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<p>Molpadida is one of eight orders in the class Holothuroidea whose phylogenetic positioning has been debated. The absence of a high-quality Molpadida genome has hindered a thorough understanding of their taxonomy and evolution. In this study, we reported the chromosome-level genome assembly of <i>Molpadia</i> sp. C3 from South China Sea, representing the first Molpadida species whose chromosome-level genome assembly became available. The <i>Molpadia</i> sp. C3 genome assembly has a total length of 2.53 Gb with a contig N50 length of 2.8 Mb and a scaffold N50 length of 107.8 Mb, encompassing 23 chromosomes, highlighting high genome continuity. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment yielded a completeness estimate of 87.4% for this assembly. We predicted a total of 38,311 protein-coding genes (PCGs), with 32,584 functionally annotated. The availability of this high-quality chromosome-level genome of <i>Molpadia</i> sp. C3 contributes to our understanding of the origin and evolution of holothuroids.</p>

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A high-quality chromosome-level genome assembly of a deep-sea sea cucumber Molpadia sp. (Molpadiidae)

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年8月3日

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  • Jing Wang,
  • Ning Xiao,
  • Zelin Duan,
  • Zhiyuan Gong,
  • Nansheng Chen

摘要

Molpadida is one of eight orders in the class Holothuroidea whose phylogenetic positioning has been debated. The absence of a high-quality Molpadida genome has hindered a thorough understanding of their taxonomy and evolution. In this study, we reported the chromosome-level genome assembly of Molpadia sp. C3 from South China Sea, representing the first Molpadida species whose chromosome-level genome assembly became available. The Molpadia sp. C3 genome assembly has a total length of 2.53 Gb with a contig N50 length of 2.8 Mb and a scaffold N50 length of 107.8 Mb, encompassing 23 chromosomes, highlighting high genome continuity. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment yielded a completeness estimate of 87.4% for this assembly. We predicted a total of 38,311 protein-coding genes (PCGs), with 32,584 functionally annotated. The availability of this high-quality chromosome-level genome of Molpadia sp. C3 contributes to our understanding of the origin and evolution of holothuroids.