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The complete chloroplast genome sequence of the medicinal plant Abrus pulchellus subsp. cantoniensis: genome structure, comparative and phylogenetic relationship analysis

Abstract

Abrus pulchellus subsp. cantoniensis, an endemic medicinal plant in southern China, is clinically used to treat jaundice hepatitis, cholecystitis, stomachache and breast carbuncle. Here, we assembled and analyzed the first complete chloroplast (cp) genome of A. pulchellus subsp. cantoniensis. The A. pulchellus subsp. cantoniensis cp genome size is 156,497 bp with 36.5% GC content. The cp genome encodes 130 genes, including 77 protein-coding genes, 30 tRNA genes and four rRNA genes, of which 19 genes are duplicated in the inverted repeats (IR) regions. A total of 30 codons exhibited codon usage bias with A/U-ending. Moreover, 53 putative RNA editing sites were predicted in 20 genes, all of which were cytidine to thymine transitions. Repeat sequence analysis identified 45 repeat structures and 125 simple-sequence repeats (SSRs) in A. pulchellus subsp. cantoniensis cp genome. In addition, 19 mononucleotides (located in atpB, trnV-UAC, ycf3, atpF, rps16, rps18, clpP, rpl16, trnG-UCC and ndhA) and three compound SSRs (located in ndhA, atpB and rpl16) showed species specificity between A. pulchellus subsp. cantoniensis and Abrus precatorius, which might be informative sources for developing molecular markers for species identification. Furthermore, phylogenetic analysis inferred that A. pulchellus subsp. cantoniensis was closely related to A. precatorius, and the genus Abrus formed a subclade with Canavalia in the Millettioid/Phaseoloid clade. These data provide a valuable resource to facilitate the evolutionary relationship and species identification of this species.

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Data transparency

The genome sequence data can be accessed via accession number MT328396 in GenBank of NCBI at https://www.ncbi.nlm.nih.gov.

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Acknowledgements

This work was supported by the Special Fund for Introducing Scientific and Technological Talents of Guangdong Academy of Agricultural Sciences (R2020YJ-YB3003) and Scientific Innovation Strategy Construction of the High-Level Academy of Agriculture Science (R2019PY-JX003).

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Conceptualization: SX and DH; Methodology: SX and MS; Software: SX; Resources: YM and YG; Writing—original draft preparation: SX; Writing—review and editing: DH and JW; Supervision: JW; Funding acquisition: SX and JW. All authors read and approved the final manuscript.

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Correspondence to Ding Huang or Jihua Wang.

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Xu, S., Sun, M., Mei, Y. et al. The complete chloroplast genome sequence of the medicinal plant Abrus pulchellus subsp. cantoniensis: genome structure, comparative and phylogenetic relationship analysis. J Plant Res 135, 443–452 (2022). https://doi.org/10.1007/s10265-022-01385-w

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  • DOI: https://doi.org/10.1007/s10265-022-01385-w

Keywords

  • Abrus pulchellus subsp. cantoniensis
  • Chloroplast genome
  • Phylogenetic analysis
  • Structural characteristics