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Nat Commun. 2016 Jun 2;7:11757. doi: 10.1038/ncomms11757.

The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts.

Author information

1
The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849, USA.
2
National Center for Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, Maryland 21702, USA.
3
Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA.
4
Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA.
5
Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1.
6
USDA, ARS, Genomics and Bioinformatics Research Unit, P.O. Box 38, Stoneville, Mississippi 38776, USA.
7
Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA.
8
USDA-ARS Warmwater Aquaculture Research Unit, P.O. Box 38, 141 Experiment Station Road, Stoneville, Mississippi 38776, USA.

Abstract

Catfish represent 12% of teleost or 6.3% of all vertebrate species, and are of enormous economic value. Here we report a high-quality reference genome sequence of channel catfish (Ictalurus punctatus), the major aquaculture species in the US. The reference genome sequence was validated by genetic mapping of 54,000 SNPs, and annotated with 26,661 predicted protein-coding genes. Through comparative analysis of genomes and transcriptomes of scaled and scaleless fish and scale regeneration experiments, we address the genomic basis for the most striking physical characteristic of catfish, the evolutionary loss of scales and provide evidence that lack of secretory calcium-binding phosphoproteins accounts for the evolutionary loss of scales in catfish. The channel catfish reference genome sequence, along with two additional genome sequences and transcriptomes of scaled catfishes, provide crucial resources for evolutionary and biological studies. This work also demonstrates the power of comparative subtraction of candidate genes for traits of structural significance.

PMID:
27249958
PMCID:
PMC4895719
DOI:
10.1038/ncomms11757
[Indexed for MEDLINE]
Free PMC Article

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