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; Geoffrey C. Waldbieser

doi:10.1038/ncomms11757

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. PhillippyXin 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, Geoffrey C. Waldbieser

Research output: Contribution to journal › Article › peer-review

251 Scopus citations

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.

Original language	English (US)
Article number	11757
Journal	Nature Communications
Volume	7
DOIs	https://doi.org/10.1038/ncomms11757
State	Published - Jun 2 2016
Externally published	Yes

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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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., ... Waldbieser, G. C. (2016). The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nature Communications, 7, Article 11757. https://doi.org/10.1038/ncomms11757

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, AM, 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, RG, Schroeder, S, Scheffler, B, Duke, MV, Ballard, L, Kucuktas, H, Kaltenboeck, L, Liu, H, Armbruster, J, Xie, Y, Kirby, ML, Tian, Y, Flanagan, ME, Mu, W & Waldbieser, GC 2016, 'The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts', Nature Communications, vol. 7, 11757. https://doi.org/10.1038/ncomms11757

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title = "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.",

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

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doi = "10.1038/ncomms11757",

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AU - Liu, Zhanjiang

AU - Liu, Shikai

AU - Yao, Jun

AU - Bao, Lisui

AU - Zhang, Jiaren

AU - Li, Yun

AU - Jiang, Chen

AU - Sun, Luyang

AU - Wang, Ruijia

AU - Zhang, Yu

AU - Zhou, Tao

AU - Zeng, Qifan

AU - Fu, Qiang

AU - Gao, Sen

AU - Li, Ning

AU - Koren, Sergey

AU - Jiang, Yanliang

AU - Zimin, Aleksey

AU - Xu, Peng

AU - Phillippy, Adam M.

AU - Geng, Xin

AU - Song, Lin

AU - Sun, Fanyue

AU - Li, Chao

AU - Wang, Xiaozhu

AU - Chen, Ailu

AU - Jin, Yulin

AU - Yuan, Zihao

AU - Yang, Yujia

AU - Tan, Suxu

AU - Peatman, Eric

AU - Lu, Jianguo

AU - Qin, Zhenkui

AU - Dunham, Rex

AU - Li, Zhaoxia

AU - Sonstegard, Tad

AU - Feng, Jianbin

AU - Danzmann, Roy G.

AU - Schroeder, Steven

AU - Scheffler, Brian

AU - Duke, Mary V.

AU - Ballard, Linda

AU - Kucuktas, Huseyin

AU - Kaltenboeck, Ludmilla

AU - Liu, Haixia

AU - Armbruster, Jonathan

AU - Xie, Yangjie

AU - Kirby, Mona L.

AU - Tian, Yi

AU - Flanagan, Mary Elizabeth

AU - Mu, Weijie

AU - Waldbieser, Geoffrey C.

PY - 2016/6/2

Y1 - 2016/6/2

N2 - 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.

AB - 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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JO - Nature Communications

JF - Nature Communications

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

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