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<p>The deep-sea environment drives unique genomic adaptations in marine organisms, but comprehensive studies in holothurians are limited. We present the first complete mitochondrial genome of the deep-sea sea cucumber <i>Psychropotes</i> sp. (17 128 bp), containing the typical 37 metazoan genes: 13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs. Comparative mitogenomic analysis revealed two notable structural innovations: the presence of three putative control regions and extensive tRNA gene rearrangements. Similar architectures were identified in the congeneric genus <i>Benthodytes</i>, suggesting a possible phylogenetic trend within this family. These structural features may reflect mechanistic adaptations to deep-sea conditions. Additionally, positive selection signals were detected in three respiratory complex genes: <i>ND2</i> (231 P), <i>ND3</i> (87 S), and <i>ND4</i> (352 G), indicating adaptive evolution in key energy metabolism pathways. A negative correlation was observed between mitochondrial guanine-cytosine content (GC content) and depth, which was potentially resulted from deep-sea physiological constraints. This study provides the first mitogenomic characterization of <i>Psychropotes</i> sp. with novel insights into the structural evolution and adaptive mechanisms of mitochondrial genomes in deep-sea holothurians, and established a foundation for further research on metazoan evolution in deep-sea ecosystems.</p>

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Deep-sea adaptation of sea cucumber Psychropotes sp.: new insights based on mitochondrial genomes

  • 期刊论文

  • 发表日期：

    2026年4月22日

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  • Boqiong Wu,
  • Chao Zhang,
  • Ruiyan Zhang,
  • Qiang Lin,
  • Yanhong Zhang

摘要

The deep-sea environment drives unique genomic adaptations in marine organisms, but comprehensive studies in holothurians are limited. We present the first complete mitochondrial genome of the deep-sea sea cucumber Psychropotes sp. (17 128 bp), containing the typical 37 metazoan genes: 13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs. Comparative mitogenomic analysis revealed two notable structural innovations: the presence of three putative control regions and extensive tRNA gene rearrangements. Similar architectures were identified in the congeneric genus Benthodytes, suggesting a possible phylogenetic trend within this family. These structural features may reflect mechanistic adaptations to deep-sea conditions. Additionally, positive selection signals were detected in three respiratory complex genes: ND2 (231 P), ND3 (87 S), and ND4 (352 G), indicating adaptive evolution in key energy metabolism pathways. A negative correlation was observed between mitochondrial guanine-cytosine content (GC content) and depth, which was potentially resulted from deep-sea physiological constraints. This study provides the first mitogenomic characterization of Psychropotes sp. with novel insights into the structural evolution and adaptive mechanisms of mitochondrial genomes in deep-sea holothurians, and established a foundation for further research on metazoan evolution in deep-sea ecosystems.