==== Front Mitochondrial DNA B Resour Mitochondrial DNA B Resour Mitochondrial DNA. Part B, Resources 2380-2359 Taylor & Francis 33366421 10.1080/23802359.2019.1670112 1670112 Version of Record Research Article Mitogenome Announcement The complete chloroplast genome sequence of a traditional Chinese medicine plant Bulbophyllum disciflorum Rolfe (Orchidaceae) Y. Tang et al. Tang Yang ab* Yang Jiapeng ab* Niu Zhitao ab Ding Xiaoyu ab a College of Life Sciences, Nanjing Normal University, Nanjing, China; b Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobium, Nanjing, China * These authors have contributed equally to this work. CONTACT Xiaoyu Ding dingxynj@263.netCollege of Life Sciences, Nanjing Normal University, Nanjing, China 9 12 2019 2020 5 1 5960 © 2019 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. 2019 The Author(s) https://creativecommons.org/licenses/by/4.0/ 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. Abstract Bulbophyllum disciflorum is one of Orchidaceae species, which has important ornamental and economic value. Here, we reported the first chloroplast genome sequence of Bulbophyllum. The genome of B. disciflorum is 148,554 bp in length, including a large single-copy (LSC) of 79,001 bp, a small single-copy (SSC) of 16,797 bp, and a pair of inverted repeat regions (IRa and IRb) of 26,378bp. It contains 108 unique genes consisting of 74 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The phylogenetic analysis revealed that Bulbophyllum is sister to the genus of Dendrobium. Keywords Bulbophyllum disciflorum traditional Chinese medicine chloroplast genome Epidendroideae National Natural Science Foundation of China10.13039/50110000180931670330 31900268 Priority Academic Program Development of Jiangsu Higher Education InstitutionsThis study was supported by grants from the National Natural Science Foundation of China [Grant No. 31670330 and No. 31900268] and the Priority Academic Program Development of Jiangsu Higher Education Institutions to XDY. ==== Body The genus Bulbophyllum, one of the largest genera in the family Orchidaceae, comprising approximately 2200 species, mainly distributed in tropical Asia, America, Africa, and Australasia. In China, there are about 110 species of this genus, some of which have been extensively used as Traditional Chinese Medicine (TCM) for hundreds of years. However, many wild Bulbophyllum species are in extreme danger of extinction. Here, we sequenced and assembled the complete chloroplast genome sequence of B. disciflorum, which is the first one in the genus, and reconstructed the phylogenetic relationship with other Orchidaceae species. Such a chloroplast genome sequence could provide abundant genetic information for identification, utilization, and breeding of Bulbophyllum species. For the DNA extraction of B. disciflorum, 2 g of fresh leaves were harvested. The plant was stored in the College of Life Sciences, Nanjing Normal University (voucher specimen No. Niu19015). Total genomic DNA was extracted using the DNeasy Plant Mini Kit (Qiagen, Dusseldorf, Germany) according to the manufacturer's instructions. Approximately, 3.5 Gb of 150 bp pair-end reads were yielded using an Illumina Hiseq4000 sequencer, and assembled on SOAP de novo (v2.04) and CLC Genomics Workbench 8.5.1 (CLC Bio, Aarhus, Denmark) as previously reported (Niu et al. 2017). The gaps and junctions between inverted repeat (IR) regions and single copy (SC) regions were confirmed by PCR amplification. Genes were annotated using DOGMA (Wyman et al. 2004) and tRNAscan-SE 1.21 (Schattner et al. 2005). The new annotated chloroplast genome sequence was deposited in GenBank (Accession No. LC498826). The newly sequenced chloroplast genome of B. disciflorum was 148,554 bp long with GC content of 37.94%. The genome consisted of an LSC region of 79,001 bp, an SSC region of 16,797 bp, and a pair of IR regions of 26,378 bp each. The chloroplast genome of B. disciflorum was well conserved, containing 30 unique tRNA genes, four unique rRNA genes, and 68 unique protein-coding genes (Figure 1). The sequence of eleven plastid NDH genes was compared to Apostasia odorata (NC_030722) which contains full set of functional NDH genes in orchids. Like other orchid species, B. disciflorum also experienced the loss of NDH genes. Among them, only the genes in IR regions contain full reading frames, whereas other ten plastid NDH genes were truncated or completely lost. Figure 1. Maximum likelihood tree of Epidendroideae species based on the whole chloroplast genome sequences with Goodyera procera and Goodyera velutina as outgroup. Numbers near the nodes represent ML bootstrap values. The phylogeny of Epidendroideae was reconstructed based on the multiple alignments of reported 11 orchid chloroplast genomes with Goodyera procera (NC_029363) and Goodyera velutina (NC_029365) as outgroup using MAFFT v. 7.427 (Nakamura et al. 2018). The best-fitting model of nucleotide substitution was GTR + I+G, as determined by the Akaike Information Criterion (AIC) in jModelTest v. 2.1.7 (Darriba et al. 2012). Maximum Likelihood (ML) analysis was conducted using RAxML 8.0.2 with 100 bootstrap replicates (Stamatakis 2014). As shown in Figure 1, the ML tree revealed: (1) the species of Epidendroideae formed a monophyly group; (2) the sister relationship between the genus of Bulbophyllum and Dendrobium was strongly supported (BS value = 100). These results were congruent with that revealed in the previous studies based on cpDNA fragments (Luo et al. 2014). Disclosure statement No potential conflict of interest was reported by the authors. ==== Refs References Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods. 9 (8 ):772. Luo J, Hou BW, Niu ZT, Liu W, Xue QY, Ding XY. 2014. Comparative chloroplast genomes of photosynthetic orchids: insights into evolution of the Orchidaceae and development of molecular markers for phylogenetic applications. PLoS One. 9 (6 ):e99016.24911363 Nakamura T, Yamada KD, Tomii K, Katoh K. 2018. Parallelization of MAFFT for large-scale multiple sequence alignments. 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