The complete chloroplast genome sequence of semi-wild soybean, Glycine gracilis (Fabales: Fabaceae)
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METHODS AND RESOURCES ARTICLE
The complete chloroplast genome sequence of semi-wild soybean, Glycine gracilis (Fabales: Fabaceae) Cheng-Wen Gao1,2 · Li-Zhi Gao1,3
Received: 10 December 2016 / Accepted: 30 December 2016 © Springer Science+Business Media Dordrecht 2017
Abstract Semi-wild soybean, Glycine gracilis, harbors unique gene resources for the soybean breeding programs, which would help to understand the process of soybean domestication. Here, we sequenced and characterized the complete chloroplast genome sequence of the semi-wild soybean. The genome of G. gracilis has 152,218 bp in length with 35.37% GC content. It contains two inverted repeats blocks of 25,574 bp, separated by the large singlecopy block of 83,175 bp and small single-copy block of 17,895 bp. A total of 111 unique genes were annotated, including 77 protein coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis of the ten sequenced Glycine chloroplast genomes revealed that the semi-wild soybean G. gracilis is closer to cultivated soybean G. max than wild soybean G. soja. The newly sequenced complete chloroplast genome of G. gracilis will provide useful resources for the further genetic characterization that would enhance the conservation of this highly endangered species. Keywords Chloroplast genome · Semi-wild soybean · Glycine gracilis · Next-generation sequencing · Conservation genetics
* Li-Zhi Gao [email protected] 1
Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
2
Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
3
Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
Semi-wild soybean (Glycine gracilis) is a unique type of soybean retaining both domesticated and wild characteristics, which provides an intermediate type as well as important material to investigate the population genetic structure of the Glycine species that would help to understand the process of soybean domestication (Chen and Nelson 2004; Hermann 1962; Yang et al. 2010). G. gracilis occurs in the northeast of China and the Yangtze regions. In the past few decades, G. gracilis has been seriously threatened by human activities. The information of chloroplast genomes has been extensively applied in understanding plant genetic diversity and evolution that are of great importance in the conservation genetics (Ye et al. 2014). To date, a total of nine complete chloroplast genomes in the genus Glycine have been reported (Saski et al. 2005; Sherman-Broyles et al. 2014; Gao and Gao 2016). However, the chloroplast genome of the semi-wild soybean G. gracilis has not yet been reported. In this study, we report and characterize the complete chloroplast genome of semi-wild soybean. Young and healthy leaf samples of G. gracilis were collected from Jinhua, Zhejiang Province, China. The qualified chloroplast DNA was extracted using CTAB DNA extraction protocol (Doyle and Doyle
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