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

Author

Listed:
  • 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
    Present address: National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA)

  • 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
    Present address: National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA)

  • 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
    Present address: Recombinetics, Inc., 1246 University Avenue W, #301, Saint Paul, Minnesota 55104, USA)

  • 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)

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.

Suggested Citation

  • 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 & Yanl, 2016. "The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts," Nature Communications, Nature, vol. 7(1), pages 1-13, September.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms11757
    DOI: 10.1038/ncomms11757
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