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<p>Plant mitochondrial genomes show significant changes, especially in Cucurbitaceae, known for large differences in size and structure. To provide novel insights into these processes, we performed high-depth sequencing (&gt; 1700x) and <i>de novo</i> assembly of the complete mitogenome of <i>Thladiantha cordifolia</i>, a previously uncharacterized member. The validated circular assembly spans 327,533&#xa0;bp with a 45.56% GC content, encoding 63 essential genes (40 protein-coding, 20 tRNA, 3 rRNA). Comparisons within Cucurbitaceae revealed frequent structural rearrangements alongside conserved regions, confirming high genomic change driven partly by repetitive DNA. Larger genomes had lower GC content (<i>r</i> = -0.92). Further analysis confirmed this resulted from genome size increasing mainly by adding non-coding DNA (<i>r</i> = 1.00 vs. size), while coding region GC content remained stable across species. Single-base SSRs were the most common repetitive DNA; <i>T. cordifolia</i> had many SSRs but few tandem repeats (TRFs) compared to <i>Cucurbita pepo</i>. Ortholog analysis (33 species) identified 14 core orthogroups but revealed significant divergence and 42 gene copies, showing dynamic gene content. Selective pressures included purifying selection (<i>cox</i>2, <i>nad</i>4) and positive selection (<i>rps</i>19<i>_copy</i>, <i>ccm</i>FC). Codon usage is linked moderately to GC content, but gene-specific patterns suggest selection on translation efficiency. We predicted 445 likely C-to-U RNA editing sites in <i>T. cordifolia</i>, often in key genes (<i>nad</i>4), while acknowledging the need for experimental validation. Bayesian phylogenetic analysis robustly placed <i>T. cordifolia</i> within Cucurbitaceae, showing affinity towards a clade including <i>Momordica</i>, <i>Lagenaria</i>, and <i>Luffa</i>. The comparative analyses offer broad insights into the complex factors driving mitochondrial genome evolution in Cucurbitaceae.</p>

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Insights into cucurbitaceae mitogenomes: gene length variation, correlation features, and phylogenetic relationship

  • 期刊论文

  • 发表日期：

    2025年6月24日

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  • Bimal K. Chetri,
  • S. S. Sonu,
  • Nicolas Dierckxsens,
  • Sudip Mitra,
  • Latha Rangan

摘要

Plant mitochondrial genomes show significant changes, especially in Cucurbitaceae, known for large differences in size and structure. To provide novel insights into these processes, we performed high-depth sequencing (> 1700x) and de novo assembly of the complete mitogenome of Thladiantha cordifolia, a previously uncharacterized member. The validated circular assembly spans 327,533 bp with a 45.56% GC content, encoding 63 essential genes (40 protein-coding, 20 tRNA, 3 rRNA). Comparisons within Cucurbitaceae revealed frequent structural rearrangements alongside conserved regions, confirming high genomic change driven partly by repetitive DNA. Larger genomes had lower GC content (r = -0.92). Further analysis confirmed this resulted from genome size increasing mainly by adding non-coding DNA (r = 1.00 vs. size), while coding region GC content remained stable across species. Single-base SSRs were the most common repetitive DNA; T. cordifolia had many SSRs but few tandem repeats (TRFs) compared to Cucurbita pepo. Ortholog analysis (33 species) identified 14 core orthogroups but revealed significant divergence and 42 gene copies, showing dynamic gene content. Selective pressures included purifying selection (cox2, nad4) and positive selection (rps19_copy, ccmFC). Codon usage is linked moderately to GC content, but gene-specific patterns suggest selection on translation efficiency. We predicted 445 likely C-to-U RNA editing sites in T. cordifolia, often in key genes (nad4), while acknowledging the need for experimental validation. Bayesian phylogenetic analysis robustly placed T. cordifolia within Cucurbitaceae, showing affinity towards a clade including Momordica, Lagenaria, and Luffa. The comparative analyses offer broad insights into the complex factors driving mitochondrial genome evolution in Cucurbitaceae.