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ARS Home » Southeast Area » Stoneville, Mississippi » Warmwater Aquaculture Research Unit » Research » Publications at this Location » Publication #317081

Research Project: Genetics, Breeding and Reproductive Physiology to Enhance Production of Catfish

Location: Warmwater Aquaculture Research Unit

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

item LIU, ZHANJIANG - Auburn University
item LIU, SHIKAI - Auburn University
item YAO, JUN - Auburn University
item BAO, LISUI - Auburn University
item JIANG, CHEN - Auburn University
item WANT, RUIJIA - Auburn University
item SUN, LUYANG - Auburn University
item LI, YUN - Auburn University
item ZHANG, YU - Auburn University
item ZHANG, JIAREN - Auburn University
item ZHOU, TAO - Auburn University
item ZENG, QIFAN - Auburn University
item FU, QIANG - Auburn University
item GAO, SEN - Auburn University
item LI, NING - Auburn University
item KOREN, SERGEY - Us Deparment Of Homeland Security
item JIANG, YANLIANG - Auburn University
item ZIMIM, ALEKSEY - University Of Maryland
item XU, PENG - Auburn University
item PHILLIPPY, ADAM - Us Deparment Of Homeland Security
item GENG, XIN - Auburn University
item SONG, LIN - Auburn University
item SUN, FANYUE - Auburn University
item LI, CHAO - Auburn University
item WANT, XIAOZHU - Auburn University
item CHEN, AILU - Auburn University
item JIN, YULIN - Auburn University
item YUAN, ZIHAO - Auburn University
item YANG, YUJIA - Auburn University
item TAN, SUXU - Auburn University
item PEATMAN, ERIC - Auburn University
item LU, JIANGUO - Auburn University
item QIN, ZHENKUI - Auburn University
item DUNHAM, REX - Auburn University
item LI, ZHAOXIA - Auburn University
item Sonstegard, Tad
item FENG, JIANBIN - Auburn University
item DANZMANN, ROY - University Of Guelph
item Schroeder, Steven - Steve
item Scheffler, Brian
item Duke, Mary
item Ballard, Linda
item KUCUKTAS, HUSEYIN - Auburn University
item KALTENBOECK, LUDMILLA - Auburn University
item LIU, HAIXIA - Auburn University
item ARMBRUSTER, JON - Auburn University
item XIE, YANGJIE - Auburn University
item Kirby, Mona
item TIAN, YI - Auburn University
item Moore Flanagan, Mary
item MU, WEIJIE - Auburn University
item Waldbieser, Geoffrey - Geoff

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/27/2016
Publication Date: 6/2/2016
Citation: Liu, Z., Liu, S., Yao, J., Bao, L., Jiang, C., Want, R., Sun, L., Li, Y., Zhang, Y., Zhang, J., Zhou, T., Zeng, Q., Fu, Q., Gao, S., Li, N., Koren, S., Jiang, Y., Zimim, A., Xu, P., Phillippy, A., Geng, X., Song, L., Sun, F., Li, C., Want, X., Chen, A., Jin, Y., Yuan, Z., Yang, Y., Tan, S., Peatman, E., Lu, J., Qin, Z., Dunham, R., Li, Z., Sonstegard, T.S., Feng, J., Danzmann, R.G., Schroeder, S.G., Scheffler, B.E., Duke, M.V., Ballard, L.L., Kucuktas, H., Kaltenboeck, L., Liu, H., Armbruster, J., Xie, Y., Kirby, M.A., Tian, Y., Moore Flanagan, M.E., Mu, W., Waldbieser, G.C. 2016. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nature Communications. 7:11757.

Interpretive Summary: Efficient whole genome analysis and selective breeding requires a reference genome assembly. ARS scientists at the Warmwater Aquaculture Research Unit and Genomics and Bioinformatics Research Unit in Stoneville, MS, the Animal Genomics and Improvement Laboratory in Beltsville, MD, collaborated with scientists at Auburn University, the Department of Homeland Security, and the University of Maryland to produce a whole genome sequence assembly for the channel catfish. Genomic DNA was utilized from “Coco”, a doubled haploid (homozygous) catfish to produce 1.3 billion DNA sequences with next-generation DNA sequencing technologies. The sequences were filtered and assembled using the MaSuRCA assembly software, and a novel method was used to fill gaps within scaffolded sequences. The team produced the most complete and continuous fish genome sequence to be assembled from next-generation technology to date. Assembly accuracy was validated using a variety of genomic resources such as sequences from DNA libraries and alignment to the catfish genetic map. The team demonstrated that the vast majority of DNA sequences from other channel catfish can be aligned to this assembly, and the catfish genome assembly contained more predicted genes than any fish genome assembly. Our analysis showed that 26,381 gene predictions could be validated from experimental gene expression data. The genome assembly will be key to the identification of sequence variation that is linked to improved performance for traits such as growth rate and carcass yield, and will permit selection of broodstock based on high resolution relationships with fish that exhibit superior performance.

Technical Abstract: Channel catfish (Ictalurus punctatus), characteristic of its scaleless skin and prominent barbels, is an ideal species to study osteogenesis, development of appendages, olfactory sensing, and immunological adaptation. It is the leading aquaculture species in the United States. A high quality reference genome sequence is essential for understanding evolution and important biological characteristics of catfishes, as well as for genetic improvement programs. Here we report the channel catfish reference genome sequence with the highest quality among genomes sequenced with next generation sequencing. A total of 26,661 protein-coding genes were annotated, the largest gene content of any diploid fish. The catfish barbels serve as olfactory and gustatory centers, providing evolutionary advantages to catfish. Interspecific comparative transcriptome analysis, coupled to regeneration experiments, provided insights into scalelessness. The lack of secretory calcium-binding phosphoprotein genes or of their expression may account for the lack of scales in channel catfish, an evolutionary characteristic shared by thousands of catfish species.