==== Front Mitochondrial DNA B Resour Mitochondrial DNA B Resour Mitochondrial DNA. Part B, Resources 2380-2359 Taylor & Francis 10.1080/23802359.2019.1687361 1687361 Version of RecordResearch Article Mitogenome Announcement Chloroplast genome of critically endangered Cotoneaster wilsonii (Rosaceae) endemic to Ulleung Island, Korea J. Y. Yang et al.Yang Ji Young a Pak Jae-Hong a Kim Seung-Chul b a Research Institute for Dok-do and Ulleung-do Island, Department of Biology, School of Life Sciences, Kyungpook National University, Daegu, Republic of Korea; b Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea CONTACT Jae-Hong Pak jhpak@knu.ac.krResearch Institute for Dok-do and Ulleung-do Island and Department of Biology, School of Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu41566, Republic of Korea; Seung-Chul Kim sonchus96@skku.edu, sonchus2009@gmail.comDepartment of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon16419, Republic of Korea 8 11 2019 2019 4 2 3892 3893 © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.2019The Author(s)This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.http://creativecommons.org/licenses/by/4.0/Abstract Cotoneaster wilsonii Nakai is an endangered species endemic to Ulleung Island, Korea. Here we reported the first complete chloroplast gnome sequences of C. wilsonii, which is 159,999 bp in total length with the large single copy (LSC) region of 87,868 bp, the small single copy (SSC) region of 19,335 bp, and two inverted repeat (IR) regions of 26,399 bp. The plastome contains 131 genes, including 84 protein-coding, eight ribosomal RNA, and 37 transfer RNA genes. The overall GC content is 42.6% and those in the LSC, SSC, and IR regions are 34.2, 30.3, and 42.6%, respectively. Phylogenetic analysis of 21 representative plastomes within the family Rosaceae suggests strongly the monophyly of Cotoneaster and C. wilsonii being sister to the clade of Cotoneaster franchetii and Cotoneaster horizontalis. Keywords Chloroplast genomeendangered speciesCotoneaster wilsoniiUlleung IslandRosaceae ==== Body The genus Cotoneaster Medik. (Rosaceae) contains numerous ornamentally important shrubs and small trees, and consists of ca. 90 species widely distributed in the northern hemisphere, with the center of diversity in the Himalayas and western China (Yü 1974; Willis 1985; Fryer and Hylmö 2009). The majority of species (ca. 90%) are apomictic and tetraploid, and relationships within Cotoneaster are poorly known due in part to many species complex groups and considerable morphological variation (Kroon 1975; Bartish et al. 2001; Talent and Dickinson 2007; Fryer and Hylmö 2009; Dickoré and Kasperek 2010). The earliest classification system based primarily on petal characters (Koehne 1893) resulted in recognization of two subgenera, and several other classification systems have recently been proposed (Yü 1963; Flinck and Hylmö 1966; Phipps et al. 1990; Fryer and Hylmö 2009). Despite several attempts to determine phylogenetic relationships among species, we know little about interspecific relationships within Cotoneaster (Bartish et al. 2001; Lo and Donoghue 2012; Li et al. 2014). In the Korean Peninsula, two species of Cotoneaster, Cotoneaster wilsonii and Cotoneaster integerrimus Medik., are known to occur. While C. integerrimus is known to occur only in North Korea, C. wilsonii is endemic to Ulleung Island, which is young oceanic and volcanic island in East Sea. About 100 individuals of C. wilsonii are found in three subpopulations of sunny cliffs at 110–130 m above sea level, and designated as critically endangered species (CR B2ab(ii)) (National Institute of Biological Resources 2014). Although Chang and Jeon (2003) questioned a distinct species status of C. wilsonii based on flavonoids and morphology, overall species relationships within Cotoneaster multiflorus complex remain to be determined. In this study, we sequenced the complete plastome of C. wilsonii, and assessed its phylogenetic position within Rosaceae. The collecting permit was obtained via the Division of Forest Biodiversity of Korea National Arboretum. Total genomic DNA (voucher specimen: SKU-Yang1804025; N37°29′9′′ E130°54′28′′) was isolated from fresh leaves using the DNeasy Plant Mini Kit (Qiagen, Carlsbad, CA). Genome sequencing was conducted using the Illumina HiSeq 4000 (Illumina Inc., San Diego, CA). A total of 31,268,870 pair-end reads were obtained and assembled de novo with Velvet v. 1.2.10 using multiple k-mer (Zerbino and Birney 2008). The tRNAs were confirmed using tRNAsacn-SE (Lowe and Eddy 1997). The complete plastome sequence of C. wilsonii (Genbank accession number: MN516695) was 159,999 bp, with large single copy (LSC; 87,868 bp), small single copy (SSC; 19,335 bp), and two inverted repeats (IRa and IRb; 26,399 bp each). The overall GC content was 42.6% (LSC, 34.3%; SSC, 30.3%; IRs, 42.6%) and the plastome contained 131 genes, including 84 protein-coding, 8 rRNA, and 37 tRNA genes. The maximum likelihood (ML) analysis was conducted using IQ-TREE v.1.4.2 (Nguyen et al. 2015) to determine phylogenetic position of C. wilsonii based on plastomes of 21 representative species of Rosaceae. The complete plastome sequences were aligned using MAFFT v.7 (Katoh and Standley 2013). The ML tree confirmed that the genus Cotoneaster is monophyletic and showed that C. wilsonii is sister to Cotoneaster franchetii and Cotoneaster horizontalis clade (Figure 1). Figure 1. The maximum-likelihood (ML) tree based on the 21 representative chloroplast genomes of Rosaceae. The bootstrap value based on 1000 replicates is shown on each node. Disclosure statement The authors report no potential conflict of interest. The authors are responsible for the content and writing of the paper. ==== Refs References Bartish IV , Hylmö B , Nybom H 2001 RAPD analysis of interspecific relationships in presumably apomictic Cotoneaster species . Euphytica . 120 (2 ):273 –280 . Chang C-S , Jeon JI 2003 Leaf floavonoids in Cotoneaster wilsonii (Rosaceae) from the island Ulleung-do, Korea . Biochem Syst Ecol . 31 (2 ):171 –179 . Dickoré WB , Kasperek G 2010 Species of Cotoneaster (Rosaceae, Maloideae) indigenous to, naturalizing or commonly cultivated in central Europe . Willdenowia . 40 (1 ):13 –45 . Flinck KE , Hylmö B 1966 A list of series and species in the genus Cotoneaster . Bot Not . 119 :445 . Fryer J , Hylmö B 2009 Cotoneasters: a comprehensive guide to shrubs for flowers, fruit and foliage . Portland, OR; London, UK : Timber Press . Katoh K , Standley DM 2013 MAFFT multiple sequence alignment software version 7: improvements in performance and usability . Mol Biol Evol . 30 (4 ):772 –780 .23329690 Koehne E 1893 Deutsch . Dendrol . 224 Kroon GH 1975 Polyploidy in Cotoneaster II . Acta Bot Neerl . 24 (5–6 ):417 –420 . Li F , Fan Q , Li Q , Chen S , Guo W , Cui D , Liao W 2014 Molecular phylogeny of Cotoneaster (Rosaceae) inferred from nuclear ITS and multiple chloroplast sequences . Plant Syst Evol . 300 (6 ):1533 –1546 . Lo EYY , Donoghue MJ 2012 Expanded phylogenetic and dating analyses of the apples and their relatives . Mol Phylogenetics Evol . 63 (2 ):230 –243 . Lowe TM , Eddy SR 1997 tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence . Nucleic Acids Res . 25 (5 ):955 –964 .9023104 National Institute of Biological Resources 2014 Cotoneaster wilsonii In: Suh M-H , Lee B-Y , Kim ST , Park C-H , Oh H-K , Kim H-Y , Lee J-H , Lee SY , editors. Korean red list of threatened species . 2nd ed Incheon (Republic of Korea) : Ministry of environment ; p. 141 . Nguyen L-T , Schmidt HA , von Haeseler A , Minh BQ 2015 IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies . Mol Biol Evol . 32 (1 ):268 –274 .25371430 Phipps JB , Kenneth RR , Paul GS , Joseph RR 1990 A checklist of the subfamily Maloideae (Rosaceae) . Can J Bot . 68 :2209 –2269 . Talent N , Dickinson TA 2007 Apomixis: evolution, mechanism and perspectives In: Grossniklaus U , Hörandl E , Sharbel T , van Dijk P , editors. Apomixis and hybridization in Rosaceae subtribe Pyrineae Dumort: a new tool promises new insights . Ruggell (Liechtenstein) : Gantner Verlag ; p. 301 –316 . Willis SY 1985 A dictionary of the flowering plants and Ferns . Cambridge (UK) : Cambridge University Press . Yü TT 1963 Taxa nova Rosacearum sinicarum . Acta Phytotaxon Sin . 8 :14 . Yü TT 1974 Rosaceae. Flora Republicae Popularis Sinicae . Beijing (China) : Science press ; p. 36 . Chinese. Zerbino DR , Birney E 2008 Velvet: algorithms for de novo short read assembly using de Bruijn graphs . Genome Res . 18 (5 ):821 –829 .18349386