The complete chloroplast genome sequence of an endangered Orchidaceae species Dendrobium monilforme and its phylogenetic
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TECHNICAL NOTE
The complete chloroplast genome sequence of an endangered Orchidaceae species Dendrobium monilforme and its phylogenetic implications Yan‑xia Gao1,2 · Yu‑yan Zhou2 · Ying Xie2 · Li Feng2 · Shi‑gang Shen1
Received: 14 July 2017 / Accepted: 9 August 2017 © Springer Science+Business Media B.V. 2017
Abstract Dendrobium monilforme is an endangered Orchidaceae species distributed in Southwest China. Here we report the complete chloroplast (cp) genome sequence and the cp genomic features of D. monilforme. The genome is 152,136 bp long with 129 genes comprising 83 proteincoding genes, 40 tRNA genes and six rRNA genes. Most of the genes occurred in a single copy, while 18 occurred in two copies. Phylogenetic analysis of a data set of six cp genomes indicated that D. monilforme is closely related to other species in the genus Dendrobium. Keywords Dendrobium monilforme · Chloroplast genome · CITES The genus Dendrobium of the family Orchidaceae includes 74 species and two varieties in China (Tsi 1999). Wild Dendrobium plants have been widely used in traditional Chinese medicine (Halberstein 2005; Shoemaker et al. 2005; Wojcikowski and Gobe 2014) and are also quite popular in flower markets. The medicinal and ornamental needs resulted in over-exploitation, and several Dendrobium species have been consequently listed as endangered taxa by the Convention on International Trade in Endangered Species Yan-xia Gao and Yu-yan Zhou have contributed equally to this study. * Yan‑xia Gao [email protected] * Shi‑gang Shen [email protected] 1
Hebei University, Baoding, China
Hebei Provincial Institute for Drug Control, Shijiazhuang 050011, China
2
of Wild Fauna and Flora (CITES) (Xiang et al. 2011). D. monilforme has been used in Chinese traditional tonics and medicines for centuries due to some pharmacological actions, including nourishing Yin, clearing away “evil-heat”, enhancing the immune system, reducing blood sugar level, preventing cancer and prolonging life (Bulpitt et al. 2007). It is also an endangered herb of which the genetic diversity study suggests urgent conservation (Ye et al. 2015). Molecular methods such as the complete chloroplast (cp) genomes have been widely used in recent years to assess plant diversity and work on evolutionary problems. In this study, we sequenced the complete chloroplast genome and reported the cp genomic features of D. monilforme. The complete cp-genome sequence has been submitted to GenBank under the accession number of MF445418. Total genomic DNA was extracted from fresh mature leaves of D. monilforme, and sequenced on Illumina Hiseq 2500 platform (San Diego, CA). Genome sequences were screened out and assembled with SOAP de novo (v2.04) and CLC genomics workbench as previously reported (Nock et al. 2011), which resulted in a complete circular sequence of 152,136 bp in length. The cp-genome was annotated with Dual Organellar Genome Annotator (DOGMA) (Wyman et al. 2004). The 152,136 bp cp-genome is made up of a large single copy region (LSC, 85,082 bp), a
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