ArticleScientific data2025
Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius.
Article in Scientific data, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Long non-coding RNA transcripts in crucian carp brain - annotation and expression patterns in anoxia and reoxygenation.RNA biology · 2026Article
- De novo Genome Assembly, Annotation, and Comparative Analysis of the Lined Sole Achirus lineatus as a Resource for Evolutionary and Environmental Genomics.Marine biotechnology (New York, N.Y.) · 2026Article
- Mitochondrial responses to anoxia-reoxygenation exposure in crucian carp (Carassius carassius).The Journal of experimental biology · 2026Article
- Fungal photobiont and microbiome genome composition in the Cladonia uncialis tripartite symbiosis.Scientific data · 2026Article
- Current State of Fish Reference Genome and Pangenome: Methodologies, Sampling Strategies, Quality Assessment and Future Perspectives to Aquaculture Breeding.Marine biotechnology (New York, N.Y.) · 2025Review
- Chromosome-level de novo genome assembly of wild, anoxia-tolerant crucian carp, Carassius carassius.Scientific data · 2025Article
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Authors and funding
5 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.