Characterization of the complete chloroplast genome of Platycarya strobilacea (Juglandaceae)
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TECHNICAL NOtE
Characterization of the complete chloroplast genome of Platycarya strobilacea (Juglandaceae) Jing Yan1 · Kai Han1 · Shuyun Zeng1 · Peng Zhao1 · Keith Woeste2 · Jianfang Li1 · Zhan-Lin Liu1
Received: 1 September 2016 / Accepted: 4 October 2016 © Springer Science+Business Media Dordrecht 2016
Abstract. The whole chloroplast genome (cp genome) sequence of Platycarya strobilacea was characterized from Illumina pair-end sequencing data. The complete cp genome was 160,994 bp in length and contained a large single copy region (LSC) of 90,225 bp and a small single copy region (SSC) of 18,371 bp, which were separated by a pair of inverted repeat regions (IRs, 26,199 bp). The genome contained 130 genes, including 85 protein-coding genes (80 PCG species), 36 tRNA genes (29 tRNA species) and 8 ribosomal RNA genes (4 rRNA species). Most genes occur as a single copy, but 15 genes are duplicated.
Zhan-Lin Liu [email protected] Jing Yan [email protected] Kai Han [email protected] Shuyun Zeng [email protected] Peng Zhao [email protected] Keith Woeste [email protected] Jianfang Li [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 Province, China
2
USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN 47907, USA
The overall AT content of the cp genome is 64 %, and the corresponding values of the LSC, SSC and IR regions are 66.4, 70.1 and 57.5 %, respectively. Phylogenetic analysis confirmed the placement of P. strobilacea near to Juglans. Keywords Platycarya strobilacea · Hickory · China · Conservation · Chloroplast genome
Platycarya strobilacea, the only species in the monotypic genus Platycarya (Juglandaceae), mainly grows as scattered individuals in evergreen forests of South China (Chen et al. 2012). As one of main components of the local vegetation, this species plays a key role in the forest ecosystems. Extracts of its fruit contain compounds used for anti-aging cosmetics (Kim et al. 2010). However, due to anthropogenic over-exploitation and fragmentation of its natural habitat, wild resources of P. strobilacea have dramatically declined and need urgent protection and restoration. An improved understanding of its genetics would contribute to the formulation of conservation strategies. In this study, we assembled and characterized the complete chloroplast genome of P. strobilacea from Illumina sequencing data. Fresh leaves of an individual were collected from Zhengpin (Shaanxi, China; 31°53′N, 109°31′E), and were used for total genomic DNA isolation. A shotgun library was prepared and sequenced on the Illumina Hiseq 2500 Sequencing System (Illumina, CA, USA). In total, 8.2G raw reads were obtained, quality-trimmed and assembled for the chloroplast genome using the program MITObim v1.8 (Hahn et al. 2013) with Juglans regia
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