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Background <p>The complexity of structural variations and long stretches of repetitive DNA make the analysis of plant mitochondrial genomes (mitogenomes) exceptionally challenging. A thorough investigation of plant mitogenomes is essential for uncovering the evolutionary processes of plant organelles and optimizing traits related to plant cellular metabolism. The genus <i>Glycine</i> includes groups with both perennial and annual life strategies, making it an ideal subject for studying the complexity and variations of plant mitogenomes during evolution across different life strategies.</p> Results <p>Here, we assembled 20 complete mitochondrial and plastid genomes of <i>Glycine</i> accessions, including both annual and perennial species using the latest organelle genome assembly tool. Significant structural variations and differences in tRNA content were observed in the mitogenomes between the two life-history strategy subgenera, while protein-coding genes and rRNAs content were highly conserved. Distinct patterns of nuclear plastid DNAs and nuclear mitochondrial DNAs (NUPTs/NUMTs) were uncovered among annual and perennial species. Genes residing in NUMTs (NUMGs) showed a substantial presence in <i>Glycine</i> accessions, with annual soybeans exhibiting a higher proportion of protein-coding genes fully integrated into the nuclear genome. Phylogenetic analysis indicated a closely related evolutionary trajectory between mitochondrial and nuclear genomes in <i>Glycine</i>, providing supplementary evidence relevant to the evolutionary history of <i>Glycine</i>.</p> Conclusions <p>This study showed the structural variations and evolutionary patterns of mitochondrial genomes between annual and perennial <i>Glycine</i> species. These findings contribute to our understanding of plant organelle complexity, variation and history of intracellular genomic integration.</p>

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Genomic variation and evolutionary patterns in organelle genomes between annual and perennial Glycine species

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年3月18日

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  • Xuchen Yang,
  • Jiaxian He,
  • Minghui Zhou,
  • Changwei Bi,
  • Jiali Kong,
  • Jie Wang,
  • Fanjiang Kong,
  • Zhiqiang Wu,
  • Zefu Wang,
  • Meina Li

摘要

Background

The complexity of structural variations and long stretches of repetitive DNA make the analysis of plant mitochondrial genomes (mitogenomes) exceptionally challenging. A thorough investigation of plant mitogenomes is essential for uncovering the evolutionary processes of plant organelles and optimizing traits related to plant cellular metabolism. The genus Glycine includes groups with both perennial and annual life strategies, making it an ideal subject for studying the complexity and variations of plant mitogenomes during evolution across different life strategies.

Results

Here, we assembled 20 complete mitochondrial and plastid genomes of Glycine accessions, including both annual and perennial species using the latest organelle genome assembly tool. Significant structural variations and differences in tRNA content were observed in the mitogenomes between the two life-history strategy subgenera, while protein-coding genes and rRNAs content were highly conserved. Distinct patterns of nuclear plastid DNAs and nuclear mitochondrial DNAs (NUPTs/NUMTs) were uncovered among annual and perennial species. Genes residing in NUMTs (NUMGs) showed a substantial presence in Glycine accessions, with annual soybeans exhibiting a higher proportion of protein-coding genes fully integrated into the nuclear genome. Phylogenetic analysis indicated a closely related evolutionary trajectory between mitochondrial and nuclear genomes in Glycine, providing supplementary evidence relevant to the evolutionary history of Glycine.

Conclusions

This study showed the structural variations and evolutionary patterns of mitochondrial genomes between annual and perennial Glycine species. These findings contribute to our understanding of plant organelle complexity, variation and history of intracellular genomic integration.