==== Front Mitochondrial DNA B Resour Mitochondrial DNA B Resour Mitochondrial DNA. Part B, Resources 2380-2359 Taylor & Francis 10.1080/23802359.2019.1669088 1669088 Version of RecordResearch Article Mitogenome Announcement The complete chloroplast genome of Dendrobium harveyanum (Orchidaceae) Z.-c. Huang et al.Huang Zhi-Cong ab Pan Yun-Yun ab Chen Gui-Zhen ab Chen Li Jun ab Wu Xin-Yi ab Huang Jie ab a Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Shenzhen, Guangdong, China; b Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, Guangdong, China CONTACT Jie Huang 13530401396@163.comShenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen518114, Guangdong, China 23 9 2019 2019 4 2 3200 3201 © 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 Dendrobium harveyanum is an endangered species of Orchidaceae. Here we report the complete chloroplast (cp) genome sequence and the cp genome features of D. harveyanum. The complete cp genome sequence of D. harveyanum is 157,292 bp in length and presented a typical quadripartite structure including one large single-copy region (LSC, 86,583 bp), one small single-copy region (SSC, 19,449 bp), and two inverted repeat regions (IRs, 25,630 bp each). The cp genome encoded 138 genes, of which 120 were unique genes. The phylogenetic relationships show that D. harveyanum is closely related to other species in Dendrobium. Keywords Dendrobium harveyanumchloroplast genomephylogeneticendangered speciesOrchidaceae ==== Body The genus Dendrobium belongs to the tribe Dendrobieae (Orchidaceae: Epidendroideae) and is one of the three largest genera in the family Orchidaceae with ∼1500 species, ranging through India across to Japan, south to Malaysia, and east to Australia, New Guinea, and the Pacific islands and is the second most common orchid genera in cultivation after the Cattleyas (Chen et al. 2009; Pridgeon et al. 2014). Since the establishment of Dendrobium by Swartz (Swartz 1799), various generic delimitations and infrageneric systems have been proposed (Li et al. 2005; Xu et al. 2014; Wang et al. 2017). Dendrobium species have an enormous economic value in global horticultural trade (Teixeira da Silva et al. 2016), and some Dendrobium species also have medicinal and pharmaceutical values (Teixeira da Silva et al. 2015). Genomic studies may contribute to the study of species identification, germplasm diversity, and genetic engineering (Lin et al. 2015). The complete chloroplast (cp) genome sequence of D. harveyanum was assembled in this study. Leaf samples of D. harveyanum were obtained from the Orchid Conservation and Research Centre of Shenzhen and specimens were deposited in the National Orchid Conservation Center herbarium (NOCC; specimen code Z.J.Liu 2509). Total genomic DNA was extracted from fresh material using the modified CTAB procedure of Doyle and Doyle (1987), and sequenced on Illumina Hiseq 2500 platform (San Diego, CA). Genome sequences were screened out and assembled with MITObim v1.8 (Hahn et al. 2013), which resulted in a complete circular sequence of 157,292 bp in length. The cp-genome was annotated with CpGAVAS (Liu et al. 2012). The cp genome sequence of D. harveyanum (MN245570) is 157,292 bp long and presented a typical quadripartite structure including one large single-copy region (LSC, 85,583 bp), one small single-copy region (SSC, 19,449 bp), and two inverted repeat regions (IRs, 25,630 bp each). The cp genome encoded 138 genes, of which 120 were unique genes (85 protein-coding genes, 31 tRNAs, and 4 rRNAs). Thirty-eight accessions of Dendrobium and two outgroups were used for the molecular analysis. The phylogenetic tree was constructed based on the maximum-likelihood (ML) method. The ML analysis was performed using the CIPRES Science Gateway web server (RAxML-HPC2 on XSEDE 8.2.10) with 1000 bootstrap replicates and settings as described by Stamatakis et al. (2008). The result showed that they were all clustered together (Figure 1). This newly reported cp genome will be helpful for further study on phylogenetic study, species identification, and genetic engineering. Figure 1. Phylogenetic position of Dendrobium harveyanum inferred by maximum-likelihood (ML) of complete cp genome. The bootstrap values are shown next to the nodes. Disclosure statement No potential conflict of interest was reported by the authors. ==== Refs References Chen SC , Liu ZJ , Zhu GH , Lang KY , Ji ZH , Luo YB , Jin XH , Cribb PJ , Wood JJ , Gale SW , et al. 2009 Orchidaceae In: Wu ZY , Raven PH , Hong D , editors. Flora of China . Vol. 25. St. Louis (MO) : Missouri Botanical Garden Press ; p. 211 –235 . Doyle JJ , Doyle JL 1987 A rapid DNA isolation procedure from small quantities of fresh leaf tissue . Phytochem Bull . 19 :11 –15 . Hahn C , Bachmann L , Chevreux B 2013 Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-a baiting and iterative mapping approach . Nucleic Acids Res . 41 :e129 .23661685 Li T , Wang J , Lu Z 2005 Accurate identification of closely related Dendrobium species with multiple species-specific gDNA probes . J Biochem Biophys Meth . 62 :111 –123 .15680281 Lin CS , Chen JJ , Huang YT , Chan MT , Daniell H , Chang WJ , Hsu CT , Liao DC , Wu FH , Lin SY , et al. 2015 The location and translocation of ndh genes of chloroplast origin in the Orchidaceae family . Sci Rep . 5 :9040 .25761566 Liu C , Shi LC , Zhu YJ , Chen HM , Zhang JH , Lin XH , Guan XJ 2012 CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences . BMC Genomics . 13 :715 .23256920 Pridgeon AM , Cribb PJ , Chase MW , Rasmussen FN 2014 Genera Orchidacearum . New York (NY); Oxford (UK) : Oxford University Press ; p. 1 –544 . Stamatakis A , Hoover P , Rougemont J 2008 A rapid bootstrap algorithm for the RAxML web-servers . System Biol . 75 :758 –771 . Swartz O 1799  Dendrobium moniliforme Nova acta Regiae . Soc Sci Upsal . 6 :85 . Teixeira da Silva JA , Jin X , Dobranszki J , Lu J , Wang H , Zotz G , Cardoso JC , Zeng S 2016 Advances in Dendrobium molecular research: applications in genetic variation, identification and breeding . Mol Phylogenet Evol . 95 :196 –216 .26493228 Teixeira da Silva JA , Tsavkelova EA , Ng TB , Parthibhan S , Dobranszki J , Cardoso JC , Rao MV , Zeng S 2015 Asymbiotic in vitro seed propagation of Dendrobium . Plant Cell Rep . 34 :1685 –1706 .26183950 Wang W , Yu HY , Li TH , Li LX , Zhang GQ , Liu ZJ , Huang TB , Zhang YX 2017 Comparative proteomics analyses of pollination response in endangered orchid species Dendrobium hrysanthum . IJMS . 18 :2496 . Xu Q , Zhang GQ , Liu ZJ , Luo YB 2014 Two new species of Dendrobium (Orchidaceae: Epidendroideae) from China: evidence from morphology and DNA . Phytotaxa . 174 :129 –143 .