Complete chloroplast genome of Caragana intermedia (Fabaceae), an endangered shrub endemic to china
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TECHNICAL NOtE
Complete chloroplast genome of Caragana intermedia (Fabaceae), an endangered shrub endemic to china Zi-long Zhang1 · Li-ying Ma1 · Hong-bin Yao1 · Xin Yang1 · Ji-huai Luo1 · Xue Gong1 · Shuo-yue Wei1 · Quan-fang Li1 · Wei Wang1 · Hong-bin Sun1
Received: 7 July 2016 / Accepted: 17 August 2016 © Springer Science+Business Media Dordrecht 2016
Abstract Caragana intermedia is an important shrub plant with high ecological and economic value. Here, we reported and analyzed the complete chloroplast (cp) genome of C. intermedia. This cp genome is relatively short (129,331 bp) because it lacks an Inverted Repeat (IR) region. It comprises 111 genes, including four unique rRNAs, 31 tRNAs, and 76 protein-coding genes. Similar to other closely related plastomes, rpl22 and rps16 are absent, and the GC content is relatively low (31.6 %). The phylogenetic analysis suggested that C. intermedia is closely related to the genera of Astragalus. Keywords Caragana intermedia · Chloroplast genome · Inverted repeat-lacking clade (IRLC)
Caragana intermedia (Fabaceae) is an important shrub species endemic to the Ordos Plateau area of China. This species plays a key role in the local desert steppe ecosystem due to its strong cold- and drought resistance. Furthermore, it’s also an important forage for live-stock, and potential energy shrub species with good economic value (Zhou et al. 2005). However, largely due to anthropogenic over-exploitation and climatic environment’s change, C. intermedia has been listed among endangered plants by local governments, and need urgent protection and restoration. The chloroplast (cp) genome information is a valuable resource for plant phylogenetics and population genetics research and may provide
Hong-bin Sun [email protected] 1
Key Laboratory of Science and Technology Research and Application, Lanzhou 730070, Gansu Province, China
valuable guidelines for the conservation of C. intermedia. In this study, we assembled and characterized the complete cp genome of C. intermedia (GenBank: KX289923) using Illumina sequencing data. Fresh leaves were collected from Wuzhai County, Shanxi Province, China, and cp DNA was extracted by using modified CTAB method (Doyle and Doyle 1987). The wholegenomic DNA data was sequenced using the Illumina Hiseq 2000 Platform (Illumina, San Diego, CA). We assembled the complete cp genome with Velvet v 1.0 software (Zerbino and Birney 2008), with the cp genomes of Astragalus mongholicus (K R296789), Medicago hybrida (NC_027153), Lathyrus pubescens (NC_027079), Glycyrrhiz a glabra (KF201590), Vigna unguiculata (K J468104), and Lotus japonicus (NC_002694) as the reference. The cp genome was annotated with the program Plann (Huang and Cronk 2015) and Sequin (http://www.ncbi.nlm.nih.gov/). A physical map of the cp genome was generated by OGDRAW (http://ogdraw.mpimp-golm.mpg.de/). To confirm the phylogenetic position of C. intermedia, its chloroplast genome was aligned with ten reported chloroplast genomes using MAFFT (Katoh and Standley 2013) and a neighbor jo
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