Chromosome-level assembly and annotation of the blue catfishIctalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies

Abstract

Background The blue catfish is of great value in aquaculture and recreational fisheries. The F1 hybrids of female channel catfish (Ictalurus punctatus) × male blue catfish (Ictalurusfurcatus) have been the primary driver of US catfish production in recent years because of superior growth, survival, and carcass yield. The channel–blue hybrid also provides an excellent model to investigate molecular mechanisms of environment-dependent heterosis. However, transcriptome and methylome studies suffered from low alignment rates to the channel catfish genome due to divergence, and the genome resources for blue catfish are not publicly available. Results The blue catfish genome assembly is 841.86 Mbp in length with excellent continuity (8.6 Mbp contig N50, 28.2 Mbp scaffold N50) and completeness (98.6% Eukaryota and 97.0% Actinopterygii BUSCO). A total of 30,971 protein-coding genes were predicted, of which 21,781 were supported by RNA sequencing evidence. Phylogenomic analyses revealed that it diverged from channel catfish approximately 9 million years ago with 15.7 million fixed nucleotide differences. The within-species single-nucleotide polymorphism (SNP) density is 0.32% between the most aquaculturally important blue catfish strains (D&B and Rio Grande). Gene family analysis discovered significant expansion of immune-related families in the blue catfish lineage, which may contribute to disease resistance in blue catfish. Conclusions We reported the first high-quality, chromosome-level assembly of the blue catfish genome, which provides the necessary genomic tool kit for transcriptome and methylome analysis, SNP discovery and marker-assisted selection, gene editing and genome engineering, and reproductive enhancement of the blue catfish and hybrid catfish.

Transcriptome Analysis Reveals Key Gene Expression Changes in Blue Catfish Sperm in Response to Cryopreservation

“…RNA-seq reads shorter than 36 bp in length were excluded from subsequent analysis. The remaining high-quality reads were mapped to the blue catfish ( Ictalurus furcatus ) reference genome [ 99 ] using TopHat (version 2.1.1) [ 100 ]. To quantify gene expression levels, read counts were summarized for each gene using HTseq (version1.0) [ 101 ].…”

Chromosome-level genome assembly of the glass catfish (<i>Kryptopterus vitreolus</i>) reveals molecular clues to its transparent phenotype

“…In the maximum-likelihood phylogenetic tree, 12 representative catfish species were diverged from zebrafish about 173.5 Mya (slightly larger than a recent report of blue catfish genome (Wang et al, 2022)), and they were mainly divided into two clades (Figure 2). Glass catfish has the closest relationship to Chinese large-mouth catfish (Silurus meridionalis) that belongs to the family of Siluridae.…”

Transcriptome analysis revealed potential mechanisms of channel catfish growth advantage over blue catfish in a tank culture environment

“…In total, 697 million 150-bp reads (209.2 Gbp of sequences) were generated ( Supplementary Table S2 ). On average, 73% of RNA-seq reads were uniquely mapped to the blue catfish reference genome ( Wang et al, 2022b ). To investigate the tissue-specific gene expression profiles in both species, a multi-dimensional scaling (MDS) plot was generated using normalized gene counts and the transcriptomic profiles clustered together by tissue in the first two dimensions ( Figure 1E ).…”

“…Low-quality bases and adapter sequences were trimmed using Trimmomatic (version 0.39), and sequencing reads shorter than 36 bp in length were excluded from subsequent analysis ( Bolger et al, 2014 ). RNA-seq reads were aligned to the blue catfish ( I. furcatus ) reference genome ( Wang et al, 2022b ) using STAR aligner version 2.7.5c ( Dobin et al, 2013 ). The gene read counts of each sample were quantified and summarized using HTseq version 1.0 ( Anders et al, 2015 ).…”