July 7, 2019  |  

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

Authors: Liu, Zhanjiang and Liu, Shikai and Yao, Jun and Bao, Lisui and Zhang, Jiaren and Li, Yun and Jiang, Chen and Sun, Luyang and Wang, Ruijia and Zhang, Yu and Zhou, Tao and Zeng, Qifan and Fu, Qiang and Gao, Sen and Li, Ning and Koren, Sergey and Jiang, Yanliang and Zimin, Aleksey and Xu, Peng and Phillippy, Adam M and Geng, Xin and Song, Lin and Sun, Fanyue and Li, Chao and Wang, Xiaozhu and Chen, Ailu and Jin, Yulin and Yuan, Zihao and Yang, Yujia and Tan, Suxu and Peatman, Eric and Lu, Jianguo and Qin, Zhenkui and Dunham, Rex and Li, Zhaoxia and Sonstegard, Tad and Feng, Jianbin and Danzmann, Roy G and Schroeder, Steven and Scheffler, Brian and Duke, Mary V and Ballard, Linda and Kucuktas, Huseyin and Kaltenboeck, Ludmilla and Liu, Haixia and Armbruster, Jonathan and Xie, Yangjie and Kirby, Mona L and Tian, Yi and Flanagan, Mary Elizabeth and Mu, Weijie and Waldbieser, Geoffrey C

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.

Journal: Nature communications
DOI: 10.1038/ncomms11757
Year: 2016

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