==== Front Mitochondrial DNA B Resour Mitochondrial DNA B Resour Mitochondrial DNA. Part B, Resources 2380-2359 Taylor & Francis 10.1080/23802359.2019.1691948 1691948 Version of RecordResearch Article Mitogenome Announcement The complete chloroplast genome of a Cymbidium Tortisepalum (Orchidaceae) male mutant X. Ma et al.Mitochondrial DNA Part Bhttps://orcid.org/0000-0002-5456-6590Sun Yangna Chen Yanqiong Lin Han Ma Xiaokai FAFU and FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology; Plant Immunity Center; The Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization (Fuzhou); College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China CONTACT Xiaokai Ma maequus@126.comFAFU and UIUC-SIB Joint Center for Genomics and Biotechnology; Plant Immunity Center; The Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization (Fuzhou); College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China 18 11 2019 2019 4 2 4087 4088 © 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 The chloroplast (cp) genome of natural male mutant Cymbidium tortisepalum ‘Guanshihe’ has been characterized using Illumina pair-end sequencing technology. The complete cp genome was 149,830 bp in length, containing a large single-copy region (LSC) of 85,131 bp and a small single-copy region (SSC) of 13,275 bp, which were separated by a pair of 25,712 bp inverted repeat regions (IRs). The genome contained 130 genes, with 111 unique genes, including 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content is 37.09% with the values of the LSC, SSC, and IR regions are 34.40%, 29.63%, and 43.45%, respectively. Further, phylogenetic analysis suggested that the plastome of C. tortisepalum male mutant ‘Guanshihe’ is close to sequenced C. sinense, C. kanran, C. tortisepalum, and C. ensifolium plastomes. Keywords Cymbidium tortisepalumfemale sterilityplastomephylogenyOrchidaceae ==== Body Cymbidium tortisepalum Lindl., is a terrestrial orchid distributed in the southern China (Chen et al. 2009). This species contains various types of novel varieties with natural mutant flowers. Because of its high ornamental value, it is widely cultivated in southeast Asian countries. Cymbidium tortisepalum male mutant ‘Guanshihe’ with female sterility is one of these famous phenotypes. However, there is no information on its plastome and its relationship to other species in the genus. Here, we first reported the complete chloroplast genome of a male mutant C. tortisepalum ‘Guanshihe’ and its phylogenetic position in Cymbidium genus. In this study, the complete chloroplast genome sequence of C. tortisepalum ‘Guanshihe’ was assembled and annotated. The specimen was collected from Dali, Yunnan, China (N 25°25′, E 100°00′) and then deposited in Fujian Agriculture and Forestry University (specimen voucher X.K. Ma 002). Total genomic DNA was extracted from dry leaves using a modified DNA extraction kit (Tiangen Biotech Ltd., Beijing, China) and sequenced based on the PE150 Illumina pair-end platform. The filtered reads were assembled using GetOrganelle pipe-line (https://github.com/Kinggerm/GetOrganelle) with a list of cp genomes in Orchidaceae as the reference. The assembled chloroplast genome was edited using Bandage software (Wick et al. 2015), and was then annotated using Geneious R11.15 (Biomatters Ltd., Auckland, New Zealand) (Kearse et al. 2012). The annotation result was used to draw the physical map using OGDRAW (http://ogdraw.mpimp-golm.mpg.de/) (Lohse et al. 2013). The novel annotated complete chloroplast genome was submitted to GenBank with accession number MN497243. The complete chloroplast genome of male mutant C. tortisepalum ‘Guanshihe’ is 149,830 base pairs (bp) in length, containing a large single-copy (LSC) region of 85,131 bp, and a small single-copy (SSC) region of 13,275 bp, which were separated by two inverted repeat (IR) regions of 25,712 bp. The new plastome possesses total 130 genes, with 111 unique genes (including 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes). Among all of these genes, seven protein-coding genes (i.e. ndhB, rpl2, rpl23, rps12, rps19, rps7 and ycf2), four rRNA genes (i.e. 4.5S, 5S, 16S, and 23S rRNA), and eight tRNA genes (i.e. trnA-UGC, trnH-GUG, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, trnV-GAC) occur in double copies. The overall GC-content of the whole plastome is 37.09%, while the corresponding values of the LSC, SSC, and IR regions are 34.40%, 29.63%, and 43.45%, respectively. To figure out its phylogenetic position, a ML tree was constructed based on published cp genome sequences of 12 Cymbidium species and two outgroup Dendrobium species using IQ-tree (Nguyen et al. 2015) with 1000 bootstrap replicates. The 15 sequences were aligned using Muscle (Edgar 2004). BMGE tools (Criscuolo and Gribaldo 2010) was then used to prune the aligned sequences. The ModelFinder module in IQ-tree was used to search the optimal nucleotide substitution model. Finally, the best model TVM + F+R2 was chosen to construct the phylogenetic tree according to BIC criteria using IQ-tree. Our results showed that the male mutant C. tortisepalum ‘Guanshihe’ is close to C. sinense, C. kanran, C. tortisepalum, and C. ensifolium with 100% bootstrap support (Figure 1). This newly reported chloroplast genome will support researchers to study the evolution of plastomes among Cymbidium species and their phylogenetic relationships. Figure 1. The maximum-likelihood (ML) tree based on 13 complete cp genome in Cymbidium, with Dendrobium nobile and D. catenatum as outgroups, boot-strap support value with 1000 replicates labeled on each node. Disclosure statement No potential conflict of interest was reported by the authors. ==== Refs References Chen X , Liu Z , Zhu GH , Lang KY , Ji ZH , Luo YB , Jin XH , Cribb PJ 2009 Orchidaceae, Flora of China . Beijing : Science Press & Missouri Botanical Garden Press , pp. 260 . Criscuolo A , Gribaldo S 2010 BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments . BMC Evol Biol . 10 (1 ):210 .20626897 Edgar RC 2004 MUSCLE: multiple sequence alignment with high accuracy and high throughput . 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