A complement factor I (CFI) gene mediates innate immune responses in yellow catfish Pelteobagrus fulvidraco

Chromosome-Level Genome Assembly of the Speckled Blue Grouper (Epinephelus cyanopodus) Provides Insight into Its Adaptive Evolution

Epinephelus cyanopodus is a coral reef-dwelling grouper with important economic and ecological value and is widely distributed in the western Pacific Ocean. The lack of genomic resources for E. cyanopodus hinders its adaptive evolution and phylogeny research. We constructed the first high-quality genome of E. cyanopodus based on DNBSEQ, PacBio, and Hic sequencing technologies, with a genome size of 998.82 Mb, contig N50 of 5.855 Mb, and scaffold N50 of 41.98 Mb. More than 99.7% of contigs were anchored to 24 pseudochromosomes, and 94.2% of BUSCO genes were found in the E. cyanopodus genome, indicating a high genome assembly completeness. A total of 26,337 protein-coding genes were predicted, of which 98.77% were functionally annotated. Phylogenetic analysis showed that E. cyanopodus separated from its closely related species Epinephelus akaara about 11.5-26.5 million years ago, and the uplift of the Indo-Australian archipelago may have provided an opportunity for its rapid radiation. Moreover, several gene families associated with innate and adaptive immunity were significantly expanded in speckled blue grouper compared to other teleost genomes. Additionally, we identified several genes associated with immunity, growth and reproduction that are under positive selection in E. cyanopodus compared to other groupers, suggesting that E. cyanopodus has evolved broad adaptability in response to complex survival environment, which may provide the genetic basis for its rapid radiation. In brief, the high-quality reference genome of the speckled blue grouper provides a foundation for research on its biological traits and adaptive evolution and will be an important genetic tool to guide aquaculture and resolve its taxonomic controversies in future studies.

Genome-wide identification of the traf gene family in yellow catfish (Pelteobagrus fulvidraco) and analysis of their expression in response to bacterial challenge

Tumour necrosis factor (TNF) receptor-associated factor (TRAF) is a receptor protein that has important functions in the immune system. Nonetheless, there have been few reports of traf genes in teleost fishes. The present study aimed to identify the traf genes from the genomic information of yellow catfish (Pelteobagrus fulvidraco). Eight traf genes were identified and named, which are distributed on different chromosomes but have similar conserved protein domains. Phylogenetic and syntenic analyses demonstrated conservation of traf genes during evolution. In addition, yellow catfish has the relatively rare traf1 and traf5 genes. Gene structure and motif analysis revealed the homology and distribution diversity of the traf genes. Quantitative real-time reverse transcription PCR was used to study the expression patterns of traf genes in healthy fish tissues and after infection by Aeromonas hydrophila. The results demonstrated significant changes in traf gene expression, indicating a potential role in innate immunity.