during the surveys was susceptible to Fusarium wilt. This finding is in agreement with some reports and greenhouse experiments on the infection of Foc on wild M. acuminata. Musa acuminata var. malaccensis from the Malaysian Peninsula was reported to be experimentally resistant (Javed et al. 2004), as was its sister variety M. acuminata var. malaccensis from Sumatra. This study and our observations during surveys indicate that Indonesia is the primary gene centre of Foc, and the most likely place to find a diverse palette of disease resistance markers for Fusarium wilt in banana. The high diversity of Foc isolates found in this study is unparalleled by the findings of any previous study (O'Donnell et al., 1998, Fourie et al., 2009) where a similar approach was used. The taking of larger numbers of samples in Indonesia inclusive of more banana cultivars, could result in an even higher diversity, as well as the discovery of yet more novel taxa belonging to FOSC. This accords with the view of Leslie & Summerell (2006), who stated that the most informative studies on the systematics and evolution of Fusarium species from natural ecosystems, as well as different agro-ecosystems, should incorporate native host populations, in order to allow discovery of the full existing species diversity (Leslie & Summerell 2006). Employing rotations with alternative crops, such as corn, sugar cane, peanuts and coffee, was found to decrease disease incidence in some plantations in Sumatra, Java, and Kalimantan. However, this practice probably has allowed for other Fusarium species, pathogenic to the rotation crops, to become established in these plantations, explaining their recovery in this study. These species include F. mangiferae, F. proliferatum F. sacchari and F. verticillioides, which are members of the Fusarium fujikuroi species complex (FFSC) and are associated with several tropical crops (Marasas et al., 2006, Ploetz, 2006) such as mango, maize, rice and sugarcane (Hsuan et al. 2011). These crops were commonly found in the areas surveyed for Fusarium wilt on bananas during this study. Fusarium proliferatum and F. oxysporum have been reported from the roots of the wild banana, M. acuminata, from Malaysia (Zakaria & Rahman 2011), which is closely related to several other M. acuminata varieties present in Sumatra and Java (Nasution 1990). This study represents the first report of both F. longipes and F. incarnatum-equiseti from banana varieties displaying symptoms of Fusarium wilt, although disease symptoms could not be induced in the pathogenicity assays undertaken here. However, both species are well-known as soil inhabitants and saprobes with a wide global distribution in tropical regions (Leslie & Summerell 2006). They could, therefore, be secondary colonisers of the decaying vascular tissue collected during the survey. The majority of the isolates that clustered outside the FOSC clade are well-known endophytes of various plant hosts, saprobes, and soil inhabitants, and are known to be non-pathogenic to banana (Waalwijk et al., 1996, O'Donnell et al., 1998). In the FOSC clade, the Indonesian isolates were equally distributed throughout the two previously known clades in FOSC (sensu O'Donnell et al. 2004). Several of these F. oxysporum isolates are known as endophytes of banana (O'Donnell et al. 1998), and are unable to induce disease on Cavendish or Gros Michel. Isolates obtained in this study that were found to be non-pathogenic to both banana cultivars tested were distantly related to the pathogenic isolates, and were more closely related to other formae speciales that are pathogenic to other crops. This finding supported the observations of Gordon & Okamoto (1992), who reported that Fusarium oxysporum f. sp. melonis, pathogenic to cucurbits, is only distantly related to non-pathogenic strains. This also supports the view that Foc and other formae speciales of F. oxysporum have a polyphyletic origin (Baayen et al., 2000, O'Donnell et al., 2009). Nine Foc lineages were revealed in this study, albeit with varying levels of statistical support, and described as new species. This conclusion was based on combinations of the genealogical approaches described by Dettmann et al. (2003) and Laurence et al. (2014), with supporting evidence from the inclusion of eight previously established lineages of FOC (O'Donnell et al., 1998, Fourie et al., 2009). A lineage is recognised as independent in this system if it is found to be concordantly supported by the majority of the loci, or is well supported by at least one locus but not contradicted by any other locus. Two previously known clades of Foc were resolved in this study (Boehm et al., 1994, Bentley et al., 1995, O'Donnell et al., 1998, Fourie et al., 2009), with the majority of the isolates fell into in Clade1, Lineage1. This lineage, classified as Foc-TR4, was found on every island surveyed, including Papua and Flores and those that were previously thought to be free of Foc-TR4. This is in agreement with some reports on Fusarium wilt in Indonesia, which note that the majority of Foc strains isolated appeared to be Foc-TR4 (O'Neill et al., 2011, Jumjunidang et al., 2012). In terms of phylogenetic diversity, Foc-TR4 isolates were less diverse than Foc-Race1, which occurred in almost all lineages. The number of diverse banana varieties sampled could be the reason for the tremendous diversity of Foc-Race1 isolates found in this study. Many of the banana sampled belong to varieties Gros Michel (AAA) or Silk (AAB), both known to be highly susceptible to Foc-Race1 (Waite & Stover 1960). The partial sequences of the three coding gene regions employed in this study, tef1, rpb1 and rpb2, are well-known to be robust for use in molecular-based identification of Fusarium species (O'Donnell et al. 2015), but are unable to distinguish all of the 24 VCGs (Puhalla, 1985, Ordonez et al., 2015) that are known to represent the widest genetic diversity of Foc. Direct VCG identification is a relatively objective but time-consuming test, and the results indicate genetic similarity rather than genetic differences (Kistler 1997). Therefore, VCGs represent good phenotypic characters for assessing diversity within populations, but genetic relationships among VCGs need to be assessed by other molecular tools. The high diversity found, based on the number of isolates recovered from different banana varieties and the high number of lineages resolved in this study, support the hypothesis that the pathogen(s) co-evolved with the host in the host's centre of origin (Ploetz & Pegg 1997). The unique agro-ecosystems and variety of ecological niches found where banana cultivation is practiced in Indonesia provide a conducive environment for the pathogen to evolve. As mentioned above, subsistence farming in Indonesia has allowed for the dissemination of banana varieties with varying degrees of tolerance and resistance to Fusarium wilt. This practice may have created a suitable environment for the incumbent pathogen to evolve and to adapt to newly introduced banana varieties. The dynamics of host diversity in these agro-ecosystems will continue to select for new pathogens (Stukenbrock & McDonald 2008), a process that, in this study, yielded a diversity of species able to infect newly introduced banana cultivars. Another scenario that could account for the high Foc diversity in Indonesia, irrespective of a lack of sexual reproduction, is horizontal gene transfer. Fusarium oxysporum has the ability to transfer specific chromosomes, sometimes containing unique pathogenicity genes, among non-pathogenic and pathogenic strains, resulting in new pathogenic lineages (Rep & Kistler 2010). This phenomenon is well recorded in Fusarium oxysporum f. sp. lycopersici, a pathogen of tomato (Ma et al. 2010). A recent study of the effector profile of different formae speciales of F. oxysporum, including Foc, indicated that these fungi have specific and unique effector profiles that reflect vertical and horizontal inheritance (van Dam et al. 2016). The endophytic character of some F. oxysporum strains, some of which are weak soil-borne pathogens (Stover 1962b), allows for relatively easy assimilation of pathogenicity genes from related pathogenic F. oxysporum strains via horizontal gene transfer (Vlaardingerbroek et al. 2016). The race concept has been used extensively in F. oxysporum classification system by plant pathologists. Based on the results of the present study, it can be inferred that the Foc-TR4 isolates evolved recently from predecessors in Foc-Race1. Foc-Race1 displayed a higher phylogenetic diversity in this study than Foc-TR4. Once established, both races apparently co-evolved in the same region, meaning that possible horizontal gene transfer could be involved in the high diversity level seen in Foc-Race1, as well as in the emergence of Foc-TR4. It was initially thought that the origin of pathogenic Foc is from non-pathogenic root inhabitants or endophytes of various wild M. acuminata plants in Java and Sulawesi that became pathogenic after their introduction to foreign banana germplasm (Buddenhagen 2007). Alternatively, native Foc-Race1 isolates may have been exposed to selection pressure through exposure to newly introduced banana varieties, as Foc-Race1 is known to infect diverse varieties like Silk (AAB), Pome (AAB), and Pisang Awak (ABB) (Waite & Stover 1960, Ploetz 2006). Isolates that clustered in the newly resolved subclade in the FOSC in this study were found to be non-pathogenic towards both Cavendish and Gros Michel. These isolates only caused initial discoloration in the corm, without any further disease development. They might be pathogenic on other germplasm, but until more banana varieties can be tested, this idea remains speculation. Our study demonstrates that the Indonesian Foc population might be the most genetically diverse ever studied. Further genetic study of this population using deeper genomic coverage should now be conducted. Pathogenicity tests using more banana varieties could be used to assess the wide range of pathogenicity. Our study gives an insight into the complexity of Fusarium wilt on banana in Indonesia. This is very important for disease management not only in Indonesia but also worldwide. As the pathogen continues to evolve, new lineages could arise and escape Indonesia. In striving to find banana resistance to Fusarium wilt, researchers should consider the high diversity of Indonesian Foc reported here as one of the main obstacles to overcome. Acknowledgements This research was supported by the KNAW-SPIN Project, “The Indonesian banana: Protecting a staple food from Panama disease collapse and exploiting its genetic diversity for discovery research”. Nani Maryani was also supported by a DIKTI (Directorate General of Higher Education, DIKTI) Scholarship, Ministry of Education, Indonesia. The authors would like to thank Dr Sarah M. Schmidt (Institute for Molecular Physiology, Heinrich-Heine-Universität Düsseldorf and Max Plank Institute for Plant Breeding Research, Köln, Germany), F. Ahmad (Research Centre for Biology, Indonesian Institute of Sciences, LIPI, Cibinong, Indonesia) and Muhammad Ilyas (Indonesian Culture Collection, INACC, LIPI, Cibinong, Indonesia) for participating in the sampling expeditions in Java, Sumatra, and Kalimantan. We also like to thank Dr Marcelo Sandoval-Denis (Westerdijk Fungal Biodiversity Institute) for helpful discussions and technical support and Dr Kerry O'Donnell (USDA) for the FOSC dataset. 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