Complete chloroplast genome sequence of Pedicularis cheilanthifolia , an alpine plant in China
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TECHNICAL NOTE
Complete chloroplast genome sequence of Pedicularis cheilanthifolia, an alpine plant in China Ruiting Zhang1 · Jiao Wang1 · Kai Han1 · Ting Ren1 · Shuyun Zeng1 · Edward Biffin2 · Zhan‑Lin Liu1
Received: 23 March 2017 / Accepted: 10 April 2017 © Springer Science+Business Media Dordrecht 2017
Abstract Pedicularis cheilanthifolia is an ecologically important species in alpine meadows of central and western China. In this study, the complete chloroplast genome (cpDNA) sequence of P. cheilanthifolia was characterized using Illumina pair-end sequencing. The cpDNA is 155,159 bp in length, and contains a pair of 25,966 bp inverted repeats (IR), one large single copy (LSC) region of 85,256 bp, and one small single copy (SSC) region of 17,971 bp. It contains 133 genes including 87 protein-coding genes (79 PCG species), 8 ribosomal RNA genes (4 RNA species), 37 transfer RNA genes (30 tRNA species) and 1 pseudogene (ndhF). The overall AT content of the whole genome is 62.3%, and the corresponding values of the LSC, SSC and IR regions are 64.3, 68.4 and 57.0%, * Zhan‑Lin Liu [email protected] Ruiting Zhang [email protected] Jiao Wang [email protected] Kai Han [email protected] Ting Ren [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
respectively. Phylogenetic analysis based on ten chloroplast genomes indicates that P. cheilanthifolia is closely related to Castilleja paramensis. Keywords Pedicularis cheilanthifolia · Alpine meadow · Complete chloroplast genome · Phylogenetic relationship The fragile ecosystem of Qinghai–Tibet Plateau (QTP) is facing grave challenges including climatic change and overgrazing, and sound environmental policies are urgently needed for this region. Pedicularis cheilanthifolia, plays an important role in soil stabilization and water retention in alpine meadows on the QTP, and is also valued for its medicinal qualities. Its population size has been decreased in recent years for overgrazing and overexploitation. Genomic data can provide effective tools for informing species conservation and restoration. In this study, we report the first complete chloroplast genome (cpDNA) of P. cheilanthifolia, which was derived using Illumina pair-end sequencing. The annotated cpDNA of P. cheilanthifolia has been deposited into GenBank with the accession number KY751712. Fresh leaves of P. cheilanthifolia were collected from Namtso (30°47′08″N, 91°04′43″E, 4700 m) and the voucher (2015QT10) was deposited at the Evolutionary Botany Laboratory (EBL), Northwest University. Genomic DNA was isolated with the CTAB method (Doyle 1987). Library preparation and high-throughput sequencing at Illumina Hiseq 2500 platform were performed by Genesky Bio-tech Co., Ltd.. In total, 22,842,472 raw reads
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