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<p>The genus <i>Erigeron</i> L. (Astereae, Asteroideae, Asteraceae), commonly known as fleabanes, comprises approximately 457 species with a near-cosmopolitan distribution. However, taxonomic discrepancies persist within the genus. In this study, the complete chloroplast (cp.) genomes of 16 <i>Erigeron</i> species were sequenced and/or de novo assembled and compared with those of nine previously reported species. The complete cp. genomes ranged from 152,108 to 153,430 base pairs (bp) in length, with a large single-copy region of 84,250–85,191&#xa0;bp, inverted repeat regions (each IRa and IRb) of 24,688–25,054&#xa0;bp, and a small single-copy region of 18,093–18,530&#xa0;bp. Each genome contained 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Comparative analyses revealed conserved gene order, GC content, codon usage patterns, simple sequence repeats, and substitution trends across <i>Erigeron</i> species. A consistently low transition-to-transversion ratio (mostly &lt;1) was observed. Analysis of selective pressure revealed gene-wide positive selection acting on <i>ycf2</i>, while some codons of <i>accD</i>, <i>ndhF</i>, <i>rbcL</i>, and <i>ycf1</i> showed signatures of positive selection. Furthermore, ten highly polymorphic loci were identified, including <i>psaC–ndhD</i>,<i> ndhD–ccsA</i>,<i> trnT–trnL</i>,<i> psbI–trnS</i>, and <i>ndhI–ndhG</i>. Phylogenetic analysis of 25 <i>Erigeron</i> species revealed paraphyly within sect. <i>Erigeron</i> and sect. <i>Trimorpha</i>. The former <i>Conyza</i> species were embedded within the <i>Erigeron</i> species. The species <i>Erigeron breviscapus</i> (Vaniot) Hand.-Mazz., which is endemic to China, showed close relationships with species of sect. <i>Trimorpha</i>. This study provides insights into the evolutionary dynamics of the cp. genome and the phylogeny of the genus, with the identified polymorphic loci offering robust and cost-effective markers for resolving phylogenetic relationships within <i>Erigeron</i>.</p>

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Comparative chloroplast genomics of Erigeron (Asteroideae, Asteraceae)

  • 期刊论文

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  • 发表日期：

    2025年10月10日

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  • Abdullah,
  • Aysha Rahmatulla,
  • Chengyu Chen,
  • Rushan Yan,
  • Irum Naz,
  • Parviz Heidari,
  • Ibrar Ahmed,
  • Atinga Vallada,
  • Xiaoxuan Tian

摘要

The genus Erigeron L. (Astereae, Asteroideae, Asteraceae), commonly known as fleabanes, comprises approximately 457 species with a near-cosmopolitan distribution. However, taxonomic discrepancies persist within the genus. In this study, the complete chloroplast (cp.) genomes of 16 Erigeron species were sequenced and/or de novo assembled and compared with those of nine previously reported species. The complete cp. genomes ranged from 152,108 to 153,430 base pairs (bp) in length, with a large single-copy region of 84,250–85,191 bp, inverted repeat regions (each IRa and IRb) of 24,688–25,054 bp, and a small single-copy region of 18,093–18,530 bp. Each genome contained 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Comparative analyses revealed conserved gene order, GC content, codon usage patterns, simple sequence repeats, and substitution trends across Erigeron species. A consistently low transition-to-transversion ratio (mostly <1) was observed. Analysis of selective pressure revealed gene-wide positive selection acting on ycf2, while some codons of accD, ndhF, rbcL, and ycf1 showed signatures of positive selection. Furthermore, ten highly polymorphic loci were identified, including psaC–ndhD, ndhD–ccsA, trnT–trnL, psbI–trnS, and ndhI–ndhG. Phylogenetic analysis of 25 Erigeron species revealed paraphyly within sect. Erigeron and sect. Trimorpha. The former Conyza species were embedded within the Erigeron species. The species Erigeron breviscapus (Vaniot) Hand.-Mazz., which is endemic to China, showed close relationships with species of sect. Trimorpha. This study provides insights into the evolutionary dynamics of the cp. genome and the phylogeny of the genus, with the identified polymorphic loci offering robust and cost-effective markers for resolving phylogenetic relationships within Erigeron.