title: The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts.
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.
authors.affiliation: 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.
authors.forename: Zhanjiang
authors.initials: Z
authors.lastname: Liu
authors.affiliation: 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.
authors.forename: Shikai
authors.initials: S
authors.lastname: Liu
authors.affiliation: 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.
authors.forename: Jun
authors.initials: J
authors.lastname: Yao
authors.affiliation: 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.
authors.forename: Lisui
authors.initials: L
authors.lastname: Bao
authors.affiliation: 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.
authors.forename: Jiaren
authors.initials: J
authors.lastname: Zhang
authors.affiliation: 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.
authors.forename: Yun
authors.initials: Y
authors.lastname: Li
authors.affiliation: 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.
authors.forename: Chen
authors.initials: C
authors.lastname: Jiang
authors.affiliation: 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.
authors.forename: Luyang
authors.initials: L
authors.lastname: Sun
authors.affiliation: 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.
authors.forename: Ruijia
authors.initials: R
authors.lastname: Wang
authors.affiliation: 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.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: 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.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhou
authors.affiliation: 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.
authors.forename: Qifan
authors.initials: Q
authors.lastname: Zeng
authors.affiliation: 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.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Fu
authors.affiliation: 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.
authors.forename: Sen
authors.initials: S
authors.lastname: Gao
authors.affiliation: 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.
authors.forename: Ning
authors.initials: N
authors.lastname: Li
authors.affiliation: National Center for Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, Maryland 21702, USA.
authors.forename: Sergey
authors.initials: S
authors.lastname: Koren
authors.affiliation: 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.
authors.forename: Yanliang
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA.
authors.forename: Aleksey
authors.initials: A
authors.lastname: Zimin
authors.affiliation: 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.
authors.forename: Peng
authors.initials: P
authors.lastname: Xu
authors.affiliation: National Center for Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, Maryland 21702, USA.
authors.forename: Adam M
authors.initials: AM
authors.lastname: Phillippy
authors.affiliation: 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.
authors.forename: Xin
authors.initials: X
authors.lastname: Geng
authors.affiliation: 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.
authors.forename: Lin
authors.initials: L
authors.lastname: Song
authors.affiliation: 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.
authors.forename: Fanyue
authors.initials: F
authors.lastname: Sun
authors.affiliation: 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.
authors.forename: Chao
authors.initials: C
authors.lastname: Li
authors.affiliation: 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.
authors.forename: Xiaozhu
authors.initials: X
authors.lastname: Wang
authors.affiliation: 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.
authors.forename: Ailu
authors.initials: A
authors.lastname: Chen
authors.affiliation: 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.
authors.forename: Yulin
authors.initials: Y
authors.lastname: Jin
authors.affiliation: 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.
authors.forename: Zihao
authors.initials: Z
authors.lastname: Yuan
authors.affiliation: 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.
authors.forename: Yujia
authors.initials: Y
authors.lastname: Yang
authors.affiliation: 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.
authors.forename: Suxu
authors.initials: S
authors.lastname: Tan
authors.affiliation: 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.
authors.forename: Eric
authors.initials: E
authors.lastname: Peatman
authors.affiliation: 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.
authors.forename: Jianguo
authors.initials: J
authors.lastname: Lu
authors.affiliation: 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.
authors.forename: Zhenkui
authors.initials: Z
authors.lastname: Qin
authors.affiliation: 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.
authors.forename: Rex
authors.initials: R
authors.lastname: Dunham
authors.affiliation: 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.
authors.forename: Zhaoxia
authors.initials: Z
authors.lastname: Li
authors.affiliation: Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA.
authors.forename: Tad
authors.initials: T
authors.lastname: Sonstegard
authors.affiliation: 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.
authors.forename: Jianbin
authors.initials: J
authors.lastname: Feng
authors.affiliation: Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1.
authors.forename: Roy G
authors.initials: RG
authors.lastname: Danzmann
authors.affiliation: Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA.
authors.forename: Steven
authors.initials: S
authors.lastname: Schroeder
authors.affiliation: USDA, ARS, Genomics and Bioinformatics Research Unit, P.O. Box 38, Stoneville, Mississippi 38776, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Scheffler
authors.affiliation: USDA, ARS, Genomics and Bioinformatics Research Unit, P.O. Box 38, Stoneville, Mississippi 38776, USA.
authors.forename: Mary V
authors.initials: MV
authors.lastname: Duke
authors.affiliation: USDA, ARS, Genomics and Bioinformatics Research Unit, P.O. Box 38, Stoneville, Mississippi 38776, USA.
authors.forename: Linda
authors.initials: L
authors.lastname: Ballard
authors.affiliation: 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.
authors.forename: Huseyin
authors.initials: H
authors.lastname: Kucuktas
authors.affiliation: 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.
authors.forename: Ludmilla
authors.initials: L
authors.lastname: Kaltenboeck
authors.affiliation: 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.
authors.forename: Haixia
authors.initials: H
authors.lastname: Liu
authors.affiliation: Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Armbruster
authors.affiliation: 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.
authors.forename: Yangjie
authors.initials: Y
authors.lastname: Xie
authors.affiliation: USDA-ARS Warmwater Aquaculture Research Unit, P.O. Box 38, 141 Experiment Station Road, Stoneville, Mississippi 38776, USA.
authors.forename: Mona L
authors.initials: ML
authors.lastname: Kirby
authors.affiliation: 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.
authors.forename: Yi
authors.initials: Y
authors.lastname: Tian
authors.affiliation: USDA-ARS Warmwater Aquaculture Research Unit, P.O. Box 38, 141 Experiment Station Road, Stoneville, Mississippi 38776, USA.
authors.forename: Mary Elizabeth
authors.initials: ME
authors.lastname: Flanagan
authors.affiliation: 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.
authors.forename: Weijie
authors.initials: W
authors.lastname: Mu
authors.affiliation: USDA-ARS Warmwater Aquaculture Research Unit, P.O. Box 38, 141 Experiment Station Road, Stoneville, Mississippi 38776, USA.
authors.forename: Geoffrey C
authors.initials: GC
authors.lastname: Waldbieser
mesh_terms: D000075342:Animal Scales / Q000033:anatomy & histology / Q000378:metabolism*; D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D002135:Calcium-Binding Proteins / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D029941:Fish Proteins / Q000235:genetics* / Q000378:metabolism; D005786:Gene Expression Regulation; D063990:Gene Ontology; D016678:Genome; D007059:Ictaluridae / Q000145:classification / Q000235:genetics*; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D010750:Phosphoproteins / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment
chemical_list: D002135:Calcium-Binding Proteins; D029941:Fish Proteins; D010750:Phosphoproteins