Characterization of the complete plastid genome of Quercus sichourensis
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TECHNICAL NOTE
Characterization of the complete plastid genome of Quercus sichourensis Hailun Su1 · Yanci Yang1 · Miaomiao Ju1 · Huimin Li1 · Guifang Zhao1 Received: 11 December 2017 / Accepted: 30 December 2017 © Springer Science+Business Media B.V., part of Springer Nature 2018
Abstract Quercus sichourensis is an endemic species in China, and is critically endangered. The complete plastid genome of Q. sichourensis was generated by Illumina pair-end sequencing in the current study. The whole plastome had a length of 160,681 bp, consisting of two copies of inverted repeat regions (25,835 bp), a large single copy region (90,154 bp) and a small single copy region (18,857 bp). The plastome encoded a total of 134 genes, comprising 86 protein-coding genes (79 PCG species), 40 tRNA genes (33 tRNA species), and 8 rRNA genes (4 rRNA species). The overall GC content of Q. sichourensis plastome is 36.9%. The maximum likelihood phylogenetic analysis based on 30 complete plastomes revealed that Q. sichourensis was strictly related to Quercus edithiae with 100% bootstrap support value. Keywords Quercus sichourensis · Critically endangered species · Plastid genome · Phylogenetic relationship Quercus sichourensis is an evergreen endemic tree species within the family Fagaceae, scattered in southwest China (Hu 1951). During the last decade, only ten individual trees were discovered in the restricted limestone seasonal rainforest in Guizhou and Yunnan Provinces (Chen et al. 2007; Xia et al. 2016). Q. sichourensis is now listed in plant species with extremely small populations (PSESP) (Ma et al. 2013) to protect the surviving trees. This species even meets the criteria for inclusion on the International Union for Conservation of Nature (IUCN) Red List of “Critically Endangered” species (Xia et al. 2016). Research has been conducted on its acorns’ biological characters that might relate to its small population size (Xia et al. 2016). However, to formulate a conservation and restoration strategy for rare species such as Q. sichourensis, genetic and genomic information would be more suitable and fundamental. In the present study, we report the complete plastid genome of Q. sichourensis (GenBank accession number: MF787253), which will provide valuable genomic information for future genetic and phylogenetic studies of this rare large tree. * Guifang Zhao [email protected] 1
Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Northern Taibai Road, Xi’an 710069, China
We extracted total genomic DNA from silica-dried leaf materials of a single individual of Q. sichourensis in Kunming Botanical Garden (Yunnan, China; E102º44′, N25º08′) using the modified CTAB method (Doyle 1987). The genomic DNA sample was sent to Biomarker Technologies, Inc. (Beijing, China) and sequenced using an Illumina Hiseq 2500 platform. We utilized NGS QC Toolkit v.2.3.3 to accomplish raw reads and remove low-quality reads through the default parameters (Patel and J
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