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<p>Recent advances in long-read sequencing and genome editing have greatly enhanced our ability to assemble plant mitochondrial genomes and perform targeted mutagenesis. However, despite these technological improvements, comprehensive analyses of the expression and conservation of mitochondrial <i>ORF</i>s beyond canonical genes remain limited. This gap continues to hinder functional studies of plant mitochondrial biology. In this study, we investigated the mitochondrial genome of tomato (cv. Micro-Tom), a model crop for functional genomics, and analyzed the expression of genes and <i>ORF</i>s across four tissues. Using Oxford Nanopore Technology (ONT)-based long-read sequencing, we assembled a complete mitochondrial genome (496,734&#xa0;bp), which contains 59 genes and 121 <i>ORF</i>s (&gt; 300&#xa0;bp). Expression profiling of mitochondrial genes across four tissues revealed consistent expression ratios between genes, suggesting limited tissue-specific transcriptional regulation. In contrast, <i>ORF</i>s exhibited a broader range of expression levels relative to canonical genes. Although most <i>ORF</i>s were expressed at levels lower than those of genes, a subset displayed expression levels that were comparable to or even higher than those of genes. Conservation analysis identified five <i>ORF</i>s that were conserved in &gt; 30% of 103 surveyed plant species. Among these, <i>ORF159</i> exhibited high expression levels in tomato and a notably low ratio of nonsynonymous to synonymous substitutions (<i>Ka</i>/<i>Ks</i>), suggesting it is under purifying selection. Taken together, these findings provide a foundation for future functional studies of the plant mitochondrial genome using advanced molecular approaches.</p>

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Genomic and transcriptomic analyses of tomato (cv. Micro-Tom) mitochondria reveal highly-expressed ORFs conserved across plant species

  • 期刊论文

  • 发表日期：

    2026年1月21日

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  • Woohyuk Choi,
  • Chaeyun Jeong,
  • Yeong Deuk Jo

摘要

Recent advances in long-read sequencing and genome editing have greatly enhanced our ability to assemble plant mitochondrial genomes and perform targeted mutagenesis. However, despite these technological improvements, comprehensive analyses of the expression and conservation of mitochondrial ORFs beyond canonical genes remain limited. This gap continues to hinder functional studies of plant mitochondrial biology. In this study, we investigated the mitochondrial genome of tomato (cv. Micro-Tom), a model crop for functional genomics, and analyzed the expression of genes and ORFs across four tissues. Using Oxford Nanopore Technology (ONT)-based long-read sequencing, we assembled a complete mitochondrial genome (496,734 bp), which contains 59 genes and 121 ORFs (> 300 bp). Expression profiling of mitochondrial genes across four tissues revealed consistent expression ratios between genes, suggesting limited tissue-specific transcriptional regulation. In contrast, ORFs exhibited a broader range of expression levels relative to canonical genes. Although most ORFs were expressed at levels lower than those of genes, a subset displayed expression levels that were comparable to or even higher than those of genes. Conservation analysis identified five ORFs that were conserved in > 30% of 103 surveyed plant species. Among these, ORF159 exhibited high expression levels in tomato and a notably low ratio of nonsynonymous to synonymous substitutions (Ka/Ks), suggesting it is under purifying selection. Taken together, these findings provide a foundation for future functional studies of the plant mitochondrial genome using advanced molecular approaches.