Characterization of the complete chloroplast genome sequence of Tsuga longibracteata W. C. Cheng (Pinaceae)
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TECHNICAL NOTE
Characterization of the complete chloroplast genome sequence of Tsuga longibracteata W. C. Cheng (Pinaceae) Lin Chen1 · Longna Li2 · Guodong Yang1 · Huirong Qian1 · Mingzhi Li3 Received: 9 December 2017 / Accepted: 30 December 2017 © Springer Science+Business Media B.V., part of Springer Nature 2018
Abstract Tsuga longibracteata W. C. Cheng is an endangered coniferous species endemic to China. Here, the complete chloroplast genome of this species was assembled and characterized from high-throughput sequencing data. The circular genome of T. longibracteata was 120,900 bp in size, with a pair of inverted repeat regions of 34,239 bp. The chloroplast genome contains 127 genes including 88 protein-coding genes (PCGs), 34 tRNAs and five rRNAs. Most of genes occurred in a single copy, while 29 PCGs, 11 tRNAs and one rRNA are totally duplicated. The overall AT content of the genome is 60.6%. A phylogenetic tree reconstructed by 20 gymnosperm chloroplast genomes reveals all the species of Pinaceae formed a monophyletic clade with high resolution value and T. longibracteata is most related with T. chinensis. This study will pave the way for future research to understand the genomic information and conservation of this endangered endemic relict plant. Keywords Tsuga longibracteata · Chloroplast genome · NOVOPlasty · Illumina sequencing · Phylogenetic analysis Tsuga longibracteata W. C. Cheng (Pinaceae) is a rare and endangered relict conifer species endemic to China and is distributed in mid-elevation mountains of subtropical coniferous or coniferous and broadleaf mixed forest in China (Fu et al. 1999). It is of great importance for studies of forest ecology, phytogeography and evolution of the Pinaceae. This species is also extremely valued for afforestation, as well as a high-quality timber tree. However, due to deforestation, habitat fragmentation and degradation, the natural populations have been dramatically decreased in recent decades and urgently need protection and restoration. A good knowledge of comprehensive genomics information would contribute to the formulation of conservation strategy. Previous studies on T. longibracteata mainly focused on its ecology (Xiao Lin Chen and Longna Li contributed equally to this work. * Lin Chen [email protected] 1
Co‑Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, People’s Republic of China
2
Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
3
Genepioneer Biotechnologies Co. Ltd, Nanjing 210014, People’s Republic of China
et al. 2016; You et al. 2013), and genetic information is still limited. The present study is the first time to assemble and characterize the complete chloroplast genome for T. longibracteata (GenBank: MG602009) from hight-hrough-put sequencing data. We believe that such information will pave the way for future studies on conservation, evaluation and utilization of T. longibracteata. Total genomic DNA was
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