Complete chloroplast genome of Sophora alopecuroides (Papilionoideae): molecular structures, comparative genome analysis
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Ó Indian Academy of Sciences (0123456789().,-volV) (0123456789().,-volV)
RESEARCH ARTICLE
Complete chloroplast genome of Sophora alopecuroides (Papilionoideae): molecular structures, comparative genome analysis and phylogenetic analysis XI ZHA, XIAOYANG WANG, JINRONG LI, FEI GAO*
and YIJUN ZHOU*
College of Life and Environmental Sciences, Minzu University of China, #27, Zhongguancun South Street, Haidian, Beijing 100081, People’s Republic of China *For correspondence. E-mail: Fei Gao, [email protected]; Yijun Zhou, [email protected]. Received 4 June 2019; revised 9 August 2019; accepted 13 November 2019 Abstract. Sophora alopecuroides belongs to the genus Sophora of the family Papilionoideae. It is mainly distributed in the desert and semidesert areas of northern China, and has high medicinal value and ecological function. Previous studies have reported the chemical composition and ecological functions of S. alopecuroides. However, only a few reports are available on the genomic information of S. alopecuroides, especially the chloroplast genome, which greatly limits the study of the evolutionary relationship between other species of Papilionoideae. Here, we report the complete chloroplast genome of S. alopecuroides. The size of the chloroplast genome is 155,207 bp, and the GC content is 36.44%. The S. alopecuroides chloroplast genome consists of 132 genes, including 83 protein-coding genes, 41 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Phylogenetic analysis revealed the taxonomic position of S. alopecuroides in Papilionoideae, and the genus Sophora and the genus Ammopiptanthus were highly related. Comparative genomics analysis revealed the gene rearrangement in the evolution of S. alopecuroides. The comparison between S. alopecuroides and the species of the Papilionoideae identified a novel 23 kb inversion between the trnC-GCA and trnF-GAA which occurred before the divergence of Sophora and Ammopiptanthus of Thermopsideae. This study provided an essential data for the understanding of phylogenetic status of S. alopecuroides. Keywords.
chloroplast genome; comparative genomics; phylogenetic analysis; IR region; Sophora alopecuroides.
Introduction Sophora alopecuroides, a perennial herb belongs to the genus Sophora of Papilionoideae, mainly distributed in the northwestern regions of Xinjiang, Qinghai, Ningxia and Tibet in China. Owning to the developed underground root system, S. alopecuroides plays an important role in soil conservation and fixation, and biological nitrogen fixation (Iinuma et al. 1995; Tanaka et al. 1998; Liang et al. 2012). S. alopecuroides contains alkaloids, flavonoid, organic acids, polysaccharides and lignans, and studies have shown that the alkaloids extracted from S. alopecuroides have various pharmacological effects such as anti-tumour, anti-arrhythmia, antibacterial, anti-toxin and immune regulation (Zhang et al. 2014a). Due to its high medicinal value and ecological significance, more and more attention has been paid to the protection and exploitation of S. alopec
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