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

被引：243

作者：

Liu, Zhanjiang ^{[1
,2
]}

Liu, Shikai ^{[1
,2
]}

Yao, Jun ^{[1
,2
]}

Bao, Lisui ^{[1
,2
]}

Zhang, Jiaren ^{[1
,2
]}

Li, Yun ^{[1
,2
]}

Jiang, Chen ^{[1
,2
]}

Sun, Luyang ^{[1
,2
]}

Wang, Ruijia ^{[1
,2
]}

Zhang, Yu ^{[1
,2
]}

Zhou, Tao ^{[1
,2
]}

Zeng, Qifan ^{[1
,2
]}

Fu, Qiang ^{[1
,2
]}

Gao, Sen ^{[1
,2
]}

Li, Ning ^{[1
,2
]}

Koren, Sergey ^{[3
,4
,11
]}

Jiang, Yanliang ^{[1
,2
]}

Zimin, Aleksey ^{[5
]}

Xu, Peng ^{[1
,2
]}

Phillippy, Adam M. ^{[3
,4
,11
]}

Geng, Xin ^{[1
,2
]}

Song, Lin ^{[1
,2
]}

Sun, Fanyue ^{[1
,2
]}

Li, Chao ^{[1
,2
]}

Wang, Xiaozhu ^{[1
,2
]}

Chen, Ailu ^{[1
,2
]}

Jin, Yulin ^{[1
,2
]}

Yuan, Zihao ^{[1
,2
]}

Yang, Yujia ^{[1
,2
]}

Tan, Suxu ^{[1
,2
]}

Peatman, Eric ^{[1
,2
]}

Lu, Jianguo ^{[1
,2
]}

Qin, Zhenkui ^{[1
,2
]}

Dunham, Rex ^{[1
,2
]}

Li, Zhaoxia ^{[1
,2
]}

Sonstegard, Tad ^{[6
,12
]}

Feng, Jianbin ^{[1
,2
]}

Danzmann, Roy G. ^{[7
]}

Schroeder, Steven ^{[6
]}

Scheffler, Brian ^{[8
]}

Duke, Mary V. ^{[8
]}

Ballard, Linda ^{[8
]}

Kucuktas, Huseyin ^{[1
,2
]}

Kaltenboeck, Ludmilla ^{[1
,2
]}

Liu, Haixia ^{[1
,2
]}

Armbruster, Jonathan ^{[9
]}

Xie, Yangjie ^{[1
,2
]}

Kirby, Mona L. ^{[10
]}

Tian, Yi ^{[1
,2
]}

Flanagan, Mary Elizabeth ^{[10
]}

机构：

[1] Auburn Univ, Fish Mol Genet & Biotechnol Lab, Sch Fisheries Aquaculture & Aquat Sci, Auburn, AL 36849 USA

[2] Auburn Univ, Program Cell & Mol Biosci, Auburn, AL 36849 USA

[3] Natl Ctr Biodefense Anal, 110 Thomas Johnson Dr, Ft Detrick, MD 21702 USA

[4] Countermeasures Ctr, 110 Thomas Johnson Dr, Ft Detrick, MD 21702 USA

[5] Univ Maryland, Inst Phys Sci & Technol, College Pk, MD 20742 USA

[6] ARS, Bovine Funct Genom Lab, USDA, 10300 Baltimore Ave, Beltsville, MD 20705 USA

[7] Univ Guelph, Dept Integrat Biol, Guelph, ON N1G 2W1, Canada

[8] ARS, USDA, Genom & Bioinformat Res Unit, POB 38, Stoneville, MS 38776 USA

[9] Auburn Univ, Dept Biol Sci, Auburn, AL 36849 USA

[10] USDA ARS Warmwater Aquaculture Res Unit, POB 38,141 Expt Stn Rd, Stoneville, MS 38776 USA

[11] NHGRI, NIH, Bethesda, MD 20892 USA

[12] Recombinetics Inc, 1246 Univ Ave W 301, St Paul, MN 55104 USA

来源：

NATURE COMMUNICATIONS | 2016年 / 7卷

基金：

美国国家科学基金会; 美国食品与农业研究所;

关键词：

SECRETORY CALCIUM-BINDING; SCPP GENE EVOLUTION; RNA-SEQ ANALYSIS; TISSUE MINERALIZATION; PHYSICAL MAP; HIGH-DENSITY; TRANSCRIPTOME; CONSTRUCTION; REGENERATION; DUPLICATION;

D O I：

10.1038/ncomms11757

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：13

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