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<p>Assembling plant mitochondrial genomes (mitogenomes) is shifting from producing a single representative circular genome to reconstructing a heteroplasmic genome landscape of multiple configurations generated by repeat-mediated recombination. In this review, I summarize the features of plant mitogenomes, evaluate current sequencing platforms relevant to mitogenome assembly, and compare mitogenome assembly pipelines. While the availability of high-accuracy long-read data is increased by the PacBio HiFi sequencing platform, nanopore-based long-read sequencing by ONT and a newcomer of MGI Tech could enter the high-accuracy long-read sequencing market. Plant mitogenome assembly pipelines evolve along with the long-read sequencing. PMAT and PMAT2 pioneered the mitogenome assembly with high-accuracy long-read sequencing data, making a base-line tool. While TIPPo and HiMT utilize k-mer-based read selection to enrich organelle-derived reads, Oatk employs syncasm assembler tailored for plant organelle genome reconstruction. Given the trends of technological advances in long-read sequencing, these pipelines are likely to remain the leading frameworks for assembling plant mitogenomes from high-accuracy long-read data.</p>

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On the Plant Mitochondrial Genome Assembly Pipelines Focusing on High-Accuracy Long-Read Data

  • 期刊论文

  • 发表日期：

    2026年1月19日

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  • Sang Chul Choi

摘要

Assembling plant mitochondrial genomes (mitogenomes) is shifting from producing a single representative circular genome to reconstructing a heteroplasmic genome landscape of multiple configurations generated by repeat-mediated recombination. In this review, I summarize the features of plant mitogenomes, evaluate current sequencing platforms relevant to mitogenome assembly, and compare mitogenome assembly pipelines. While the availability of high-accuracy long-read data is increased by the PacBio HiFi sequencing platform, nanopore-based long-read sequencing by ONT and a newcomer of MGI Tech could enter the high-accuracy long-read sequencing market. Plant mitogenome assembly pipelines evolve along with the long-read sequencing. PMAT and PMAT2 pioneered the mitogenome assembly with high-accuracy long-read sequencing data, making a base-line tool. While TIPPo and HiMT utilize k-mer-based read selection to enrich organelle-derived reads, Oatk employs syncasm assembler tailored for plant organelle genome reconstruction. Given the trends of technological advances in long-read sequencing, these pipelines are likely to remain the leading frameworks for assembling plant mitogenomes from high-accuracy long-read data.