Characterization of the complete chloroplast genome of Carpinus putoensis
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METHODS AnD RESOUrCES ArTICLE
Characterization of the complete chloroplast genome of Carpinus putoensis Shuo Feng1 · Xiuyue Xie1 · Mingcheng Wang1 · Yongzhi Yang1
Received: 20 August 2016 / Accepted: 23 August 2016 © Springer Science+Business Media Dordrecht 2016
Abstract The whole chloroplast (cp) genome sequence of Carpinus putoensis has been characterized from Illumina pair-end sequencing. The complete cp genome was 159,673 bp in length, containing a large single copy region (LSC) of 89,020 bp and a small single copy region (SSC) of 18,568 bp, which were separated by a pair of 26,044 and 26,043 bp inverted repeat regions (IRs). The genome contained 128 genes, including 83 protein-coding genes (75 PCG species), 36 tRNA genes (29 tRNA species) and 8 ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 16 gene species occur in double copies. The overall AT content of C. putoensis chloroplast genome is 63.6 %, while the corresponding values of the LSC, SSC and IR regions are 65.8, 69.8 and 57.5 %, respectively. Further, phylogenetic analysis suggested that C. putoensis is closely related to Ostrya rehderiana. Keywords Carpinus putoensis · Chloroplast genome · Phylogenetic analysis
Carpinus putoensis, a critically endangered species, is endemic to Putuo Island of the Zhoushan Archipelago, Zhejiang Province, China. The wild C. putoensis tree, as
Electronic supplementary material The online version of this article (doi:10.1007/s12686-016-0604-1) contains supplementary material, which is available to authorized users.
Yongzhi Yang [email protected] 1
State Key Laboratory of Grassland Agro-Ecosystem, College of Life Science, Lanzhou University, Lanzhou, China
a single mature individual species preserved on the top of Foding Mountain, is under first-grade state protection. This single tree was discovered in the early 1930s and since then no more wild individuals have been found (Shaw et al. 2014). This species is monoecious, in theory it is able to reproduce sexually in the wild, but it has a very low rate of seed production due to strong winds during flowering. Natural regeneration therefore is extremely poor and almost no seedlings are found under the tree. C. putoensis is currently listed as a critically endangered species in the IUCN red list (IUCN 2016; Shaw et al. 2014). Therefore, a good knowledge of its genetics would contribute to the formulation of conservation strategy. In this study, we assembled and characterized the complete chloroplast genome sequence of C. putoensis based on the Illumina pair-end sequencing data. Fresh leaves of an individual were collected from Hangzhou Botanical Garden (Zhejiang, China; 30°15′N, 120°16′E), and were used for total genomic DNA extraction with the modified CTAB method (Doyle 1987). The whole-genome sequencing was conducted with 150 bp pair-end reads on the Illumina Hiseq Platform (Illumina, San Diego, CA). In total, about 900 million high quality base pairs (Gb) of sequence data were obtained and used for the c
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