
==== Front
IMA Fungus
IMA Fungus
IMA Fungus
2210-6340
2210-6359
BioMed Central London

39252145
160
10.1186/s43008-024-00160-x
Research
Exploration on cold adaptation of Antarctic lichen via detection of positive selection genes
Wang Yanyan 12
Zhang Yaran 12
Li Rong 13
Qian Ben 12
Du Xin 24
Qiu Xuyun 12
Chen Mengmeng 12
Shi Guohui 1
Wei Jiangchun 12
http://orcid.org/0000-0001-5470-9590
Wei Xin-Li weixl@im.ac.cn

12
Wu Qi wuq@im.ac.cn

12
1 grid.9227.e 0000000119573309 State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
2 https://ror.org/05qbk4x57 grid.410726.6 0000 0004 1797 8419 University of Chinese Academy of Sciences, Beijing, 100049 China
3 https://ror.org/0040axw97 grid.440773.3 0000 0000 9342 2456 School of Life Sciences, Yunnan University, Kunming, 650500 China
4 grid.9227.e 0000000119573309 Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
9 9 2024
9 9 2024
2024
15 2922 11 2023
19 8 2024
© The Author(s) 2024
2024
https://creativecommons.org/licenses/by/4.0/ Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Lichen as mutualistic symbiosis is the dominant organism in various extreme terrestrial environment on Earth, however, the mechanisms of their adaptation to extreme habitats have not been fully elucidated. In this study, we chose the Antarctic dominant lichen species Usnea aurantiacoatra to generate a high-quality genome, carried out phylogenetic analysis using maximum likelihood and identify genes under positive selection. We performed functional enrichment analysis on the positively selected genes (PSGs) and found that most of the PSGs focused on transmembrane transporter activity and vacuole components. This suggest that the genes related to energy storage and transport in Antarctic U. aurantiacoatra were affected by environmental pressure. Inside of the 86 PSGs screened, two protein interaction networks were identified, which were RNA helicase related proteins and regulator of G-protein signaling related proteins. The regulator of the G-protein signaling gene (UaRGS1) was chosen to perform further verification by the lichen genetic manipulation system Umbilicaria muhlenbergii. Given that the absence of UmRgs1 resulted in elevated lethality to cold shock, the role for UaRgs1 in Antarctic U. aurantiacoatra resistance to cold can be inferred. The investigation of lichen adaptation to extreme environments at the molecular level will be opened up.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43008-024-00160-x.

Keywords

Lichen-forming fungi
Polar region
Genome
Genomic syntenic alignment
Protein interaction network
G-protein signaling
Strategic Priority Research Program of ScienceXDB31000000 Wu Qi http://dx.doi.org/10.13039/501100001809 National Natural Science Foundation of China 32170082 91746119 32070096 Wang Yanyan Wei Xin-Li Wu Qi Space Application System of China Manned Space ProgramKJZ-YY-WSM05 Wei Xin-Li Strategic Priority Research Program of Science XDA28030401 Wu Qi http://dx.doi.org/10.13039/100014718 Innovative Research Group Project of the National Natural Science Foundation of China 32170015 Wu Qi Senior User Project of RV KEXUEKEXUE2019GZ05 Wu Qi issue-copyright-statement© International Mycological Association 2024
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pmcINTRODUCTION

Lichens are stable mutualistic symbiosis composed of fungi and algae or cyanobacteria, also including a diverse microbiome (Honegger 1991, Lücking and Nelsen 2018, Hawksworth and Grube 2020; Zhang et al. 2023). In lichens, lichen-forming fungi (LFF) provide protection to algae, whereas the algae provide photosynthetic nutrition for the LFF. This symbiotic form allows lichens to be widely distributed in extreme environments worldwide, including polar, plateau, and desert regions. For this reason, lichens are known as “pioneer organisms” of the terrestrial ecosystem and stress-tolerant extremophiles (Yang et al. 2023). Taking the Antarctica as an example, it is the coldest continent in the world with 99.8% of the area covered by ice (Burton-Johnson et al. 2016). In its northern region, there are some ice-free and relatively mild sites called the Maritime Antarctica such as Fildes Peninsula of King George Island (Fig. 1a), where is characterized by annual mean temperature − 3 to − 4 °C, sometimes lower than − 10 to − 12 °C in over 8-month-long winter, and common freeze–thaw cycle. However, lichens not only can survive but also are predominant organisms with over 400 species in Antarctic vegetation here, as comparison, only two vascular plant species exist (Øvstedal and Smith 2001).Fig. 1 Antarctic Usnea aurantiacoatra and its genome annotations. a Location of the Fildes Peninsula on the Antarctic continent and the sampling site of U. aurantiacoatra. The sampling site is marked with solid red circles. b Habitat of U. aurantiacoatra in Ardley Island, which looks like a grassland from a distance. And the morphology of saxicolous lichen thallus in the field. c Genome annotations of U. aurantiacoatra (NJ115-6). Circos representation of detailed information about the genome. a: Contigs over 500 Kb are labeled with names; b: Gene length; c: gene density (gene numbers per 100 Kb); d: GC abundance (GC percentage per 100 Kb); e: duplicate density (duplicate numbers per 100 Kb). d Abundance of repetitive elements in six lichen genomes. The repetitive elements in U. aurantiacoatra was nearly 40 Mbp, which far exceeds the amount in the other five genomes

Although knowledge of the lichens has been accumulated on biodiversity and conservation (Romeike et al. 2002; Wauchope et al. 2019), as well as how they are influenced by Antarctic climate change (Sancho et al. 2017), the mechanism by which lichen species are adaptive to such an extreme environment and dominate the terrestrial vegetation is yet to be fully elucidated. The corresponding researches were only reported on animals (Li et al. 2014a; Daane and Detrich 2022) and green algae (Zhang et al. 2020) here. To our knowledge, no Antarctic lichen genome has yet been sequenced and analyzed. Moreover, the number of sequenced genomes is still too little in relation to the great variety of lichen species. The lack of enough genetic information, as well as limitations such as slow growth and difficulty in genetic manipulation, have slowed down the development of research on lichen resistance mechanism. In this context, genomics will be a more effective and feasible strategy.

Through our field investigation in the Fildes Peninsula of King George Island in Antarctica, we found the lichen species Usnea aurantiacoatra thriving there, and covering the ground gravel like grassland (Fig. 1a-1b), suggesting strong adaptation to the polar environment. Biogeographic and phylogenetic studies also indicated some special characteristics of this lichen. Firstly, majority of usneoid lichens distributed in low- and medium-latitude regions, including most species of Usnea and other related genera, whereas only several Usnea species including U. aurantiacoatra are confined in Antarctica. Secondly, these Usnea species confined in Antarctica and high-latitude represent one separate subclade, suggesting a significant genetic differentiation from the usneoid ancestors (Øvstedal and Smith 2001; Wirtz et al. 2006; Thell et al. 2012; Divakar et al. 2017). Based on these comprehensive characteristics, U. aurantiacoatra was chosen as our research model for cold adaptation of lichens.

In this study, three LFFs were de novo whole-genome sequenced, yielding a high-quality genome of U. aurantiacoatra. Genomic syntenic alignment was comprehensively performed in six usneoid LFFs, yielding a list of positively selected genes for environmental adaptation in U. aurantiacoatra. We performed functional enrichment and protein interaction network analysis and found that positively selected genes cluster into vacuole components, transporter proteins, RNA helicase, and G-protein signaling. We chose to use Umbilicaria muhlenbergii for functional validation of positively selected genes because U. muhlenbergii has genetic manipulation system (Wang et al. 2020, 2023), and it also grows extensively in cold region like U. aurantiacoatra, both of which belong to Lecanoromycetes. Protein interaction network analyses indicated that UaRGS1 may play an important role in the adaptation of U. aurantiacoatra to the Antarctic environment, and that deletion of its ortholog, UmRGS1, in U. muhlenbergii resulted in the inability of U. muhlenbergii to tolerate cold-shock. Our results provided evidence for understanding the adaptation of U. aurantiacoatra to Antarctic environments and would open up the study of adaptive mechanisms in lichens at molecular level.

METHODS

Sample information

The Usnea aurantiacoatra lichen sample (NJ115-6) in minor amount was collected from the Fildes Peninsula, King George Island in Antarctica (Fig. 1a-1b, Table S1). The other two usneoid lichens, Dolichousnea longissima (coll.no. SC-9, syn. Usnea longissima) and an unknown Usnea species (coll.no. SC-4), were collected from the Sichuan Province of China (Table S1), considering their cold habitat source due to the high altitudes, and close phylogeny to U. aurantiacoatra. All samples were identified based on morphological observation and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences, which were amplified using ITS4/ITS5 (White et al. 1990), and the sequencing results were blasted in the NCBI database.

DNA extraction

The thallus of U. aurantiacoatra (NJ115-6), D. longissima (SC-9), and U. sp. (SC-4) were surface-cleaned and sterilized by immersion in 75% ethanol for 1 min, 1% sodium hypochlorite for 1 min, and sterile water for 1 min. Samples were then aired on sterile filter paper for half a day in a clean bench. The U. aurantiacoatra (NJ115-6) sample was directly sent to Nextomics Biosciences in Wuhan, China, and the thallus of D. longissima (SC-9) and that of U. sp. (SC-4) were sent to Majorbio in Shanghai, China, for DNA extraction and genomic sequencing.

De novo whole-genome sequencing

A sequencing strategy, combining second-generation, Hi-C, and third-generation sequencing techniques, was used for the sequencing of usneoid lichen genomes. After quality checking, the qualified genomic DNA was used to construct a non-replication large-fragment genomic library with ~ 20 Kbp fragment sizes. The pooled library was bound to a polymerase and loaded onto a PacBio Sequel, after which PacBio Sequel SMRT Sequencing was performed. Hi-C libraries were prepared with independently extracted genomic DNA of the U. aurantiacoatra sample, and an Illumina sequencing library was constructed with a mean fragment size of ~ 350 bp for further Illumina Hiseq X10 sequencing. Hi-C and Illumina Hiseq sequencing data were used for genome-assisted assembly. For genomic DNA from samples of U. sp. (SC-4) and D. longissima (SC-9), independent Illumina Hiseq2500 sequencing was performed with 300- and 380-bp sequencing libraries, respectively, which was used for further de novo genome assembly.

Genome resources available in public databases

Genome information of Evernia prunastri (Meiser et al. 2017), Usnea florida (https://mycocosm.jgi.doe.gov/Usnflo1/Usnflo1.home.html), and Alectoria sarmentosa (Liu et al. 2019a) used for comparative genome analysis were download from JGI (Grigoriev et al. 2014) and NCBI database. Genome information of Letharia lupina (McKenzie et al. 2020), Imshaugia aleurites (PRJEB42325), Gomphillus americanus (PRJEB42325), Alectoria fallacina (PRJEB42325), Bacidia gigantensis (Allen et al. 2021), Physcia stellaris (Wilken et al. 2020), Letharia columbiana (McKenzie et al. 2020), and Lasallia pustulata (Merges et al. 2023) used for analyzing amino acid residues of positively selected genes were downloaded from NCBI database.

Genome assembly and annotation

The initial genome assembly was performed using FALCON software (Chin et al. 2013). For Hi-C data, Bowtie2 (v.2.3.2) (Langmead and Salzberg 2012) and HiC-Pro (v.2.8.1) (Servant et al. 2015) were applied for mapping reads, identifying valid interaction paired reads, and clustering scaffolds, respectively. Contigs with depths less than 50 × coverage were filtered out to exclude low-coverage genome sequences particularly potential algal genome sequences. FCS-GX was used to reconfirm the low degree of contamination from algae genomes (Astashyn et al. 2024). The final assembly was polished using independently sequenced Illumina Hiseq raw reads.

For protein-coding gene prediction, Augustus (Stanke et al. 2006) and GeneID (Parra et al. 2000) were used for de novo annotation, whereas GeMoMa (Keilwagen et al. 2016) and Genewise (Birney et al. 2004) were used for homologous annotation. The EVidenceModeler method (Haas et al. 2008) was used to integrate the two results for genomes sequenced in this study, including U. aurantiacoatra (NJ115-6), U. sp. (SC-4) and D. longissima (SC-9). The Funannotate (v1.8.13) with Usnea florida as the training model was used for genomes of Evernia prunastri and Alectoria sarmentosa. For D. longissima (SC-9), ORFs with both a start codon and a stop codon were retained to exclude incomplete annotations caused by short scaffolds.

For repeat sequence annotation, RepeatMasker (v.4.1.2) (Chen 2004), RepeatModeler (v.2.0.2) (Flynn et al. 2020), RepeatProteinMasker (v.4.1.2) (Chen 2004), and TandemRepeatFinder (v.4.09) (Benson 1999) were used with the repeat sequence database constructed with the U. aurantiacoatra (NJ115-6) assembly itself.

For ncRNA annotation, Rfam (Griffiths-Jones et al. 2005), tRNAscan-SE (Lowe and Eddy 1997), and RNAmmer (Lagesen et al. 2007) were used. For protein coding gene annotation, the first approach was to query the whole protein sequence to Swissprot (Bairoch et al. 2005) and KEGG (Ogata et al. 1999) databases, whereas the second approach was to use InterProScan (Zdobnov and Apweiler 2001) to identify conserved protein domains and annotate gene function. A circos plot (Krzywinski et al. 2009) was used to visualize the genomic landscape of related annotations.

Orthologous gene identifications by genome syntenic alignment

We performed genomic syntenic alignment for six lichen genomes, including U. aurantiacoatra (NJ115-6), U. sp. (SC-4), U. florida (ATCC18376), D. longissima (SC-9), E. prunastri (FR SP7-11), and A. sarmentosa (MAF-Lich 21536), using LASTZ (version 1.04.00) (Chen et al. 2019; Hecker and Hiller 2020). The genome of U. florida was used as the reference genome, and the other five genomes were aligned to it. The five pair-align results were combined to obtain a final multispecies alignment as a multiple alignment format file. Then, the corresponding U. florida annotated coding sequence was used as reference to retrieve orthologous DNA sequences from the multiple alignment format file. This dataset of orthologous sequences of the six species included 12,243 genes and was a start-up orthologue dataset for further analyses.

Evolutionary genetic analyses for adaptive selection

For positive selection analyses using PAML (v4.8), two tree-setting strategies were considered. Focusing on U. aurantiacoatra as the foreground branch, strategy #1 used all five species as background branches, and strategy #2 excluded D. longissima from the five species, using only four species as background branches. The reason to consider using strategy #2 was because the obvious fast growth rate of D. longissima (1–3 cm per year) compared with U. aurantiacoatra (4.3–5.5 mm per year) (Keon 2009; Esseen et al. 1981; Jansson et al. 2009; Li et al. 2014b). The results of the two tree strategies were combined to a final result. For each strategy, the same “more than 20% of the alignment in a gap” screening criterion was implemented. The result dataset of the two strategies included 5674 and 6202 orthologous genes, respectively, and their concatenated set was 6226 genes.

Based on the reconstructed phylogenomic tree, positively selected genes (PSGs) were identified using the branch-site model of the codon evolution with model = 2 and Nssites = 2, whereas for the branch model, the parameters were the null model (model = 0) versus the alternative model (model = 2). Genes with omega value (dN/dS) larger than 1 and statistically significant between foreground and background branch were regarded as PSGs. In PAML, a chi-square test is used to exam the statistical significance of the omega larger than 1. Besides, an FDR test was performed to exclude potential false positive PSGs.

To further confirm the target PSGs and find its potential amino acid residues where positive evolution occurs, eight additional lichen species with available genome data from Lecanoromycetes were added, including Letharia lupina (McKenzie et al. 2020), Imshaugia aleurites (PRJEB42325), Gomphillus americanus (PRJEB42325), Alectoria fallacina (PRJEB42325), Bacidia gigantensis (Allen et al. 2021), Physcia stellaris (Wilken et al. 2020), Letharia columbiana (McKenzie et al. 2020), and Lasallia pustulata (Merges et al. 2023). Orthologous genes of the target PSGs were identified from the total 14 genomes by a reciprocal BLAST strategy of INPARANOID algorithm (Remm et al. 2001). The potential amino acid residues were aligned to check their evolution and possible substitution variations.

Protein interaction network

Protein interaction network analyses were performed in EMBL’s STRING (http://string.embl.de). Four different fungal model species were implemented as background genomes for analyses, including Aspergillus nidulans, Cryptococcus neoformans, Neurospora crassa, and Saccharomyces cerevisiae. For analyses the PSGs in U. aurantiacoatra, a 0.40 default interaction score of medium confidence was used. Domain analyses were performed in the SMART online website (http://smart.embl.de/smart/), with PFAM and signal peptide items checked.

Generation of ΔUmrgs1 mutant for functional verification

The UaRGS1 ortholog in Umbilicaria muhlenbergii, UmRGS1, was identified by searching the genome (unpublished data) using a reciprocal BLAST strategy (Remm et al. 2001). The split-marker approach was applied to knock out UmRGS1 in U. muhlenbergii. Upstream and downstream flanking sequences of UmRGS1 were amplified using primers 1F/2R and 3F/4R (Table S2), respectively. The resulting PCR fragments were ligated onto the hph cassette amplified from pCX63 (Zhao et al. 2005) with primers HT-F/HY-R and YG-F/HT-R. The final UmRGS1 gene replacement fragments were transformed into protoplasts generated by Driselase (Sigma-Aldrich), as described previously (Wang et al. 2020). Hygromycin-resistant transformants were screened by using PCR with primers 5F/6R, 7F/HY-R, YG-F/8R, and H850/H852 (Fig. S1).

The lichen-forming fungus U. muhlenbergii strain (wild type) and UmRGS1 gene knockout mutant strains (LR2, LR5, and LR8) were routinely cultivated on potato dextrose agar medium at 20 °C for 7 days. To detect the survival rate of ultra-low-temperature stress, 2 × 103 cells of the U. muhlenbergii JL3 strain and ΔUmrgs1 mutants were subjected to six freeze–thaw cycles of liquid nitrogen without any protective agent. Cold-shocked cells were recovered on PDA medium at 20 °C for 10 days. Each experiment was performed in triplicate to count the number of colonies on the recovered plates.

RESULTS

De novo genome assembly combined multi-sequencing technologies yield high-quality genome of Usnea aurantiacoatra

To obtain a high-quality reference genome, we sequenced Antarctica U. aurantiacoatra (NJ115-6) (Fig. 1a-1b) using three sequencing techniques of PacBio, HiSeq (Illumina) and Hi-C. First, we assembled the genome sequences with 61.01 Gbp PacBio data using FALCON, and obtained a draft genome with a size of 81.0 Mbp (187 contigs; contig N50 944.85 Kbp) after removing the potential contaminant and redundant sequences. Then, we corrected the contigs with 86.83 Gb HiSeq data using pilon (v.1.24) (Walker et al. 2014). Finally, we linked the corrected contigs to scaffolds with 73.71 Gb Hi-C data using Bowtie2 (v.2.3.2), HiC-Pro (v.2.8.1), and LACHESIS (Burton et al. 2013), and obtained a total of 81.4 Mb genome sequences (121 scaffolds; Scaffold N50 1.59 Mb; Fig. 1c; Fig. S2; Table 1).Table 1 Genome assembly statistics of usneoid lichens sequenced in this study

	U. aurantiacoatra (NJ115-6)	U. sp. (SC-4)	D. longissimi (SC-9)	
Total Bases (Gbp)	86.83	9.83	11.50	
Assembly size (Mbp)	81.40	40.60	67.30	
No. Scaffolds	121	8966	59,938	
Scaffolds N50 (Kbp)	1590	13.90	1.80	
BUSCO (%)	97.36	88.51	54.22	
Duplicated BUSCO (%)	16.41	0.47	1.70	
Predicted genes	13,534	13,191	12,475	
Accession	GWHBJEF00000000	GSA: CRA007127	GSA: CRA007127	

We also performed Hiseq sequencing of the genome of two other usneoid lichen U. sp. (SC-4) and D. longissima (SC-9). We sequenced the genomic DNA (9.83 Gb for SC-4; 11.5 Gb for SC-9), and assembled a total of 40.6 Mb of SC-4 (contig N50 10.5 Kbp; scaffold N50 13.9 Kbp) and 67.3 Mbp of SC-9 (contig N50 1.3 Kbp; scaffold N50 1.8 Kbp) genome sequences using SOAPdenovo2, respectively (Table 1). Gene annotation obtained 13,534 protein-coding genes for U. aurantiacoatra, 13,191 genes for U. sp., and 12,475 genes for D. longissima (Table 1).

To carry out a comparative genome analysis, genome of Usnea florida (ATCC18376), Evernia prunastri (FR SP7-11), and Alectoria sarmentosa (MAF-Lich 21536), which belong to the same family (Parmeliaceae) as the three usneoid lichens mentioned above, were selected from the published genomic data. Of these six genomes, U. aurantiacoatra genome was the largest, almost double the size of the LFF genomes that have been published so far. To uncover the reason for the highly expanded genome size of U. aurantiacoatra, repeat sequence annotation was performed in these six LFF genomes. Comparison showed that the repeat sequences of U. aurantiacoatra were significantly higher than those of the other five genomes, with the greatest expansion of long terminal repeat (LTR) and unknown repeat sequences (Fig. 1d). The total size of all types of repeat sequence was about 40 Mbp, the same as the genome sizes of other lichen species except U. aurantiacoatra. Considering similar gene number in the six genomes (Table 1), it can be concluded that the large genome size in U. aurantiacoatra is due to amplification of repeat sequences. We also performed BUSCO assessment of the three usneoid LFF genome data obtained in this study, U. aurantiacoatra has the more complete genome (Fig. S3).

Genome signatures for adaptive selection of U. aurantiacoatra

In search of adaptive selection traits at genomic level, 6226 concatenated genes obtained by two tree-setting strategies (Fig. 2a) were used for positive selection analysis by PAML, and were corrected the p-values with false discovery rate (FDR) analysis (Fig. 2b). There were 178 PSGs with corrected p-values < 0.1 under both strategies (Fig. 2b), removing 35 pseudogenes yielded 143 PSGs (Fig. 2c), which included 86 PSGs paired with genes annotated by EVidenceModeler (Table S3).Fig. 2 Positive selection related to the adaption to extreme Antarctic environments. a Workflow of evolutionary genetic analyses for adaptive selection. Genomic syntenic alignment found 12,243 orthologs in six genomes, which were filtered for two tree-building strategies. The concatenation obtained by both strategies was used for adaptive analysis, resulting in 178 potential positively selected genes (PSGs). b The p-values of the potential PSGs obtained by two strategies were corrected for false discovery rate (FDR) analysis. Red and blue dots indicated PSGs with p-values < 0.1 in strategy I and II, respectively. Yellow dots were PSGs with corrected p-values < 0.1 under both strategies, which were used for subsequent analysis. c Pie chart showing the number of pseudogenes, annotated genes, and non-annotated genes in 178 potential PSGs. d Box plot of mean dN/dS shows a significantly high mean ω value in U. aurantiacoatra (p < 0.01)

We calculated ω ratios (dN/dS) for 6226 orthologous genes, and comparisons revealed that the average value of the ω ratios for U. aurantiacoatra was significantly higher than that of other LFF (p < 0.01, Fig. 2d, Table S4–S5), indicating that negative selection in this species is universally more relaxed than other species.

Functional enrichment and protein interaction network of positively selected genes

To acquire the biological processes and functions in which the above PSGs were involved, we performed functional enrichment analysis using clusterProfiler (Wu et al. 2021) with GO categories and KEGG pathways. By functional enrichment of 86 PSGs with a Q-value < 0.05, it showed that most of these proteins were associated with transmembrane transporter functions and vacuole components, and cyanoamino acid metabolism was also enriched (Table S6).

To identify potential functional information related to adaptive selection, protein-associated network analysis was carried out with EMBL’s STRING platform using four model fungal species (Aspergillus nidulans, Cryptococcus neoformans, Neurospora crassa, Saccharomyces cerevisiae). Of the 4 model fungi species in STRING, we identified 6 protein interaction networks, which included 35 genes of the 86 PSGs (Table S7). PSGs in four of these protein interaction networks were enriched in the GO category described above, which were related to transmembrane transporter activity or/and vacuole component (Fig. 3). The other two protein interaction networks that were not enriched by KEGG or GO were the G-protein-signaling and RNA helicase (Fig. 3). The RNA helicase network involves 12 proteins with functions related to the processing and maturation of rRNA and tRNA modification in the initiation of protein translation (Fig. 3). The G-protein-signaling network contains three proteins, regulator of G-protein-signaling, casein kinase I, and carboxypeptidase (Fig. 3).Fig. 3 Protein interaction networks of positively selected genes (PSGs) in Usnea aurantiacoatra. A total of 35 PSGs were in six protein interaction networks, four of which were enriched for vacuole component and transmembrane transporter activity. In addition to this, a larger protein interaction network centered on RNA helicase, and another network of three proteins centered on regulator of G-protein signaling

Effects of regulator of G-protein-signaling in cold resistance

To characterize PSGs as evidence of environmental adaption in Antarctic U. aurantiacoatra, we selected regulator of G-protein-signaling to further study, and named this protein as UaRgs1. Since U. aurantiacoatra cannot be genetically manipulated, we chose to knock out the homologous of UaRGS1 in Umbilicaria muhlenbergii (UmRGS1). Three separate ΔUmrgs1 deletion mutants (LR2, LR5, and LR8) were generated and validated by PCR using anchor primers (Fig. S1; Table S2). We chose LR2 as the representative of mutants for the further cold resistant verification considering the consistent phenotype among the three mutants. Knockout of the UmRGS1 did not affect the growth phenotype of U. muhlenbergii. To determine whether UmRgs1 was critical for cold shock, the liquid nitrogen freeze–thaw experiment was performed on the wild-type strain and ΔUmrgs1 mutants. After three parallel experiments, the average number of wild-type and ΔUmrgs1 mutant colonies was 94 and 33 on the recovery medium, respectively (Fig. 4a; Table S8). The survival rate of wild-type strain (4.7%) was nearly three times that of the ΔUmrgs1 mutant (1.65%), with a significant difference between them (p = 0.001), indicating that the ΔUmrgs1 mutant is more sensitive to rapid freeze–thaw temperature changes than the wild-type. Therefore, we can deduce that UaRgs1 may have similar and even stronger function in Antarctic U. aurantiacoatra for resistance of the freeze–thaw sharp temperature changes.Fig. 4 Functional verification of UmRGS1 in rock tripe Umbilicaria muhlenbergii. a Survival colonies and survival rate of wild-type strain and ΔUmrgs1 mutant after six liquid nitrogen freeze–thaw cycles. Error bars represent SD, unpaired T-test with Welch’s correction, p = 0.001, n = 3 independent experiments. b Domain architecture of UaRgs1 and the locations of three amino acid residues undergo positive evolution. c Phylogenetic tree constructed by UaRgs1 with its homologous in 13 other lichen-forming fungal genomes. List on the right were the amino acids and corresponding codons for the three positive selection sites in UaRgs1. d Multiple alignment of the same set of protein sequences, with asterisks marking the sites of three amino acids, and amino acid position 519 was in conserved domain

We also identified potential amino acid residues where positive evolution occurs on UaRgs1 (Fig. 4b). A phylogenetic tree and multiple alignment using additional UaRgs1 orthologous in 13 LFFs, showed that amino acid 519 site, located in the DEP domain, was highly conserved but changed in Antarctic U. aurantiacoatra (Fig. 4c-4d), suggesting that the adaptive selection is associated with the biochemical and molecular function of the gene. Another branch site analysis for these 14 Rgs genes was conducted and the outcome showed that site 519 was under positive selection, which enhanced out conclusion.

DISCUSSION

The three poles, Antarctica, Arctic and the Third Pole (i.e., the Tibetan Plateau and its surroundings), are the coldest environment on the Earth, of which Antarctica is the most severe one and recorded the lowest air temperature. Lichens, as the pioneer organisms, can dominantly survive in such extreme environments and contribute substantial biodiversity of their flora, for which a set of cold tolerance mechanisms are needed. Previous studies on the Antarctic lichens mainly focused on the correlation of lichen biodiversity and conservation with climate change (Sancho et al. 2017; Romeike et al. 2002; Wauchope et al. 2019). A related study revealed differences in biosynthetic gene clusters between Umbilicaria pustulata lichens in Mediterranean and cold-temperate regions (Singh et al. 2021). This suggests that there must be a large number of environmental adaptation genes in Antarctic lichen genome. In this case, Usnea aurantiacoatra was chosen as a model mainly due to our field investigation and the good matching between divergent time of this lichen and the paleoclimate and paleogeology of Antarctica discovered by our study, which indicated that it is very likely to have a strong adaption to the Antarctic extreme environment driven by natural selection.

The approaches identifying natural selection at the molecular evolution level involves estimation of synonymous and nonsynonymous substitution rates and detection of positive selection in protein-coding DNA sequences among species (Yang 2007). We comprehensively compared the genomes between U. aurantiacoatra and those lichens mainly living in the temperate regions, then attempted to remove D. longissima with different growth rates when analyzing PSGs. The results of the two strategies were slightly different (Fig. S4), but the results obtained from different background branches may be both meaningful. We used a combination (the union) of the two strategies to ensure that genes selected by either strategy would be included in the final set of result genes.

The identified 86 PSGs possibly related to cold adaptation mainly enriched in lytic and storage vacuole components. The fungal vacuole serves as both the main compartment for division and a reservoir for the storage of small molecules, such as polyphosphate, amino acids, divalent calcium, and other small molecules (Klionsky et al. 1990). In some fungi, genes controlling the formation of vacuole play an important role in resistance to stresses (Son et al. 2018; Wilken et al. 2020; Zhu et al. 2023). Antarctic lichens need to undergo long periods of dormancy, and it is hypothesized from our results that U. aurantiacoatra enhance its vacuole function under selective pressure.

Two other potentially important mechanisms were found through protein network analysis. RNA helicase at the center of the largest protein interaction network, has been intensively studied in both eukaryotes (O’Day et al. 1996) and bacteria (Liu et al. 2021). This gene involves in the maturation of 35S-pre-rRNA and is required for cleavages leading to mature 18S rRNA in cell nucleus, which plays a critical role for the biogenesis of ribosomes. RNA helicase has been shown to be related to thermo-tolerance in rice (Wang et al. 2016) and cold tolerance in glacial psychrophilic Flavobacterium (Liu et al. 2021). Besides, the tRNA methyltransferase gene interacted with RNA helicase (Fig. 3) has also been verified to be related with temperature changes in bacteria and yeast (Lorenz et al. 2017, Hori 2014). In LFF Cladonia grayi, rRNA and the biogenesis of ribosomes have been suggested to be closely related with stress resistance (Armaleo et al. 2019). Our results provide further evidence of the importance of the RNA helicase associated protein network in resistance.

In this study, we chose to perform an extended analysis of regulator of the G-protein signaling (RGS) in another protein network, because G-protein and RGS belong to important pathways that receive external signals in fungi (Lengeler et al. 2000; Zhong and Neubig 2001; McCudden et al. 2005). Orthologous genes of UaRGS1 involves in the regulation of growth, sporulation, and pathogenicity in model fungi (Chan and Otte 1982; Yu et al. 1996; Ballon et al. 2006; Liu et al. 2007), but there is no experimental evidence that it is related to external low-temperature stimuli or other environmental stress. Here, we verified the new function of RGS related to the ultra-low temperature tolerance. Furthermore, it is worth mentioning that there is a casein kinase I gene in the UaRgs1 protein interaction network (Fig. 3). Casein kinase I is conserved from plants to animals, it performed a number of cellular processes, including DNA repair, cell cycle, cytokinesis, vesicular trafficking, and circadian rhythm (Park et al. 2012; Marzoll et al. 2022). The protein interaction network analysis allows further enrichment of PSGs and can shed more light on the cellular processes in which environmentally adapted genes are involved. The identification of RGS and casein kinase I interaction network in PSGs is more indicative of G-protein signaling pathways that were subjected to selective pressures. Both RGS and casein kinase I are important factors upstream of cellular signaling pathways, and in the case of RGS, as a negative regulator of G-proteins, it is responsible for making the cell to respond correctly to a variety of signals, not just adaptation to cold stress, and it is possible that it will have similar results across different external stresses.

Besides, there is also some other genomic signatures suggesting that the LFF genome is under adaptive selection. The assembly size of U. aurantiacoatra is two times as large as those of other relative lichen species, which is caused by LTR amplification and unknown repeat sequences. The LTR amplification is one of the main drivers leading to the big size of eukaryotic genome (Liu et al. 2019b). LTRs show considerable enrichment in lncRNA transcripts compared with non-LTR elements in mouse and human (Kannan et al. 2015; Kapusta et al. 2013; Kelley and Rinn 2012). Most of LTRs transcribed in lncRNAs serve as exons (Kannan et al. 2015), specific families have been co-opted as promoters (Thompson et al. 2016). In plants such as mangrove trees (Lyu et al. 2018), palm (Schley et al. 2022) and bamboo (Papolu et al. 2021), LTR copy number has been reported to crucially associated with adaptation to various environmental stress including aridity or heat. Plenty of evidence suggests that LTR in Plants involves in the modulation of gene expression in response to several stimuli, notably stresses and external challenges (Bui and Grandbastien 2012). In Medicago sativa, LTR has been reported to be related to cold tolerance. Study of Sicilian blood oranges (Citrus sinensis) illustrated the strength of the LTR as a promoter and as an upstream activating sequence is of cold dependency (Butelli et al. 2012). Therefore, it is reasonable to presume that in the U. aurantiacoatra as the symbiont of lichen-forming fungus and plant (alga), the existence of abundant LTR is related to the tolerance of cold environment.

CONCLUSIONS

In summary, based on our genomic sequencing and bioinformatic analyses, we exhibited several potential mechanisms on how U. aurantiacoatra achieved its adaptation to Antarctic environments. We also performed functional validation of one of the genes that has not yet been reported to be associated with stress, further determining the accuracy of the screened PSGs. This study can serve as a good start to understand the environmental adaptions of lichens, and provide the basis and clues for further studies on LFF resistance mechanisms.

Supplementary Information

Supplementary Material 1: Figure S1. Gene replacement of UmRGS1. a Diagram of the UmRGS1 gene and primers used to generated the ΔUmrgs1 mutant. HY and YG are fragments of the hph cassette conferring resistance to hygromycin. b Mutant detected with four pairs of anchor primers. Figure S2. GC content-sequencing depth distribution of three usneoid lichen-forming fungi. a The left and right panels represent the results of U. aurantiacoatra (NJ115-6) using Illumina and Nanopore sequencing platforms, respectively. b GC-depth of Illumina-sequencing U. sp. (SC-4). c GC-depth of Illumina-sequencing D. longissima (SC-9). Figure S3. Integrity and characterization of U. aurantiacoatra genome. a BUSCO assessment of three usneoid LFF genomes with the highest completeness of U. aurantiacoatra. b Gene feature distribution of U. aurantiacoatra. Figure S4. The differences between ω and p values of two strategies. a Comparison of ω values of two strategies. b Comparison of p values of two strategies.

Supplementary Material 1: Table S1. Information on lichen samples used in this study. Table S2. PCR primers used in this study. Table S3. List of positively selected genes and annotation in Antarctic Usnea aurantiacoatra. Table S4. Results of branch site analysis for strategy 1. Table S5. Results of branch site analysis for strategy 2. Table S6. Results of positively selected genes enrichment in GO ontology and KEGG pathway in Antarctic Usnea aurantiacoatra. Table S7. Protein interaction networks and annotation of positively selected genes in Antarctic Usnea aurantiacoatra. Table S8. Survival colonies and survival rates of WT and the ΔUmrgs1 mutant after ultra-low-temperature shock.

Abbreviations

PSG Positively selected gene

RGS Regulator of the G-protein signaling

LFF Lichen-forming fungi

PAML Phylogenetic analysis by maximum likelihood

LTR Long terminal repeat

FDR False discovery rate

Acknowledgements

We thank Dr. Weicheng Wang for his help in collecting samples, Ms. Qiuxia Yang for her assistance in micromanipulation on the lichen thallus, and Dr. Huizhong Fan for the help in dealing with the pipeline of positive selection. We are grateful to the Chinese Arctic and Antarctic Administration for the help in carrying out the project in the Great Wall Station during the 32nd and 34th Chinese National Antarctic Expedition.

Author contributions

X.W., Q.W., and Y. W. conceived and designed the study; X.W. and Y.W. collected samples; Y.W., R.L., B.Q., X.Q., and X.W. performed the experiments; Y.W., Y.Z., X.W., X.D., M.C., and Q.W. analyzed the data; Q.W. wrote the manuscript draft; Q.W., X.W., Y.W., Y.Z., and G.S. revised the draft; all authors approved the final manuscript.

Funding

This work was supported by the Strategic Priority Research Program of Science (grant number XDB31000000); the National Natural Science Foundation of China (grant number 32170082); Space Application System of China Manned Space Program (KJZ-YY-WSM05); the Strategic Priority Research Program of Science (grant number XDA28030401); the National Natural Science Foundation of China (grant numbers 91746119, 32170015, 32070096); and the Senior User Project of RV KEXUE (grant number KEXUE2019GZ05).

Availability of data and materials

The whole genome sequence data of U. aurantiacoatra (NJ115-6) have been deposited in the Genome Warehouse in National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, under accession number GWHBJEF00000000 that is publicly accessible at https://ngdc.cncb.ac.cn/gwh. The raw sequence data of Usnea sp. (SC-4) and D. longissima (SC-9) have been deposited in the Genome Sequence Archive in National Genomics Data Center, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (GSA: CRA007127) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa. The sequence of UmRGS1 is available in the GenBank Nucleotide Database under accession number ON649705.

Declarations

Ethics approval and consent to participate

Not applicable.

Adherence to national and international regulations

The authors confirm that this manuscript respects Plant Health and Quarantine and the Nagoya Protocol to the Convention on Biological Diversity.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Yanyan Wang and Yaran Zhang contributed equally to this work.
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References

Allen JL Jones SJM McMullin RT Draft genome sequence of the lichenized fungus Bacidia gigantensis Microbiol Resour Announc 2021 10 e0068621 10.1128/MRA.00686-21 34734769
Allen JL, Jones SJM, McMullin RT (2021) Draft genome sequence of the lichenized fungus Bacidia gigantensis. Microbiol Resour Announc 10:e006862134734769 10.1128/MRA.00686-21
Armaleo D Müller O Lutzoni F Andrésson ÓS Blanc G Bode HB Collart FR Dal Grande F Dietrich F Grigoriev IV Joneson S Kuo A Larsen PE Logsdon JM Lopez D Martin F May SP Mcdonald TR Merchant SS Miao V Morin E Oono R Pellegrini M Rubinstein N Sanchez-Puerta MV Savelkoul E Schmitt I Slot JC Soanes D Szovenyi P Talbot NJ Veneault-Fourrey C Xavier BB The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata BMC Genomics 2019 20 605 637 10.1186/s12864-019-5629-x 31337355
Armaleo D, Müller O, Lutzoni F, Andrésson ÓS, Blanc G, Bode HB, Collart FR, Dal Grande F, Dietrich F, Grigoriev IV, Joneson S, Kuo A, Larsen PE, Logsdon JM, Lopez D, Martin F, May SP, Mcdonald TR, Merchant SS, Miao V, Morin E, Oono R, Pellegrini M, Rubinstein N, Sanchez-Puerta MV, Savelkoul E, Schmitt I, Slot JC, Soanes D, Szovenyi P, Talbot NJ, Veneault-Fourrey C, Xavier BB (2019) The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC Genomics 20:605–63731337355 10.1186/s12864-019-5629-x
Astashyn A Tvedte ES Sweeney D Sapojnikov V Bouk N Joukov V Mozes E Strope PK Sylla PM Wagner L Bidwell SL Brown LC Clark K Davis EW Smith-White B Hlavina W Pruitt KD Schneider VA Murphy TD Rapid and sensitive detection of genome contamination at scale with FCS-GX Genome Biol 2024 25 60 10.1186/s13059-024-03198-7 38409096
Astashyn A, Tvedte ES, Sweeney D, Sapojnikov V, Bouk N, Joukov V, Mozes E, Strope PK, Sylla PM, Wagner L, Bidwell SL, Brown LC, Clark K, Davis EW, Smith-White B, Hlavina W, Pruitt KD, Schneider VA, Murphy TD (2024) Rapid and sensitive detection of genome contamination at scale with FCS-GX. Genome Biol 25:6038409096 10.1186/s13059-024-03198-7
Bairoch A Apweiler R Wu CH Barker WC Boeckmann B Ferro S Gasteiger E Huang HZ Lopez R Magrane M Martin MJ Natale DA O’Donovan C Redaschi N Yeh LSL The universal protein resource (UniProt) Nucleic Acids Res 2005 33 D154 D159 10.1093/nar/gki070 15608167
Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang HZ, Lopez R, Magrane M, Martin MJ, Natale DA, O’Donovan C, Redaschi N, Yeh LSL (2005) The universal protein resource (UniProt). Nucleic Acids Res 33:D154–D15915608167 10.1093/nar/gki070
Ballon DR Flanary PL Gladue DP Konopka JB Dohlman HG Thorner J DEP-domain-mediated regulation of GPCR signaling responses Cell 2006 126 1079 1093 10.1016/j.cell.2006.07.030 16990133
Ballon DR, Flanary PL, Gladue DP, Konopka JB, Dohlman HG, Thorner J (2006) DEP-domain-mediated regulation of GPCR signaling responses. Cell 126:1079–109316990133 10.1016/j.cell.2006.07.030
Benson G Tandem repeats finder: a program to analyze DNA sequences Nucleic Acids Res 1999 27 573 580 10.1093/nar/27.2.573 9862982
Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–5809862982 10.1093/nar/27.2.573
Birney E Clamp M Durbin R GeneWise and genomewise Genome Res 2004 14 988 995 10.1101/gr.1865504 15123596
Birney E, Clamp M, Durbin R (2004) GeneWise and genomewise. Genome Res 14:988–99515123596 10.1101/gr.1865504
Bui QT Grandbastien M-A Grandbastien M-A Casacuberta JM LTR retrotransposons as controlling elements of genome response to stress? Plant transposable elements: impact on genome structure and function 2012 Berlin, Heidelberg Springer
Bui QT, Grandbastien M-A (2012) LTR retrotransposons as controlling elements of genome response to stress? In: Grandbastien M-A, Casacuberta JM (eds) Plant transposable elements: impact on genome structure and function. Springer, Berlin, Heidelberg
Burton JN Adey A Patwardhan RP Qiu R Kitzman JO Shendure J Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions Nat Biotechnol 2013 31 1119 1125 10.1038/nbt.2727 24185095
Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J (2013) Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat Biotechnol 31:1119–112524185095 10.1038/nbt.2727
Burton-Johnson A Black M Fretwell PT Kaluza-Gilbert J An automated methodology for differentiating rock from snow, clouds and sea in Antarctica from Landsat 8 imagery: a new rock outcrop map and area estimation for the entire Antarctic continent Cryosphere 2016 10 1665 1677 10.5194/tc-10-1665-2016
Burton-Johnson A, Black M, Fretwell PT, Kaluza-Gilbert J (2016) An automated methodology for differentiating rock from snow, clouds and sea in Antarctica from Landsat 8 imagery: a new rock outcrop map and area estimation for the entire Antarctic continent. Cryosphere 10:1665–167710.5194/tc-10-1665-2016
Butelli E Licciardello C Zhang Y Liu J Mackay S Bailey P Reforgiato-Recupero G Martin C Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges Plant Cell 2012 24 1242 1255 10.1105/tpc.111.095232 22427337
Butelli E, Licciardello C, Zhang Y, Liu J, Mackay S, Bailey P, Reforgiato-Recupero G, Martin C (2012) Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell 24:1242–125522427337 10.1105/tpc.111.095232
Chan RK Otte CA Isolation and genetic analysis of Saccharomyces cerevisiae mutants supersensitive to G1 arrest by a factor and alpha factor pheromones Mol Cell Biol 1982 2 11 20 7050665
Chan RK, Otte CA (1982) Isolation and genetic analysis of Saccharomyces cerevisiae mutants supersensitive to G1 arrest by a factor and alpha factor pheromones. Mol Cell Biol 2:11–207050665
Chen N Using RepeatMasker to identify repetitive elements in genomic sequences Curr Protoc Bioinform 2004 5 4 10 10.1002/0471250953.bi0410s05
Chen N (2004) Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinform 5:4–1010.1002/0471250953.bi0410s05
Chen L Qiu Q Jiang Y Wang K Lin Z Li Z Bibi F Yang Y Wang J Nie W Su W Liu G Li Q Fu W Pan X Liu C Yang J Zhang C Yin Y Wang Y Zhao Y Zhang C Wang Z Qin Y Liu W Wang B Ren Y Zhang R Zeng Y da Fonseca RR Wei B Li R Wan W Zhao R Zhu W Wang Y Duan S Gao Y Zhang YE Chen C Hvilsom C Epps CW Chemnick LG Dong Y Mirarab S Siegismund HR Ryder OA Gilbert MTP Lewin HA Zhang G Heller R Wang W Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits Science 2019 364 eaav6202 10.1126/science.aav6202 31221828
Chen L, Qiu Q, Jiang Y, Wang K, Lin Z, Li Z, Bibi F, Yang Y, Wang J, Nie W, Su W, Liu G, Li Q, Fu W, Pan X, Liu C, Yang J, Zhang C, Yin Y, Wang Y, Zhao Y, Zhang C, Wang Z, Qin Y, Liu W, Wang B, Ren Y, Zhang R, Zeng Y, da Fonseca RR, Wei B, Li R, Wan W, Zhao R, Zhu W, Wang Y, Duan S, Gao Y, Zhang YE, Chen C, Hvilsom C, Epps CW, Chemnick LG, Dong Y, Mirarab S, Siegismund HR, Ryder OA, Gilbert MTP, Lewin HA, Zhang G, Heller R, Wang W (2019) Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits. Science 364:eaav620231221828 10.1126/science.aav6202
Chin CS Alexander DH Marks P Klammer AA Drake J Heiner C Clum A Copeland A Huddleston J Eichler EE Turner SW Korlach J Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data Nat Methods 2013 10 563 569 10.1038/nmeth.2474 23644548
Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–56923644548 10.1038/nmeth.2474
Daane JM Detrich HW Adaptations and diversity of Antarctic fishes: a genomic perspective Ann Rev Anim Biosci 2022 10 39 62 10.1146/annurev-animal-081221-064325 34748709
Daane JM, Detrich HW (2022) Adaptations and diversity of Antarctic fishes: a genomic perspective. Ann Rev Anim Biosci 10:39–6234748709 10.1146/annurev-animal-081221-064325
Divakar PK Crespo A Kraichak E Leavitt SD Singh G Schmitt I Lumbsch HT Using a temporal phylogenetic method to harmonize family-and genus-level classification in the largest clade of lichen-forming fungi Fungal Divers 2017 84 101 117 10.1007/s13225-017-0379-z
Divakar PK, Crespo A, Kraichak E, Leavitt SD, Singh G, Schmitt I, Lumbsch HT (2017) Using a temporal phylogenetic method to harmonize family-and genus-level classification in the largest clade of lichen-forming fungi. Fungal Divers 84:101–11710.1007/s13225-017-0379-z
Esseen P-A Ericson L Lindström H Zackrisson O Occurrence and ecology of usnea longissima in central Sweden Lichenologist 1981 13 177 190 10.1017/S0024282981000224
Esseen P-A, Ericson L, Lindström H, Zackrisson O (1981) Occurrence and ecology of usnea longissima in central Sweden. Lichenologist 13:177–19010.1017/S0024282981000224
Flynn JM Hubley R Goubert C Rosen J Clark AG Feschotte C Smit AF RepeatModeler2 for automated genomic discovery of transposable element families Proc Natl Acad Sci USA 2020 117 9451 9457 10.1073/pnas.1921046117 32300014
Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, Smit AF (2020) RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci USA 117:9451–945732300014 10.1073/pnas.1921046117
Griffiths-Jones S Moxon S Marshall M Khanna A Eddy SR Bateman A Rfam: annotating non-coding RNAs in complete genomes Nucleic Acids Res 2005 33 D121 D124 10.1093/nar/gki081 15608160
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33:D121–D12415608160 10.1093/nar/gki081
Grigoriev IV Nikitin R Haridas S Kuo A Ohm R Otillar R Riley R Salamov A Zhao XL Korzeniewski F Smirnova T Nordberg H Dubchak I Shabalov I MycoCosm portal: gearing up for 1000 fungal genomes Nucleic Acids Res 2014 42 D699 D704 10.1093/nar/gkt1183 24297253
Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, Riley R, Salamov A, Zhao XL, Korzeniewski F, Smirnova T, Nordberg H, Dubchak I, Shabalov I (2014) MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res 42:D699–D70424297253 10.1093/nar/gkt1183
Haas BJ Salzberg SL Zhu W Pertea M Allen JE Orvis J White O Buell CR Wortman JR Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments Genome Biol 2008 9 R7 10.1186/gb-2008-9-1-r7 18190707
Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR (2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol 9:R718190707 10.1186/gb-2008-9-1-r7
Hawksworth DL Grube M Lichens redefined as complex ecosystems New Phytol 2020 227 1281 1283 10.1111/nph.16630 32484275
Hawksworth DL, Grube M (2020) Lichens redefined as complex ecosystems. New Phytol 227:1281–128332484275 10.1111/nph.16630
Hecker N Hiller M A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers GigaScience 2020 9 giz159 10.1093/gigascience/giz159 31899510
Hecker N, Hiller M (2020) A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers. GigaScience 9:giz15931899510 10.1093/gigascience/giz159
Honegger R Margulis L Fester R Symbiosis and fungal evolution: symbiosis and morphogenesis Evolution and speciation: symbiosis as a source of evolutionary innovation 1991 MIT Press
Honegger R (1991) Symbiosis and fungal evolution: symbiosis and morphogenesis. In: Margulis L, Fester R (eds) Evolution and speciation: symbiosis as a source of evolutionary innovation. MIT Press
Hori H Methylated nucleosides in tRNA and tRNA methyltransferases Front Genet 2014 5 144 10.3389/fgene.2014.00144 24904644
Hori H (2014) Methylated nucleosides in tRNA and tRNA methyltransferases. Front Genet 5:14424904644 10.3389/fgene.2014.00144
Jansson KU Palmqvist K Esseen P-A Growth of the old forest lichen Usnea longissima at forest edges Lichenologist 2009 41 663 672 10.1017/S0024282909008536
Jansson KU, Palmqvist K, Esseen P-A (2009) Growth of the old forest lichen Usnea longissima at forest edges. Lichenologist 41:663–67210.1017/S0024282909008536
Kannan S Chernikova D Rogozin IB Poliakov E Managadze D Koonin EV Milanesi L Transposable element insertions in long intergenic non-coding RNA genes Front in Bioeng Biotechnol 2015 3 71 10.3389/fbioe.2015.00071
Kannan S, Chernikova D, Rogozin IB, Poliakov E, Managadze D, Koonin EV, Milanesi L (2015) Transposable element insertions in long intergenic non-coding RNA genes. Front in Bioeng Biotechnol 3:7110.3389/fbioe.2015.00071
Kapusta A Kronenberg Z Lynch VJ Zhuo X Ramsay L Bourque G Yandell M Feschotte C Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs PLoS Genet 2013 9 e1003470 10.1371/journal.pgen.1003470 23637635
Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C (2013) Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet 9:e100347023637635 10.1371/journal.pgen.1003470
Keilwagen J Wenk M Erickson JL Schattat MH Grau J Hartung F Using intron position conservation for homology-based gene prediction Nucleic Acids Res 2016 44 e89 10.1093/nar/gkw092 26893356
Keilwagen J, Wenk M, Erickson JL, Schattat MH, Grau J, Hartung F (2016) Using intron position conservation for homology-based gene prediction. Nucleic Acids Res 44:e8926893356 10.1093/nar/gkw092
Kelley D Rinn J Transposable elements reveal a stem cell-specific class of long noncoding RNAs Genome Biol 2012 13 R107 10.1186/gb-2012-13-11-r107 23181609
Kelley D, Rinn J (2012) Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol 13:R10723181609 10.1186/gb-2012-13-11-r107
Keon D Growth of Usnea longissima across a variety of habitats in the oregon coast range Bryologist 2009 105 233 242 10.1639/0007-2745(2002)105[0233:GOULAA]2.0.CO;2
Keon D (2009) Growth of Usnea longissima across a variety of habitats in the oregon coast range. Bryologist 105:233–24210.1639/0007-2745(2002)105[0233:GOULAA]2.0.CO;2
Klionsky DJ Herman PK Emr SD The fungal vacuole-composition, function, and biogenesis Microbiol Rev 1990 54 266 292 10.1128/mr.54.3.266-292.1990 2215422
Klionsky DJ, Herman PK, Emr SD (1990) The fungal vacuole-composition, function, and biogenesis. Microbiol Rev 54:266–2922215422 10.1128/mr.54.3.266-292.1990
Krzywinski M Schein J Birol I Connors J Gascoyne R Horsman D Jones SJ Marra MA Circos: an information aesthetic for comparative genomics Genome Res 2009 19 1639 1645 10.1101/gr.092759.109 19541911
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–164519541911 10.1101/gr.092759.109
Lagesen K Hallin P Rodland EA Stærfeldt HH Rognes T Ussery DW RNAmmer: consistent and rapid annotation of ribosomal RNA genes Nucleic Acids Res 2007 35 3100 3108 10.1093/nar/gkm160 17452365
Lagesen K, Hallin P, Rodland EA, Stærfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–310817452365 10.1093/nar/gkm160
Langmead B Salzberg SL Fast gapped-read alignment with Bowtie 2 Nat Methods 2012 9 357 U54 10.1038/nmeth.1923 22388286
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357-U5422388286 10.1038/nmeth.1923
Lengeler KB Davidson RC D’Souza C Harashima T Shen WC Wang P Pan XW Waugh M Heitman J Signal transduction cascades regulating fungal development and virulence Microbiol Mol Biol Rev 2000 64 746 785 10.1128/MMBR.64.4.746-785.2000 11104818
Lengeler KB, Davidson RC, D’Souza C, Harashima T, Shen WC, Wang P, Pan XW, Waugh M, Heitman J (2000) Signal transduction cascades regulating fungal development and virulence. Microbiol Mol Biol Rev 64:746–78511104818 10.1128/MMBR.64.4.746-785.2000
Li C Zhang Y Li JW Kong LS Hu HF Pan HL Xu LH Deng Y Li QY Jin LJ Yu H Chen Y Liu BH Yang LF Liu SP Zhang Y Lang YS Xia JQ He WM Shi Q Subramanian S Millar CD Meader S Rands CM Fujita MK Greenwold MJ Castoe TA Pollock D Gu WJ Nam K Ellegren H Ho SYW Burt DW Ponting CP Jarvis ED Gilbert MTP Yang HM Wang J Lambert DM Wang J Zhang GJ Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment Gigascience 2014 3 1 15 10.1186/2047-217X-3-27 24460651
Li C, Zhang Y, Li JW, Kong LS, Hu HF, Pan HL, Xu LH, Deng Y, Li QY, Jin LJ, Yu H, Chen Y, Liu BH, Yang LF, Liu SP, Zhang Y, Lang YS, Xia JQ, He WM, Shi Q, Subramanian S, Millar CD, Meader S, Rands CM, Fujita MK, Greenwold MJ, Castoe TA, Pollock D, Gu WJ, Nam K, Ellegren H, Ho SYW, Burt DW, Ponting CP, Jarvis ED, Gilbert MTP, Yang HM, Wang J, Lambert DM, Wang J, Zhang GJ (2014a) Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. Gigascience 3:1–1524460651 10.1186/2047-217X-3-27
Li Y Kromer B Schukraft G Bubenzer O Huang M-R Wang Z-M Bian L-G Li C-S Growth rate of Usnea aurantiacoatra (Jacq.) Bory on Fildes Peninsula, Antarctica and its climatic background PLoS ONE 2014 9 e100735 10.1371/journal.pone.0100735 24968131
Li Y, Kromer B, Schukraft G, Bubenzer O, Huang M-R, Wang Z-M, Bian L-G, Li C-S (2014b) Growth rate of Usnea aurantiacoatra (Jacq.) Bory on Fildes Peninsula, Antarctica and its climatic background. PLoS ONE 9:e10073524968131 10.1371/journal.pone.0100735
Liu H Suresh A Willard FS Siderovski DP Lu S Naqvi NI Rgs1 regulates multiple Gα subunits in Magnaporthe pathogenesis, asexual growth and thigmotropism EMBO J 2007 26 690 700 10.1038/sj.emboj.7601536 17255942
Liu H, Suresh A, Willard FS, Siderovski DP, Lu S, Naqvi NI (2007) Rgs1 regulates multiple Gα subunits in Magnaporthe pathogenesis, asexual growth and thigmotropism. EMBO J 26:690–70017255942 10.1038/sj.emboj.7601536
Liu FF Chen SF Ferreira MA Chang RL Sayari M Kanzi AM Wingfield BD Wingfield MJ Pizarro D Crespo A Divakar PK de Beer ZW Duong TA Draft genome sequences of five Calonectria species from Eucalyptus plantations in China, Celoporthe dispersa, Sporothrix phasma and Alectoria sarmentosa IMA Fungus 2019 10 1 13 10.1186/s43008-019-0023-5 32647610
Liu FF, Chen SF, Ferreira MA, Chang RL, Sayari M, Kanzi AM, Wingfield BD, Wingfield MJ, Pizarro D, Crespo A, Divakar PK, de Beer ZW, Duong TA (2019a) Draft genome sequences of five Calonectria species from Eucalyptus plantations in China, Celoporthe dispersa, Sporothrix phasma and Alectoria sarmentosa. IMA Fungus 10:1–1332647610 10.1186/s43008-019-0023-5
Liu Y Ul Qamar MT Feng JW Ding YD Wang S Wu GZ Ke LJ Xu Q Chen LL Comparative analysis of miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species BMC Plant Biol 2019 19 1 16 30606102
Liu Y, Ul Qamar MT, Feng JW, Ding YD, Wang S, Wu GZ, Ke LJ, Xu Q, Chen LL (2019b) Comparative analysis of miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species. BMC Plant Biol 19:1–1630606102
Liu Q Li W Liu D Li LY Li J Lv N Liu F Zhu BL Zhou YG Xin YH Dong XZ Light stimulates anoxic and oligotrophic growth of glacial Flavobacterium strains that produce zeaxanthin ISME J 2021 15 1844 1857 10.1038/s41396-020-00891-w 33452478
Liu Q, Li W, Liu D, Li LY, Li J, Lv N, Liu F, Zhu BL, Zhou YG, Xin YH, Dong XZ (2021) Light stimulates anoxic and oligotrophic growth of glacial Flavobacterium strains that produce zeaxanthin. ISME J 15:1844–185733452478 10.1038/s41396-020-00891-w
Lorenz C Lünse CE Mörl M tRNA modifications: impact on structure and thermal adaptation Biomolecules 2017 7 35 10.3390/biom7020035 28375166
Lorenz C, Lünse CE, Mörl M (2017) tRNA modifications: impact on structure and thermal adaptation. Biomolecules 7:3528375166 10.3390/biom7020035
Lowe TM Eddy SR tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence Nucleic Acids Res 1997 25 955 964 10.1093/nar/25.5.955 9023104
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–9649023104 10.1093/nar/25.5.955
Lücking R Nelsen MP Krings M Harper CJ Cúneo NR Rothwell GW Ediacarans, Protolichens, and lichen-derived Penicillium: a critical reassessment of the evolution of lichenization in fungi Transformative paleobotany 2018 Academic Press
Lücking R, Nelsen MP (2018) Ediacarans, Protolichens, and lichen-derived Penicillium: a critical reassessment of the evolution of lichenization in fungi. In: Krings M, Harper CJ, Cúneo NR, Rothwell GW (eds) Transformative paleobotany. Academic Press
Lyu HM He ZW Wu CI Shi SH Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes New Phytol 2018 217 428 438 10.1111/nph.14784 28960318
Lyu HM, He ZW, Wu CI, Shi SH (2018) Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes. New Phytol 217:428–43828960318 10.1111/nph.14784
Marzoll D Serrano FE Shostak A Schunke C Diernfellner ACR Brunner M Casein kinase 1 and disordered clock proteins form functionally equivalent, phospho-based circadian modules in fungi and mammals Proc Natl Acad Sci USA 2022 119 e2118286119 10.1073/pnas.2118286119 35217617
Marzoll D, Serrano FE, Shostak A, Schunke C, Diernfellner ACR, Brunner M (2022) Casein kinase 1 and disordered clock proteins form functionally equivalent, phospho-based circadian modules in fungi and mammals. Proc Natl Acad Sci USA 119:e211828611935217617 10.1073/pnas.2118286119
McCudden CR Hains MD Kimple RJ Siderovski DP Willard FS G-protein signaling: back to the future Cell Mol Life Sci 2005 62 551 577 10.1007/s00018-004-4462-3 15747061
McCudden CR, Hains MD, Kimple RJ, Siderovski DP, Willard FS (2005) G-protein signaling: back to the future. Cell Mol Life Sci 62:551–57715747061 10.1007/s00018-004-4462-3
McKenzie SK Walston RF Allen JL Complete, high-quality genomes from long-read metagenomic sequencing of two wolf lichen thalli reveals enigmatic genome architecture Genomics 2020 112 3150 3156 10.1016/j.ygeno.2020.06.006 32504651
McKenzie SK, Walston RF, Allen JL (2020) Complete, high-quality genomes from long-read metagenomic sequencing of two wolf lichen thalli reveals enigmatic genome architecture. Genomics 112:3150–315632504651 10.1016/j.ygeno.2020.06.006
Meiser A Otte J Schmitt I dal Grande F Sequencing genomes from mixed DNA samples—evaluating the metagenome skimming approach in lichenized fungi Sci Rep 2017 7 14881 10.1038/s41598-017-14576-6 29097759
Meiser A, Otte J, Schmitt I, dal Grande F (2017) Sequencing genomes from mixed DNA samples—evaluating the metagenome skimming approach in lichenized fungi. Sci Rep 7:1488129097759 10.1038/s41598-017-14576-6
Merges D dal Grande F Valim H Singh G Schmitt I Gene abundance linked to climate zone: parallel evolution of gene content along elevation gradients in lichenized fungi Front Microbiol 2023 14 1097787 10.3389/fmicb.2023.1097787 37032854
Merges D, dal Grande F, Valim H, Singh G, Schmitt I (2023) Gene abundance linked to climate zone: parallel evolution of gene content along elevation gradients in lichenized fungi. Front Microbiol 14:109778737032854 10.3389/fmicb.2023.1097787
O’Day CL Chavanikamannil F Abelson J 18S rRNA processing requires the RNA helicase-like protein Rrp3 Nucleic Acids Res 1996 24 3201 3207 10.1093/nar/24.16.3201 8774901
O’Day CL, Chavanikamannil F, Abelson J (1996) 18S rRNA processing requires the RNA helicase-like protein Rrp3. Nucleic Acids Res 24:3201–32078774901 10.1093/nar/24.16.3201
Ogata H Goto S Sato K Fujibuchi W Bono H Kanehisa M KEGG: Kyoto encyclopedia of genes and genomes Nucleic Acids Res 1999 27 29 34 10.1093/nar/27.1.29 9847135
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M (1999) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27:29–349847135 10.1093/nar/27.1.29
Øvstedal DO Smith RL Lichens of Antarctica and South Georgia: a guide to their identification and ecology 2001 Cambridge University Press
Øvstedal DO, Smith RL (2001) Lichens of Antarctica and South Georgia: a guide to their identification and ecology. Cambridge University Press
Papolu PK Ramakrishnan M Wei Q Vinod KK Zou LH Yrjala K Kalendar R Zhou MB Long terminal repeats (LTR) and transcription factors regulate PHRE1 and PHRE2 activity in Moso bamboo under heat stress BMC Plant Biol 2021 21 585 10.1186/s12870-021-03339-1 34886797
Papolu PK, Ramakrishnan M, Wei Q, Vinod KK, Zou LH, Yrjala K, Kalendar R, Zhou MB (2021) Long terminal repeats (LTR) and transcription factors regulate PHRE1 and PHRE2 activity in Moso bamboo under heat stress. BMC Plant Biol 21:58534886797 10.1186/s12870-021-03339-1
Park YI Do KH Kim IS Park HH Structural and functional studies of casein kinase I-like protein from rice Plant Cell Physiol 2012 53 304 311 10.1093/pcp/pcr175 22199373
Park YI, Do KH, Kim IS, Park HH (2012) Structural and functional studies of casein kinase I-like protein from rice. Plant Cell Physiol 53:304–31122199373 10.1093/pcp/pcr175
Parra G Blanco E Guigó R GeneID in Drosophila Genome Res 2000 10 511 515 10.1101/gr.10.4.511 10779490
Parra G, Blanco E, Guigó R (2000) GeneID in Drosophila. Genome Res 10:511–51510779490 10.1101/gr.10.4.511
Remm M Storm CEV Sonnhammer ELL Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J Mol Biol 2001 314 1041 1052 10.1006/jmbi.2000.5197 11743721
Remm M, Storm CEV, Sonnhammer ELL (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314:1041–105211743721 10.1006/jmbi.2000.5197
Romeike J Friedl T Helms G Ott S Genetic diversity of algal and fungal partners in four species of Umbilicaria (Lichenized ascomycetes) along a transect of the Antarctic Peninsula Mol Biol Evol 2002 19 1209 1217 10.1093/oxfordjournals.molbev.a004181 12140232
Romeike J, Friedl T, Helms G, Ott S (2002) Genetic diversity of algal and fungal partners in four species of Umbilicaria (Lichenized ascomycetes) along a transect of the Antarctic Peninsula. Mol Biol Evol 19:1209–121712140232 10.1093/oxfordjournals.molbev.a004181
Sancho LG Pintado A Navarro F Ramos M de Pablo MA Blanquer JM Raggio J Valladares F Green TGA Recent warming and cooling in the Antarctic Peninsula Region has rapid and large effects on lichen vegetation Sci Rep 2017 7 5689 10.1038/s41598-017-05989-4 28740147
Sancho LG, Pintado A, Navarro F, Ramos M, de Pablo MA, Blanquer JM, Raggio J, Valladares F, Green TGA (2017) Recent warming and cooling in the Antarctic Peninsula Region has rapid and large effects on lichen vegetation. Sci Rep 7:568928740147 10.1038/s41598-017-05989-4
Schley RJ Pellicer J Ge XJ Barrett C Bellot S Guignard MS Novak P Suda J Fraser D Baker WJ Dodsworth S Macas J Leitch AR Leitch IJ The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity New Phytol 2022 236 433 446 10.1111/nph.18323 35717562
Schley RJ, Pellicer J, Ge XJ, Barrett C, Bellot S, Guignard MS, Novak P, Suda J, Fraser D, Baker WJ, Dodsworth S, Macas J, Leitch AR, Leitch IJ (2022) The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity. New Phytol 236:433–44635717562 10.1111/nph.18323
Servant N Varoquaux N Lajoie BR Viara E Chen CJ Vert JP Heard E Dekker J Barillot E HiC-Pro: an optimized and flexible pipeline for Hi-C data processing Genome Biol 2015 16 1 11 10.1186/s13059-015-0831-x 25583448
Servant N, Varoquaux N, Lajoie BR, Viara E, Chen CJ, Vert JP, Heard E, Dekker J, Barillot E (2015) HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol 16:1–1125583448 10.1186/s13059-015-0831-x
Singh G Calchera A Schulz M Drechsler M Bode HB Schmitt I dal Grande F Climate-specific biosynthetic gene clusters in populations of a lichen-forming fungus Environ Microbiol 2021 23 4260 4275 10.1111/1462-2920.15605 34097344
Singh G, Calchera A, Schulz M, Drechsler M, Bode HB, Schmitt I, dal Grande F (2021) Climate-specific biosynthetic gene clusters in populations of a lichen-forming fungus. Environ Microbiol 23:4260–427534097344 10.1111/1462-2920.15605
Son Y-E Jung WH Oh S-H Kwak J-H Cárdenas ME Park H-S Mon1 is essential for fungal virulence and stress survival in Cryptococcus neoformans Mycobiology 2018 46 114 121 10.1080/12298093.2018.1468053 29963312
Son Y-E, Jung WH, Oh S-H, Kwak J-H, Cárdenas ME, Park H-S (2018) Mon1 is essential for fungal virulence and stress survival in Cryptococcus neoformans. Mycobiology 46:114–12129963312 10.1080/12298093.2018.1468053
Stanke M Schöffmann O Morgenstern B Waack S Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources BMC Bioinform 2006 7 1 11 10.1186/1471-2105-7-62
Stanke M, Schöffmann O, Morgenstern B, Waack S (2006) Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinform 7:1–1110.1186/1471-2105-7-62
Thell A Crespo A Divakar PK Kärnefelt I Leavitt SD Lumbsch HT Seaward MR A review of the lichen family Parmeliaceae–history, phylogeny and current taxonomy Nordic J Bot 2012 30 641 664 10.1111/j.1756-1051.2012.00008.x
Thell A, Crespo A, Divakar PK, Kärnefelt I, Leavitt SD, Lumbsch HT, Seaward MR (2012) A review of the lichen family Parmeliaceae–history, phylogeny and current taxonomy. Nordic J Bot 30:641–66410.1111/j.1756-1051.2012.00008.x
Thompson PJ Macfarlan TS Lorincz MC Long terminal repeats: from parasitic elements to building blocks of the transcriptional regulatory repertoire Mol Cell 2016 62 766 776 10.1016/j.molcel.2016.03.029 27259207
Thompson PJ, Macfarlan TS, Lorincz MC (2016) Long terminal repeats: from parasitic elements to building blocks of the transcriptional regulatory repertoire. Mol Cell 62:766–77627259207 10.1016/j.molcel.2016.03.029
Walker BJ Abeel T Shea T Priest M Abouelliel A Sakthikumar S Cuomo CA Zeng QD Wortman J Young SK Earl AM Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement PLoS ONE 2014 9 e112963 10.1371/journal.pone.0112963 25409509
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng QD, Wortman J, Young SK, Earl AM (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9:e11296325409509 10.1371/journal.pone.0112963
Wang D Qin BX Li X Tang D Zhang Y Cheng ZK Xue YB Nucleolar DEAD-Box RNA helicase TOGR1 regulates thermotolerant growth as a pre-rRNA chaperone in rice Plos Genet 2016 12 e1005844 10.1371/journal.pgen.1005844 26848586
Wang D, Qin BX, Li X, Tang D, Zhang Y, Cheng ZK, Xue YB (2016) Nucleolar DEAD-Box RNA helicase TOGR1 regulates thermotolerant growth as a pre-rRNA chaperone in rice. Plos Genet 12:e100584426848586 10.1371/journal.pgen.1005844
Wang Y Wei X Bian Z Wei J Xu JR Coregulation of dimorphism and symbiosis by cyclic AMP signaling in the lichenized fungus Umbilicaria muhlenbergii Proc Natl Acad Sci USA 2020 117 23847 23858 10.1073/pnas.2005109117 32873646
Wang Y, Wei X, Bian Z, Wei J, Xu JR (2020) Coregulation of dimorphism and symbiosis by cyclic AMP signaling in the lichenized fungus Umbilicaria muhlenbergii. Proc Natl Acad Sci USA 117:23847–2385832873646 10.1073/pnas.2005109117
Wang Y Li R Wang D Qian B Bian Z Wei J Wei X Xu J-R Regulation of symbiotic interactions and primitive lichen differentiation by UMP1 MAP kinase in Umbilicaria muhlenbergii Nat Commun 2023 14 6972 10.1038/s41467-023-42675-8 37914724
Wang Y, Li R, Wang D, Qian B, Bian Z, Wei J, Wei X, Xu J-R (2023) Regulation of symbiotic interactions and primitive lichen differentiation by UMP1 MAP kinase in Umbilicaria muhlenbergii. Nat Commun 14:697237914724 10.1038/s41467-023-42675-8
Wauchope HS Shaw JD Terauds A A snapshot of biodiversity protection in Antarctica Nat Commun 2019 10 946 10.1038/s41467-019-08915-6 30808907
Wauchope HS, Shaw JD, Terauds A (2019) A snapshot of biodiversity protection in Antarctica. Nat Commun 10:94630808907 10.1038/s41467-019-08915-6
White TJ Bruns T Lee S Taylor J Innis MA Gelfand DH Sninsky JJ White TJ Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics PCR Protocols 1990 Academic Press
White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR Protocols. Academic Press
Wilken PM Aylward J Chand R Grewe F Lane FA Sinha S Ametrano C Distefano I Divakar PK Duong TA Huhndorf S Kharwar RN Lumbsch HT Navathe S Pérez CA Ramírez-Berrutti N Sharma R Sun YK Wingfield BD Wingfield MJ IMA genome-F13: draft genome sequences of Ambrosiella cleistominuta, Cercospora brassicicola, C. citrullina, Physcia stellaris, and Teratosphaeria pseudoeucalypti IMA Fungus 2020 11 1 17 10.1186/s43008-020-00039-7 32617253
Wilken PM, Aylward J, Chand R, Grewe F, Lane FA, Sinha S, Ametrano C, Distefano I, Divakar PK, Duong TA, Huhndorf S, Kharwar RN, Lumbsch HT, Navathe S, Pérez CA, Ramírez-Berrutti N, Sharma R, Sun YK, Wingfield BD, Wingfield MJ (2020) IMA genome-F13: draft genome sequences of Ambrosiella cleistominuta, Cercospora brassicicola, C. citrullina, Physcia stellaris, and Teratosphaeria pseudoeucalypti. IMA Fungus 11:1–1732617253 10.1186/s43008-020-00039-7
Wirtz N Printzen C Sancho LG Lumbsch TH The phylogeny and classification of Neuropogon and Usnea (Parmeliaceae, Ascomycota) revisited Taxon 2006 55 367 376 10.2307/25065584
Wirtz N, Printzen C, Sancho LG, Lumbsch TH (2006) The phylogeny and classification of Neuropogon and Usnea (Parmeliaceae, Ascomycota) revisited. Taxon 55:367–37610.2307/25065584
Wu T Hu E Xu S Chen M Guo P Dai Z Feng T Zhou L Tang W Zhan L Fu X Liu S Bo X Yu G clusterProfiler 4.0: a universal enrichment tool for interpreting omics data Innovation (camb) 2021 2 100141 34557778
Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, Feng T, Zhou L, Tang W, Zhan L, Fu X, Liu S, Bo X, Yu G (2021) clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation (camb) 2:10014134557778
Yang Z PAML 4: phylogenetic analysis by maximum likelihood Mol Biol Evol 2007 24 8 1586 1591 10.1093/molbev/msm088 17483113
Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24(8):1586–159117483113 10.1093/molbev/msm088
Yang QX Wang YY Lücking R Lumbsch HT Du ZY Chen YK Bai M Ren D Wei JC Li H Wang YJ Wei XL The Jurassic epiphytic macrolichen reveals the oldest lichen-plant interaction in a Mesozoic forest ecosystem iScience 2023 26 105770 10.1016/j.isci.2022.105770 36590161
Yang QX, Wang YY, Lücking R, Lumbsch HT, Du ZY, Chen YK, Bai M, Ren D, Wei JC, Li H, Wang YJ, Wei XL (2023) The Jurassic epiphytic macrolichen reveals the oldest lichen-plant interaction in a Mesozoic forest ecosystem. iScience 26:10577036590161 10.1016/j.isci.2022.105770
Yu JH Wieser J Adams TH The Aspergillus FlbA RGS domain protein antagonizes G protein signaling to block proliferation and allow development EMBO J 1996 15 5184 5190 10.1002/j.1460-2075.1996.tb00903.x 8895563
Yu JH, Wieser J, Adams TH (1996) The Aspergillus FlbA RGS domain protein antagonizes G protein signaling to block proliferation and allow development. EMBO J 15:5184–51908895563 10.1002/j.1460-2075.1996.tb00903.x
Zdobnov EM Apweiler R InterProScan - an integration platform for the signature-recognition methods in InterPro Bioinformatics 2001 17 847 848 10.1093/bioinformatics/17.9.847 11590104
Zdobnov EM, Apweiler R (2001) InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17:847–84811590104 10.1093/bioinformatics/17.9.847
Zhang ZH Qu CF Zhang KJ He YY Zhao X Yang LX Zheng Z Ma XY Wang XX Wang WY Wang K Li D Zhang LP Zhang X Su DY Chang X Zhou MY Gao D Jiang WK Leliaert F Bhattacharya D de Clerck O Zhong BJ Miao JL Adaptation to extreme Antarctic environments revealed by the genome of a sea ice green alga Curr Biol 2020 30 3330 3341 10.1016/j.cub.2020.06.029 32619486
Zhang ZH, Qu CF, Zhang KJ, He YY, Zhao X, Yang LX, Zheng Z, Ma XY, Wang XX, Wang WY, Wang K, Li D, Zhang LP, Zhang X, Su DY, Chang X, Zhou MY, Gao D, Jiang WK, Leliaert F, Bhattacharya D, de Clerck O, Zhong BJ, Miao JL (2020) Adaptation to extreme Antarctic environments revealed by the genome of a sea ice green alga. Curr Biol 30:3330–334132619486 10.1016/j.cub.2020.06.029
Zhang TT, Grube M, Wei XL (2023) Host selection tendency of key microbiota in arid desert lichen crusts. iMeta e138
Zhao X Kim Y Park G Xu J-R A mitogen-activated protein kinase cascade regulating infection-related morphogenesis in Magnaporthe grisea Plant Cell 2005 17 1317 1329 10.1105/tpc.104.029116 15749760
Zhao X, Kim Y, Park G, Xu J-R (2005) A mitogen-activated protein kinase cascade regulating infection-related morphogenesis in Magnaporthe grisea. Plant Cell 17:1317–132915749760 10.1105/tpc.104.029116
Zhong HL Neubig RR Regulator of G protein signaling proteins: novel multifunctional drug targets J Pharmacol Exp Ther 2001 297 837 845 11356902
Zhong HL, Neubig RR (2001) Regulator of G protein signaling proteins: novel multifunctional drug targets. J Pharmacol Exp Ther 297:837–84511356902
Zhu Y Zhou D Bai NS Liu Q Zhao N Yang J SNARE protein AoSec22 orchestrates mycelial growth, vacuole assembly, trap formation, stress response, and secondary metabolism in Arthrobotrys oligospora J Fungi 2023 9 75 91 10.3390/jof9010075
Zhu Y, Zhou D, Bai NS, Liu Q, Zhao N, Yang J (2023) SNARE protein AoSec22 orchestrates mycelial growth, vacuole assembly, trap formation, stress response, and secondary metabolism in Arthrobotrys oligospora. J Fungi 9:75–9110.3390/jof9010075
