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Background&#xa0; <p><i>Strobilanthes cusia</i> is a perennial herbaceous plant that is an important medicinal and natural dye plant. The genome of <i>S. cusia</i> has been reported, including the nuclear and chloroplast genomes, but the pan-plastome (pan-plastid genome) that can help our understanding of the intraspecific variation has not yet been studied. Here, the pan-plastome, constructed from different samples collected from diverse locations, is reported for the first time.</p> Results <p>Sixty-four <i>S. cusia</i> samples were resequenced and assembled in this work, and the published <i>S. cusia</i> genome was downloaded from NCBI and used as a reference. The sizes of the 65 plastomes ranged from 144,107 to 144,174&#xa0;bp, and the region that had the highest degree of variation was the small single copy, with a coefficient of variation value of 0.03. A total of 101 nucleotide polymorphism sites were identified, comprising 38 insertion and deletion events and 63 single nucleotide variants (SNVs). Additionally, certain group-specific repetitive sequences were discovered, and sample Sc45 contained two SNVs and a unique insertion that resulted in a shortened mutation in one copy of the <i>ndhB</i> gene. Using a number of methods, including phylogenetic tree construction, population structure analysis, and principal component analysis, the population was evidently divided into two clusters, comprising three groups (C1-1, C1-2, and C2). There were 50 samples in group C2, compared to 7 and 8 samples in group C1-1 and group C1-2, respectively. After conducting a haplotype analysis, it was shown that the majority of the 29 samples gathered from Fujian Province, together with a few samples from other provinces, formed a core super haplotype inside group C2. Samples from Yunnan Province made up the majority of the samples in group C1-1 and group C1-2.</p> Conclusion <p>Construction of the pan-plastome and the analysis of the population structure of <i>S. cusia</i> plastomes provide important resources for our knowledge of <i>S. cusia</i> evolution and its future breeding projects.</p>

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The pan-plastome of Strobilanthes cusia provided new information about the genetic diversity and cultivation history of an important medicinal and natural dye plant

  • 期刊论文

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  • 发表日期：

    2026年1月16日

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  • Zhicong Lin,
  • Yu Chen,
  • Fengzhou Xu,
  • Hailan Lin,
  • Shunquan Lin,
  • Shoukai Lin,
  • Jincheng Wu

摘要

Background 

Strobilanthes cusia is a perennial herbaceous plant that is an important medicinal and natural dye plant. The genome of S. cusia has been reported, including the nuclear and chloroplast genomes, but the pan-plastome (pan-plastid genome) that can help our understanding of the intraspecific variation has not yet been studied. Here, the pan-plastome, constructed from different samples collected from diverse locations, is reported for the first time.

Results

Sixty-four S. cusia samples were resequenced and assembled in this work, and the published S. cusia genome was downloaded from NCBI and used as a reference. The sizes of the 65 plastomes ranged from 144,107 to 144,174 bp, and the region that had the highest degree of variation was the small single copy, with a coefficient of variation value of 0.03. A total of 101 nucleotide polymorphism sites were identified, comprising 38 insertion and deletion events and 63 single nucleotide variants (SNVs). Additionally, certain group-specific repetitive sequences were discovered, and sample Sc45 contained two SNVs and a unique insertion that resulted in a shortened mutation in one copy of the ndhB gene. Using a number of methods, including phylogenetic tree construction, population structure analysis, and principal component analysis, the population was evidently divided into two clusters, comprising three groups (C1-1, C1-2, and C2). There were 50 samples in group C2, compared to 7 and 8 samples in group C1-1 and group C1-2, respectively. After conducting a haplotype analysis, it was shown that the majority of the 29 samples gathered from Fujian Province, together with a few samples from other provinces, formed a core super haplotype inside group C2. Samples from Yunnan Province made up the majority of the samples in group C1-1 and group C1-2.

Conclusion

Construction of the pan-plastome and the analysis of the population structure of S. cusia plastomes provide important resources for our knowledge of S. cusia evolution and its future breeding projects.