Characterization of the complete chloroplast genome of Cephalotaxus sinensis (Cephalotaxaceae), an endangered species en
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TECHNICAL NOTE
Characterization of the complete chloroplast genome of Cephalotaxus sinensis (Cephalotaxaceae), an endangered species endemic to China Xu Qiang1 · Yun Yang1 · Yun Jia1 · Ting Ren1 · Guo‑Qing Bai1,2 Received: 13 December 2017 / Accepted: 30 December 2017 © Springer Science+Business Media B.V., part of Springer Nature 2018
Abstract Cephalotaxus sinensis, is an endangered species endemic to China. Here, the complete chloroplast genome (plastome) of C. sinensis was obtained by using Illumina pair-end sequencing. The total genome size is 134,621 bp in length, and encodes 114 genes, including 82 protein-coding genes, 28 transfer RNA genes and four ribosomal RNA genes. The nucleotide composition is asymmetric (32.5% A, 17.7% C, 17.5% G and 32.9% T) with an overall G+C content of 35.2%. Unexpectedly, we observed the plastome lacks typical inverted repeat regions, which is consistent with C. oliveri plastome in the genus Cephalotaxus. Furthermore, a total of 38 simple sequences repeats were identified in the plastome of C. sinensis. The phylogenetic analysis based on 14 plastomes revealed that C. sinensis is closely related to C. oliveri. Keywords Chloroplast genome · Cephalotaxus sinensis · Relict species · Illumina sequencing Cephalotaxus sinensis, belonging to Cephalotaxaceae family, is an endangered conifer species endemic to China (Fu et al. 1999). This species is scattered along the Yangtze River Basin, occurring in moist areas and plays a vital role of wood production (Wang and Wang 1992). However, the population size of this species has been dramatically decreased on account of unreasonable deforestation and habitat deterioration and it has been listed in The IUCN Red List (Farjon et al. 2013). Therefore, the urgent conservation and management strategies should be established for this species. The complete plastome could provide valuable genomic information for the conservation and restoration of rarely relict species. Here, we characterized the complete plastome of the C. sinensis (GenBank: MF977938) based on Illumina pair-end sequencing. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12686-017-0978-8) contains supplementary material, which is available to authorized users. * Guo‑Qing Bai [email protected] 1
Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China
Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Institute of Botany of Shaanxi Province, Xi’an 710061, China
2
Young leaves of a C. sinensis individual were collected from Xi’an Botanical Garden, Shaanxi province. DNA extraction and Illumina sequencing were conducted by Novogene Technologies Inc. (Tianjin, China). Wholegenome sequencing was performed with 150 bp pair-end reads on the Illumina Hiseq 2500 platform. The sequencing raw reads were trimmed using NGSQC Toolkit_v.2.3.3 with the default parameters (Patel and Jain 2012). Subse
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