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Backgrounds <p>The Korean black pine (<i>Pinus thunbergii</i>) is a coastal conifer native to East Asia, including Korea, China, and Japan. Mitochondria and chloroplast in plants are semi-autonomous organelle that encode a small set of proteins and modulate nuclear genome expressions with retrograde signaling to coordinate stress responses and photosynthesis. Although the chloroplast genome of <i>P. thunbergii</i> has been previously characterized, a complete mitochondrial genome has not yet been reported, limiting genomic insights into the evolutionary dynamics of the genus <i>Pinus</i>.</p> Results <p>We assembled the mitogenome using a hybrid sequencing approach that integrates Nanopore long reads with Illumina short reads. The mitogenome comprises two distinct chromosomes—a circular chromosome (~ 2.24&#xa0;Mb) and a linear chromosome (~ 0.31&#xa0;Mb)—with a total length of 2,553,981&#xa0;bp (46.86% of GC), which is two times larger than mitogenome of <i>P. taeda</i> (1.2&#xa0;Mb). These genomes encode 41 protein-coding genes (PCGs), 17 tRNA genes, and three rRNA genes. Based on these PCGs, we predicted 861 potential C-to-U RNA editing sites. Relative synonymous codon usage (RSCU) analysis identified that 30 codon values exceed 1; among these, 86.6% of codons ended with A/T bases, except UUG (Leu), UCC (Ser), ACC (Thr), and UAG (Ter). Only <i>atp1</i> is exposed to purifying selection (Ka/Ks &lt; 1). Comparative genomics revealed that 15 fragments were transferred to chromosome 1 and two fragments were transferred to chromosome 2 from the chloroplast of <i>P. thunbergii</i> (Accession number MW599991.31). Moreover, collinearity analysis showed that 217 fragments were similar to the mitogenome of <i>P. taeda</i>, which accounts for 23.92% of the <i>P. thunbergii</i> mitogenome. Phylogenetic analysis with 15 PCGs confirmed the taxonomic position within the family Pinaceae. Notably, <i>rps3</i> showed a similar distribution to the phylogenetic tree of 30 PCGs.</p> Conclusions <p>In this study, we present the first complete mitogenome of <i>P. thunbergii</i>, analyze mitochondrial genomic characters, confirm horizontal gene transfer from the chloroplast genome, and reveal similarity and close phylogenetic affinity with <i>P. taeda</i>. This study expands the current organellar genomic resources and provides a foundation for evolutionary research in the genus <i>Pinus</i>. Moreover, the discovery of a multi-chromosomal architecture opens new avenues for investigating genome rearrangement and complex evolutionary dynamics across gymnosperm lineages.</p>

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The first complete assembly and analysis of mitochondrial genome of Pinus thunbergii in Pinaceae

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月1日

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  • Seong-Wook Kang,
  • Hanna Shin,
  • Seol-Jong Kim,
  • Junki Lee,
  • Kyeong-Seong Cheon

摘要

Backgrounds

The Korean black pine (Pinus thunbergii) is a coastal conifer native to East Asia, including Korea, China, and Japan. Mitochondria and chloroplast in plants are semi-autonomous organelle that encode a small set of proteins and modulate nuclear genome expressions with retrograde signaling to coordinate stress responses and photosynthesis. Although the chloroplast genome of P. thunbergii has been previously characterized, a complete mitochondrial genome has not yet been reported, limiting genomic insights into the evolutionary dynamics of the genus Pinus.

Results

We assembled the mitogenome using a hybrid sequencing approach that integrates Nanopore long reads with Illumina short reads. The mitogenome comprises two distinct chromosomes—a circular chromosome (~ 2.24 Mb) and a linear chromosome (~ 0.31 Mb)—with a total length of 2,553,981 bp (46.86% of GC), which is two times larger than mitogenome of P. taeda (1.2 Mb). These genomes encode 41 protein-coding genes (PCGs), 17 tRNA genes, and three rRNA genes. Based on these PCGs, we predicted 861 potential C-to-U RNA editing sites. Relative synonymous codon usage (RSCU) analysis identified that 30 codon values exceed 1; among these, 86.6% of codons ended with A/T bases, except UUG (Leu), UCC (Ser), ACC (Thr), and UAG (Ter). Only atp1 is exposed to purifying selection (Ka/Ks < 1). Comparative genomics revealed that 15 fragments were transferred to chromosome 1 and two fragments were transferred to chromosome 2 from the chloroplast of P. thunbergii (Accession number MW599991.31). Moreover, collinearity analysis showed that 217 fragments were similar to the mitogenome of P. taeda, which accounts for 23.92% of the P. thunbergii mitogenome. Phylogenetic analysis with 15 PCGs confirmed the taxonomic position within the family Pinaceae. Notably, rps3 showed a similar distribution to the phylogenetic tree of 30 PCGs.

Conclusions

In this study, we present the first complete mitogenome of P. thunbergii, analyze mitochondrial genomic characters, confirm horizontal gene transfer from the chloroplast genome, and reveal similarity and close phylogenetic affinity with P. taeda. This study expands the current organellar genomic resources and provides a foundation for evolutionary research in the genus Pinus. Moreover, the discovery of a multi-chromosomal architecture opens new avenues for investigating genome rearrangement and complex evolutionary dynamics across gymnosperm lineages.