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

Zhanjiang Liu (), Shikai Liu, Jun Yao, Lisui Bao, Jiaren Zhang, Yun Li, Chen Jiang, Luyang Sun, Ruijia Wang, Yu Zhang, Tao Zhou, Qifan Zeng, Qiang Fu, Sen Gao, Ning Li, Sergey Koren, Yanliang Jiang, Aleksey Zimin, Peng Xu, Adam M. Phillippy, Xin Geng, Lin Song, Fanyue Sun, Chao Li, Xiaozhu Wang, Ailu Chen, Yulin Jin, Zihao Yuan, Yujia Yang, Suxu Tan, Eric Peatman, Jianguo Lu, Zhenkui Qin, Rex Dunham, Zhaoxia Li, Tad Sonstegard, Jianbin Feng, Roy G. Danzmann, Steven Schroeder, Brian Scheffler, Mary V. Duke, Linda Ballard, Huseyin Kucuktas, Ludmilla Kaltenboeck, Haixia Liu, Jonathan Armbruster, Yangjie Xie, Mona L. Kirby, Yi Tian, Mary Elizabeth Flanagan, Weijie Mu and Geoffrey C. Waldbieser
Additional contact information
Zhanjiang Liu: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Shikai Liu: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Jun Yao: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Lisui Bao: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Jiaren Zhang: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Yun Li: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Chen Jiang: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Luyang Sun: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Ruijia Wang: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Yu Zhang: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Tao Zhou: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Qifan Zeng: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Qiang Fu: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Sen Gao: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Ning Li: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Sergey Koren: National Center for Biodefense Analysis and Countermeasures Center
Yanliang Jiang: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Aleksey Zimin: Institute for Physical Science and Technology, University of Maryland
Peng Xu: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Adam M. Phillippy: National Center for Biodefense Analysis and Countermeasures Center
Xin Geng: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Lin Song: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Fanyue Sun: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Chao Li: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Xiaozhu Wang: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Ailu Chen: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Yulin Jin: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Zihao Yuan: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Yujia Yang: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Suxu Tan: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Eric Peatman: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Jianguo Lu: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Zhenkui Qin: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Rex Dunham: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Zhaoxia Li: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Tad Sonstegard: Bovine Functional Genomics Laboratory, Agricultural Research Service
Jianbin Feng: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Roy G. Danzmann: University of Guelph
Steven Schroeder: Bovine Functional Genomics Laboratory, Agricultural Research Service
Brian Scheffler: USDA, ARS, Genomics and Bioinformatics Research Unit
Mary V. Duke: USDA, ARS, Genomics and Bioinformatics Research Unit
Linda Ballard: USDA, ARS, Genomics and Bioinformatics Research Unit
Huseyin Kucuktas: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Ludmilla Kaltenboeck: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Haixia Liu: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Jonathan Armbruster: Auburn University
Yangjie Xie: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Mona L. Kirby: USDA-ARS Warmwater Aquaculture Research Unit
Yi Tian: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Mary Elizabeth Flanagan: USDA-ARS Warmwater Aquaculture Research Unit
Weijie Mu: The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Geoffrey C. Waldbieser: USDA-ARS Warmwater Aquaculture Research Unit

Nature Communications, 2016, vol. 7, issue 1, 1-13

Abstract: 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.

Date: 2016
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DOI: 10.1038/ncomms11757

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