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

Liu, Zhanjiang, Liu, Shikai, Yao, Jun, Bao, Lisui, Zhang, Jiaren, Li, Yun, Jiang, Chen, Sun, Luyang, Wang, Ruijia, Zhang, Yu, Zhou, Tao, Zeng, Qifan, Fu, Qiang, Gao, Sen, Li, Ning, Koren, Sergey, Jiang, Yanliang, Zimin, Aleksey, Xu, Peng, Phillippy, Adam M., Geng, Xin, Song, Lin, Sun, Fanyue, Li, Chao, Wang, Xiaozhu, Chen, Ailu, Jin, Yulin, Yuan, Zihao, Yang, Yujia, Tan, Suxu, Peatman, Eric, Lu, Jianguo, Qin, Zhenkui, Dunham, Rex, Li, Zhaoxia, Sonstegard, Tad, Feng, Jianbin, Danzmann, Roy G., Schroeder, Steven, Scheffler, Brian, Duke, Mary V., Ballard, Linda, Kucuktas, Huseyin, Kaltenboeck, Ludmilla, Liu, Haixia, Armbruster, Jonathan, Xie, Yangjie, Kirby, Mona L., Tian, Yi, Flanagan, Mary Elizabeth, Mu, Weijie, Waldbieser, Geoffrey C.·2016·Nature Communications
DOI 10.1038/ncomms11757PMC PMC4895719
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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.

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  • The monophyly hypothesis of Siluriphysi (comprising Gymnotiformes and Siluriformes) was originally proposed based on morphological characteristics including the electroreception system and has long been widely accepted.

    “Within the Otocephala clade, the monophyly hypothesis of Siluriphysi (comprising Gymnotiformes and Siluriformes), originally proposed based on morphological characteristics including the electroreception system,45,46,47 has long been widely accepted.”

    From A genomic compendium of hundreds of teleost fishes reveals their evolutionary landscape (2026) · cites this paper as [47]

    The Abstract identifies Siluriformes as catfish, but does not discuss Siluriphysi or its proposed monophyly. Searches for Gymnotiformes, electroreception, and morphological evidence found no passage addressing the hypothesis’s origin or how widely it was accepted. (LLM, conf=0.76)

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Metadata

Authors
Liu, Z., Liu, S., Yao, J., Bao, L., Zhang, J., Li, Y., Jiang, C., Sun, L., Wang, R., Zhang, Y., Zhou, T., Zeng, Q., Fu, Q., Gao, S., Li, N., Koren, S., Jiang, Y., Zimin, A., Xu, P., Phillippy, A. M., Geng, X., Song, L., Sun, F., Li, C., Wang, X., Chen, A., Jin, Y., Yuan, Z., Yang, Y., Tan, S., Peatman, E., Lu, J., Qin, Z., Dunham, R., Li, Z., Sonstegard, T., Feng, J., Danzmann, R. G., Schroeder, S., Scheffler, B., Duke, M. V., Ballard, L., Kucuktas, H., Kaltenboeck, L., Liu, H., Armbruster, J., Xie, Y., Kirby, M. L., Tian, Y., Flanagan, M. E., Mu, W., & Waldbieser, G. C.
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2016-06-02
Volume
7
Issue
1
ISSN
2041-1723
DOI
10.1038/ncomms11757
PMC
PMC4895719
Cited by
254
References
4
Language
en
Licence

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