Laura Marian Valencia Pesqueira

• Pesqueira, Laura Marian Valencia; Hoff, Siv Nam Khang; Tørresen, Ole Kristian; Jentoft, Sissel & Nilsson, Sjannie Lefevre (2025). Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius. Scientific Data. 12. doi: 10.1038/s41597-025-04813-3. Fulltekst i vitenarkiv Vis sammendrag

  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.

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• Lefevre, Sjannie; Pesqueira, Laura Marian Valencia & Jentoft, Sissel (2024). De novo assembly of the crucian carp genome for the study of anoxia tolerance. Fulltekst i vitenarkiv Vis sammendrag

  The crucian carp (Carassius carassius) is a fish with a remarkable anoxia tolerance, enabling it to survive the Norwegian winters in the wild, where seasonal anoxia is common in small lakes and ponds. While the physiological mechanisms are well documented, there is still a need for better understanding regulation at the molecular and genetic level, and a fully sequenced, assembled and annotated genome will facilitate such studies. To obtain a high-quality genome assembly, we sequenced crucian carp genomic DNA using chromosome conformation capture (HiC), PacBio long-read sequencing, and short-read sequencing for error correction. The structural and functional annotation were produced using RNA-seq data, teleost ortholog proteins, and UTRs were annotated with the PASA-pipeline and long-read RNA sequencing (Iso-seq data). Functional annotation of proteins predicted by the structural gene models were obtained by performing protein motif searches using Diamond blast, InterProScan and UniProt. With this new genome assembly with structural and functional annotation of a wild specimen of Norwegian crucian carp, we can begin to formulate more hypotheses about mechanisms that support the physiological adaptations that the crucian carp employs in order to tolerate survival in anoxic environments. Furthermore, the crucian carp has a recent whole-genome duplication (shared with some other cyprinids like common carp and goldfish), which provides the opportunity for diversified functions of the multiple gene paralogs; diversions that can be further studied with a high-quality reference genome.

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