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<p>Crucian carp (<i>Carassius carassius</i>), a member of the carp family (Cyprinidae), is known for its remarkable anoxia tolerance. The physiological responses and adaptations to anoxia are well documented, but there is a need for better understanding of the molecular regulation and evolutionary mechanisms behind these adaptations. Here we present a high-quality, functionally annotated, chromosome-level genome assembly that can facilitate such further studies. Genomic DNA was obtained from a wild-caught crucian carp specimen and used for PacBio long-read, Illumina short-read and Hi-C sequencing. Short-read mRNA data were used for structural annotation using the BRAKER3 pipeline, while PacBio long-read RNA sequencing data were used for annotation of untranslated regions and refinement of gene-isoform relationships, using the PASA pipeline. The full assembly had a contig-level N50 of 15Mbp in 290 scaffolds and 98.6% of the total length (1.65Gbp) placed in 50 chromosomes. Structural annotation resulted in 82,557 protein-coding transcripts (in 45,667 genes), with a BUSCO completeness of 99.6% and of which 77,370 matched a protein in the UniProtKB/Swiss-Prot database.</p>

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Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年3月24日

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  • Laura Marian Valencia-Pesqueira,
  • Siv Nam Khang Hoff,
  • Ole K. Tørresen,
  • Sissel Jentoft,
  • Sjannie Lefevre

摘要

Crucian carp (Carassius carassius), a member of the carp family (Cyprinidae), is known for its remarkable anoxia tolerance. The physiological responses and adaptations to anoxia are well documented, but there is a need for better understanding of the molecular regulation and evolutionary mechanisms behind these adaptations. Here we present a high-quality, functionally annotated, chromosome-level genome assembly that can facilitate such further studies. Genomic DNA was obtained from a wild-caught crucian carp specimen and used for PacBio long-read, Illumina short-read and Hi-C sequencing. Short-read mRNA data were used for structural annotation using the BRAKER3 pipeline, while PacBio long-read RNA sequencing data were used for annotation of untranslated regions and refinement of gene-isoform relationships, using the PASA pipeline. The full assembly had a contig-level N50 of 15Mbp in 290 scaffolds and 98.6% of the total length (1.65Gbp) placed in 50 chromosomes. Structural annotation resulted in 82,557 protein-coding transcripts (in 45,667 genes), with a BUSCO completeness of 99.6% and of which 77,370 matched a protein in the UniProtKB/Swiss-Prot database.