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<p>Wild relatives within the economically vital gourd family (Cucurbitaceae) are critical genetic resources for understanding crop evolution and improving agricultural resilience. The genus <i>Thladiantha</i>, a close relative of bitter gourds (<i>Momordica</i>), remains a largely untapped source of agrobiodiversity. In this study, we characterized the first complete plastome of <i>Thladiantha cordifolia</i> to resolve its phylogenetic position, investigate evolutionary dynamics across the Cucurbitaceae, and identify genomic features valuable for conservation. The 157,230&#xa0;bp plastome, containing 133 genes, showed a highly conserved structure compared to the significant rearrangements and gene orientation changes observed across 57 other Cucurbitaceae species, positioning it as a key reference for&#xa0;evolutionary research. Our phylogenetic analyses robustly place <i>Thladiantha</i> as a sister group to <i>Momordica</i>, clarifying a key relationship relevant to the domestication history of the family. Evidence of adaptive evolution was identified, with the <i>psaI</i> gene showing strong signals of positive selection (Ka/Ks = 2.51), highlighting how this wild relative has adapted to its environment. Furthermore, we identified numerous species-specific simple sequence repeats (SSRs), providing a suite of molecular markers for future genetic diversity assessment, gene bank management, and conservation genetics. This work establishes the <i>T. cordifolia</i> plastome as a vital genetic resource, providing fundamental insights into the evolution of a major crop family and delivering tangible tools to support the study and preservation of its agrobiodiversity.</p>

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Plastome genomics of the crop wild relative Thladiantha cordifolia illuminates the evolution and phylogeny of the gourd family (Cucurbitaceae)

  • 期刊论文

  • 发表日期：

    2025年8月5日

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  • Bimal K. Chetri,
  • S. S. Sonu,
  • Rahul G. Shelke,
  • Sudip Mitra,
  • Latha Rangan

摘要

Wild relatives within the economically vital gourd family (Cucurbitaceae) are critical genetic resources for understanding crop evolution and improving agricultural resilience. The genus Thladiantha, a close relative of bitter gourds (Momordica), remains a largely untapped source of agrobiodiversity. In this study, we characterized the first complete plastome of Thladiantha cordifolia to resolve its phylogenetic position, investigate evolutionary dynamics across the Cucurbitaceae, and identify genomic features valuable for conservation. The 157,230 bp plastome, containing 133 genes, showed a highly conserved structure compared to the significant rearrangements and gene orientation changes observed across 57 other Cucurbitaceae species, positioning it as a key reference for evolutionary research. Our phylogenetic analyses robustly place Thladiantha as a sister group to Momordica, clarifying a key relationship relevant to the domestication history of the family. Evidence of adaptive evolution was identified, with the psaI gene showing strong signals of positive selection (Ka/Ks = 2.51), highlighting how this wild relative has adapted to its environment. Furthermore, we identified numerous species-specific simple sequence repeats (SSRs), providing a suite of molecular markers for future genetic diversity assessment, gene bank management, and conservation genetics. This work establishes the T. cordifolia plastome as a vital genetic resource, providing fundamental insights into the evolution of a major crop family and delivering tangible tools to support the study and preservation of its agrobiodiversity.