The complete chloroplast genome sequence of wild soybean, Glycine soja
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METHODS AND RESOURCES ARTICLE
The complete chloroplast genome sequence of wild soybean, Glycine soja Cheng‑Wen Gao1,2 · Li‑Zhi Gao2,3
Received: 16 November 2016 / Accepted: 3 December 2016 / Published online: 9 December 2016 © Springer Science+Business Media Dordrecht 2016
Abstract Wild soybean Glycine soja is the presumed wild ancestor of cultivated soybean G. max, which harbors abundant and unique gene resources for soybean breeding programs. Here we report the chloroplast genome sequence of G. soja using next-generation sequencing technology. The complete chloroplast genome size is 152,217 bp. The genome includes of a pair of inverted repeats (IRs) of 25,574 bp, which is separated by a large single-copy region of 83,174 bp and a small single-copy region of 17,895 bp. The genome contains a total of 111 unique genes, including 77 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenomic analysis based on complete chloroplast genome sequences revealed that G. soja is closely related to G. max in the genus Glycine. The newly sequenced complete chloroplast genome of G. soja will provide useful genetic resources that will help to obtain our knowledge of genetic diversity of G. soja and potentially help to conserve the precious natural populations of wild soybean. Keywords Glycine soja · Chloroplast genome · Nextgeneration sequencing · Conservation genetics
* Li‑Zhi Gao [email protected] 1
Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650504, China
2
Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China
3
Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
Introduction The genus Glycine includes at least 28 species divided into two subgenera: Glycine and Soja. The annual species include the cultivated soybean, G. max, and wild soybean, G. soja; they both belong to the subgenus Soja in the genus Glycine and are native to eastern Asia. G. soja is generally considered to be the progenitor of cultivated soybean (Hymowitz 1970). Unfortunately, a large number of wild soybean populations are severely endangered and even have become extinct. Thus, it is a great challenge for us to efficiently protect wild soybean resources from loss. The information of chloroplast genomes has been extensively applied in plant biology, such as the utility for phylogenetic inference (Ruhfel et al. 2014), biotechnological applications (Sabir et al. 2014), and species identification (Kane et al. 2012). To date, a total of eight complete chloroplast genomes in the genus Glycine have been reported (Saski et al. 2005; Sherman-Broyles et al. 2014), excluding the most important wild soybean G. soja. In this study, we report and characterize the complete nucleotide sequence of G. soja chloroplast genome. Young and healthy leaf samples of G. soja were collected from Miyun, Beijing City, China. High-quality chloroplast DNA was extracted following
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