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Cited by 18Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsFish Biology and Ecology Studies

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

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Wang, Haolong, Su, Baofeng, Butts, Ian A E, Dunham, Rex A, Wang, Xu·2022·GigaScience
DOI 10.1093/gigascience/giac070PMC PMC9270728
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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.

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Cited by

Sorted by citations

Authors
Wang, H., Su, B., Butts, I. A. E., Dunham, R. A., & Wang, X.
Affiliations
  • Auburn University (US)
  • HudsonAlpha Institute for Biotechnology (US)
Corresponding author
Wang, Xu
ORCID
Venue
GigaScience
Publisher
Oxford University Press (OUP)
Published
2022
Volume
11
ISSN
2047-217X (ISSN-L)
DOI
10.1093/gigascience/giac070
PMC
PMC9270728
OpenAlex
W4284992769
Cited by
18
References
0
Citations by year
2026: 1 · 2025: 6 · 2024: 5 · 2023: 5 · 2022: 1
FWCI
1.39
Type
journal article
Language
en
Open access
Licence
Locations
  • GigaScience (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • U.S. Department of Agriculture (1018100)
  • National Science Foundation (OIA1928770)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Fish Biology and Ecology Studies
Keywords
blue catfish, Ictalurus furcatus, chromosome-level genome assembly, genome annotation, hybrid catfish, heterosis, epigenetics, methylome, single nucleotide polymorphisms, gene family expansion, immune-related genes, disease resistance, phylogenomics, marker-assisted selection, genome editing
MeSH terms
Animals, Catfishes, Chromosomes, Female, Hybrid Vigor, Ictaluridae, Male, Reproduction, Aquaculture, Polymorphism, Single Nucleotide, Epigenesis, Genetic

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