Genome sequencing and transcriptome analysis provide an insight into the hypoxia resistance of Channa asiatica

• Published in: International journal of biological macromolecules 2024-12, Vol.282 (Pt 6), p.137306, Article 137306
• Main Authors: Zhou, Chaowei, Li, Junting, Duan, Yuting, Fu, Suxing, Li, Hejiao, Zhou, Yinhua, Gao, He, Zhou, Xinghua, Liu, Haiping, Lei, Luo, Chen, Jie, Yuan, Dengyue
• Format: Article
• Language: English
• Subjects: Animals; Channa asiatica; de novo genome assembly; Fishes - genetics; Gene Expression Profiling; Gene family expansion; Genome; Hypoxia - genetics; Hypoxia - metabolism; Hypoxia tolerance; Molecular Sequence Annotation; Oxidative Stress - genetics; Transcriptome; Transcriptome analysis
• ISSN: 0141-8130; 1879-0003; 1879-0003
• DOI: 10.1016/j.ijbiomac.2024.137306

Channa asiatica is an economically valuable fish species and excellent model for studying hypoxic tolerance. However, the underlying genetic and molecular mechanisms are poorly understood. In this study, we assembled a high-quality C. asiatica genome (23 chromosomes, totaling 722 Mb) using a combination of Illumina short-read, PacBio long-read, and Hi-C sequencing. Repetitive elements accounted for 28.39%of the C. asiatica genome, and 23,949 protein-coding genes were predicted, with 96.63 % of these functionally annotated. Moreover, a comparative genomic analysis of 12 fish genomes showed that gene families associated with oxygen binding and transport were expanded in C. asiatica. In addition, transcriptome analysis revealed that multiple oxidative stress pathways were activated when C. asiatica was exposed to air. In conclusion, this study provided high-quality genome assembly and transcriptome data, both serving as critical resources for researching the genetic basis of hypoxic tolerance in C. asiatica.