Valencia-Pesqueira Laura Marian, Hoff Siv Nam Khang, Tørresen Ole K, Jentoft Sissel, Lefevre Sjannie
Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway.
Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
Sci Data. 2025 Mar 24;12(1):491. doi: 10.1038/s41597-025-04813-3.
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.
鲫鱼（Carassius carassius）是鲤科（Cyprinidae）的一员，以其卓越的耐缺氧能力而闻名。对缺氧的生理反应和适应已有充分记录，但仍需要更好地理解这些适应背后的分子调控和进化机制。在此，我们展示了一个高质量、具有功能注释的染色体水平的基因组组装，它有助于进一步开展此类研究。基因组DNA取自一个野生捕获的鲫鱼样本，并用于PacBio长读长测序、Illumina短读长测序和Hi-C测序。短读长mRNA数据使用BRAKER3流程进行结构注释，而PacBio长读长RNA测序数据则使用PASA流程进行非翻译区注释和基因异构体关系的优化。完整组装在290个支架中的重叠群水平N50为15Mbp，总长度（1.65Gbp）的98.6%定位在50条染色体上。结构注释产生了82,557个蛋白质编码转录本（存在于45,667个基因中），BUSCO完整性为99.6%，其中77,370个与UniProtKB/Swiss-Prot数据库中的蛋白质匹配。
