Characterization of the complete chloroplast genome of the Cortusa matthioli subsp. pekinensis (Primulaceae)
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TECHNICAL NOTE
Characterization of the complete chloroplast genome of the Cortusa matthioli subsp. pekinensis (Primulaceae) Jiao Wang1 · Ruiting Zhang1 · Ting Ren1 · Kai Han1 · Shuyun Zeng1 · Edward Biffin2 · Zhan‑Lin Liu1
Received: 13 December 2016 / Accepted: 4 April 2017 © Springer Science+Business Media Dordrecht 2017
Abstract The complete chloroplast genome sequence of Cortusa matthioli subsp. pekinensis has been characterized using Illumina pair-end sequencing. The circular genome is 152,239 bp in length, containing a pair of inverted repeats (IRs) of 25,677 bp, separated by a large single copy (LSC) and a small single copy (SSC) region of 83,026 and 17,859 bp, respectively. It contains 131 genes, including 85 protein-coding genes (78 PCG species), 37 transfer RNA genes (28 tRNA species) and eight ribosomal RNA genes (four rRNA species). The most of gene species occur as a single copy, while 18 genes are duplicated. The nucleotide composition is asymmetric (31.1% A, 19.0% C, 18.2% G and 31.7% T) with an overall AT content of 62.8%. The corresponding values for the LSC, SSC and IR regions are * Zhan‑Lin Liu [email protected] Jiao Wang [email protected] Ruiting Zhang [email protected] Ting Ren [email protected] Kai Han [email protected] Shuyun Zeng [email protected] Edward Biffin [email protected] 1
Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi’an 710069, Shaanxi, China
2
State Herbarium of South Australia, Adelaide 5001, Australia
64.7, 69.8 and 57.2%, respectively. Phylogenetic analysis suggested that C. matthioli subsp. pekinensis is closely related to Primula species. Keywords Complete chloroplast genome · Phylogenetic relationship · Cortusa matthioli subsp. pekinensis Cortusa matthioli subsp. pekinensis is a rare subalpine perennial herb distributed predominantly in several mountains with high altitude in North China (Hu 1990). Alpine and subalpine species, like C. matthioli subsp. pekinensis, are potentially sensitive to global climatic change and are at higher risk of extinction due to habitat loss and low competition. The sky-island distribution pattern of alpine and subalpine species can also restrict genetic exchange among natural populations driving population divergence and adaptation to heterogenous habitats (Ramírez-Amezcua et al. 2016). An understanding of genetic variability is urgently needed to formulate appropriate conservation management strategies. In this study, we assembled and characterized the complete chloroplast genome (cpDNA) of C. matthioli subsp. pekinensis using next generation sequencing. Fresh leaves of a single individual of C. matthioli subsp. pekinensis were sampled from Taibai Mountain, China (N34°01′, E107°42′, 2800 m). The voucher specimen (2016P03, Z-L Liu) was deposited in the Evolutionary Botany Laboratory (EBL), College of Life Science, Northwest University. Extraction of genomic DNA and Illumina Hiseq 2500 sequencing
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