Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius
Abstract 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 me...
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Nature Portfolio
2025-03-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-04813-3 |
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| author | Laura Marian Valencia-Pesqueira Siv Nam Khang Hoff Ole K. Tørresen Sissel Jentoft Sjannie Lefevre |
| author_facet | Laura Marian Valencia-Pesqueira Siv Nam Khang Hoff Ole K. Tørresen Sissel Jentoft Sjannie Lefevre |
| author_sort | Laura Marian Valencia-Pesqueira |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-7b0136364a67474e82647182db4e7ba9 |
| institution | OA Journals |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Nature Portfolio |
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| spelling | doaj-art-7b0136364a67474e82647182db4e7ba92025-08-20T02:10:20ZengNature PortfolioScientific Data2052-44632025-03-0112111410.1038/s41597-025-04813-3Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassiusLaura Marian Valencia-Pesqueira0Siv Nam Khang Hoff1Ole K. Tørresen2Sissel Jentoft3Sjannie Lefevre4Section for Physiology and Cell Biology, Department of Biosciences, University of OsloCentre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of OsloCentre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of OsloCentre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of OsloSection for Physiology and Cell Biology, Department of Biosciences, University of OsloAbstract 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.https://doi.org/10.1038/s41597-025-04813-3 |
| spellingShingle | Laura Marian Valencia-Pesqueira Siv Nam Khang Hoff Ole K. Tørresen Sissel Jentoft Sjannie Lefevre Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius Scientific Data |
| title | Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius |
| title_full | Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius |
| title_fullStr | Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius |
| title_full_unstemmed | Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius |
| title_short | Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius |
| title_sort | chromosome level de novo genome assembly of wild anoxia tolerant crucian carp carassius carassius |
| url | https://doi.org/10.1038/s41597-025-04813-3 |
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