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Main conclusion <p>This study provides insights into the chloroplast genome evolution of Triumfetta, identifies polymorphic loci for molecular marker development, and offers preliminary phylogenomic evidence on the evolutionary relationships within the genus.</p> Abstract <p>The genus <i>Triumfetta</i> Plum. ex L. (Grewioideae, Malvaceae) is a pantropical group comprising approximately 177 species. Despite its diversity, its chloroplast&#xa0;(cp) genomics remain unstudied. To investigate evolutionary dynamics and phylogenetic relationships within <i>Triumfetta</i>, complete cp genomes of eight species were de novo assembled and compared with two publicly available genomes. These cp genomes were 160,075 to 160,604 base pairs (bp) long and consisted of a large single-copy region (89,006–89,386&#xa0;bp), a small single-copy region (20,142–20,266&#xa0;bp), and a pair of inverted repeats (IRa and IRb, 25,440–25,498&#xa0;bp), encoding 112 unique genes (78 protein-coding, 30 transfer RNA, and 4 ribosomal RNA). Comparative analyses showed high similarity in GC content, IR contraction/expansion, codon usage, substitution patterns, and repeat structures. An inversion was identified in the LSC region of <i>Triumfetta tomentosa</i>, reversing six genes: <i>trnC</i>, <i>petN</i>, <i>psbM</i>, <i>trnD</i>, <i>trnY</i>, and <i>trnE</i>, without gene loss. Six genes (<i>psbK</i>, <i>rpl20</i>, <i>rpl23</i>, <i>rps16</i>, <i>rps7</i>, and <i>ycf2</i>) showed signatures of positive selection, suggesting potential roles in adaptation. Ten polymorphic loci were identified across intergenic and coding regions, including <i>trnR-atpA</i>, <i>rpl33-rps18</i>, <i>ccsA-ndhD</i>, <i>clpP</i>, <i>rpl22</i>, and <i>ycf1</i>, representing useful markers for DNA barcoding and population genetics. Phylogenetic analysis revealed <i>Triumfetta</i> is monophyletic and closely related to <i>Corchorus</i> L. <i>Triumfetta</i> species formed two distinct clades, reflecting a clear biogeographic divergence: one comprising African and Asian species, and the other consisting exclusively of Australian species. This study provides the first insights into cp genome variation and phylogenetic relationships in <i>Triumfetta</i>, offering resources for further phylogenetic, barcoding, and conservation research.</p>

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Molecular evolution of chloroplast genome in Triumfetta (Grewioideae, Malvaceae)

  • 期刊论文

  • 发表日期：

    2025年8月14日

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  • Rushan Yan,
  • Yujie Zeng,
  • Chengyu Chen,
  • Abdur Rab,
  • Hui Li,
  • Raza Ullah,
  • Madiha Islam,
  • Ying Cui,
  • Mengyang Liu,
  • Xiaoxuan Tian

摘要

Main conclusion

This study provides insights into the chloroplast genome evolution of Triumfetta, identifies polymorphic loci for molecular marker development, and offers preliminary phylogenomic evidence on the evolutionary relationships within the genus.

Abstract

The genus Triumfetta Plum. ex L. (Grewioideae, Malvaceae) is a pantropical group comprising approximately 177 species. Despite its diversity, its chloroplast (cp) genomics remain unstudied. To investigate evolutionary dynamics and phylogenetic relationships within Triumfetta, complete cp genomes of eight species were de novo assembled and compared with two publicly available genomes. These cp genomes were 160,075 to 160,604 base pairs (bp) long and consisted of a large single-copy region (89,006–89,386 bp), a small single-copy region (20,142–20,266 bp), and a pair of inverted repeats (IRa and IRb, 25,440–25,498 bp), encoding 112 unique genes (78 protein-coding, 30 transfer RNA, and 4 ribosomal RNA). Comparative analyses showed high similarity in GC content, IR contraction/expansion, codon usage, substitution patterns, and repeat structures. An inversion was identified in the LSC region of Triumfetta tomentosa, reversing six genes: trnC, petN, psbM, trnD, trnY, and trnE, without gene loss. Six genes (psbK, rpl20, rpl23, rps16, rps7, and ycf2) showed signatures of positive selection, suggesting potential roles in adaptation. Ten polymorphic loci were identified across intergenic and coding regions, including trnR-atpA, rpl33-rps18, ccsA-ndhD, clpP, rpl22, and ycf1, representing useful markers for DNA barcoding and population genetics. Phylogenetic analysis revealed Triumfetta is monophyletic and closely related to Corchorus L. Triumfetta species formed two distinct clades, reflecting a clear biogeographic divergence: one comprising African and Asian species, and the other consisting exclusively of Australian species. This study provides the first insights into cp genome variation and phylogenetic relationships in Triumfetta, offering resources for further phylogenetic, barcoding, and conservation research.