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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.

SUBMITTER: Liu Z

PROVIDER: S-EPMC4895719 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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

Liu Zhanjiang Z Liu Shikai S Yao Jun J Bao Lisui L Zhang Jiaren J Li Yun Y Jiang Chen C Sun Luyang L Wang Ruijia R Zhang Yu Y Zhou Tao T Zeng Qifan Q Fu Qiang Q Gao Sen S Li Ning N Koren Sergey S Jiang Yanliang Y Zimin Aleksey A Xu Peng P Phillippy Adam M AM Geng Xin X Song Lin L Sun Fanyue F Li Chao C Wang Xiaozhu X Chen Ailu A Jin Yulin Y Yuan Zihao Z Yang Yujia Y Tan Suxu S Peatman Eric E Lu Jianguo J Qin Zhenkui Z Dunham Rex R Li Zhaoxia Z Sonstegard Tad T Feng Jianbin J Danzmann Roy G RG Schroeder Steven S Scheffler Brian B Duke Mary V MV Ballard Linda L Kucuktas Huseyin H Kaltenboeck Ludmilla L Liu Haixia H Armbruster Jonathan J Xie Yangjie Y Kirby Mona L ML Tian Yi Y Flanagan Mary Elizabeth ME Mu Weijie W Waldbieser Geoffrey C GC

Nature communications 20160602

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 experimen ...[more]

PMID: 27249958

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Project description:BackgroundWalking catfish (Clarias batrachus) is a freshwater fish capable of air-breathing and locomotion on land. It usually inhabits various low-oxygen habitats, burrows inside the mudflat, and sometimes "walks" to search for suitable environments during summer. It has evolved accessory air-breathing organs for respiring air and corresponding mechanisms to survive in such challenging environments. Thereby, it serves as a great model for understanding adaptations to terrestrial life.ResultsComparative genomics with channel catfish (Ictalurus punctatus) revealed specific adaptations of C. batrachus in DNA repair, enzyme activator activity, and small GTPase regulator activity. Comparative analysis with 11 non-air-breathing fish species suggested adaptive evolution in gene expression and nitrogenous waste metabolic processes. Further, myoglobin, olfactory receptor related to class A G protein-coupled receptor 1, and sulfotransferase 6b1 genes were found to be expanded in the air-breathing walking catfish genome, with 15, 15, and 12 copies, respectively, compared to non-air-breathing fishes that possess only 1-2 copies of these genes. Additionally, we sequenced and compared the transcriptomes of the gill and the air-breathing organ to characterize the mechanism of aerial respiration involved in elastic fiber formation, oxygen binding and transport, angiogenesis, ion homeostasis and acid-base balance. The hemoglobin genes were expressed dramatically higher in the air-breathing organ than in the gill of walking catfish.ConclusionsThis study provides an important genomic resource for understanding the adaptive mechanisms of walking catfish to terrestrial environments. It is possible that the coupling of enhanced abilities for oxygen storage and oxygen transport through genomic expansion of myoglobin genes and transcriptomic up-regulation of hemoglobin and angiogenesis-related genes are important components of the molecular basis for adaptation of this aquatic species to terrestrial life.

Dataset Information

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

Publications

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

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