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Complete chloroplast genome of Sophora alopecuroides (Papilionoideae): molecular structures, comparative genome analysis and phylogenetic analysis

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Abstract

Sophora alopecuroides belongs to the genus Sophora of the family Papilionoideae. It is mainly distributed in the desert and semi-desert 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.

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Acknowledgements

This research was funded by the National Natural Science Foundation of China, grant numbers 31770363 and 31670335, and the Ministry of Education of China through 111 and Double First-Class Projects, grant numbers B08044 and Yldxxk201819.

Author information

Correspondence to Fei Gao or Yijun Zhou.

Additional information

Corresponding editor: H. A. Ranganath

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Zha, X., Wang, X., Li, J. et al. Complete chloroplast genome of Sophora alopecuroides (Papilionoideae): molecular structures, comparative genome analysis and phylogenetic analysis. J Genet 99, 13 (2020). https://doi.org/10.1007/s12041-019-1173-3

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Keywords

  • chloroplast genome
  • comparative genomics
  • phylogenetic analysis
  • IR region
  • Sophora alopecuroides.