Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions

Authors: Waldbieser, Geoffrey - Geoff; LIU, SHIKAI - Ocean University Of China; YUAN, ZIHAO - Auburn University; Older, Caitlin; GAO, DONGYA - Syracuse University; SHI, CHENYU - Ocean University Of China; Bosworth, Brian; LI, NING - Auburn University; BOA, LISUI - Auburn University; Kirby, Mona; JIN, YULIN - Auburn University; Wood, Monica; Scheffler, Brian; Simpson, Sheron; YOUNGBLOOD, RAMEY - Mississippi State University; Duke, Mary; Ballard, Linda; PHILLIPY, ADAM - National Institutes Of Health (NIH); KOREN, SERGEY - National Institutes Of Health (NIH); LIU, ZHANJIANG - Syracuse University

Submitted to: BMC Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/8/2023
Publication Date: 4/3/2023
Citation: Waldbieser, G.C., Liu, S., Yuan, Z., Older, C.E., Gao, D., Shi, C., Bosworth, B.G., Li, N., Boa, L., Kirby, M.A., Jin, Y., Wood, M.L., Scheffler, B.E., Simpson, S.A., Youngblood, R.C., Duke, M.V., Ballard, L.L., Phillipy, A., Koren, S., Liu, Z. 2023. Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions. BMC Biology. 21:67. https://doi.org/10.1186/s12915-023-01556-8.
DOI: https://doi.org/10.1186/s12915-023-01556-8

Interpretive Summary: Channel and blue catfish are native to North America and are key to U.S. aquaculture. In order to efficiently implement genomic selection in these species, we require accurate, complete genome assemblies. Scientists at the USDA, ARS, Warmwater Aquaculture Research Unit in Stoneville, Mississippi, and collaborators utilized state-of-the-art molecular technologies and bioinformatics to produce highly complete DNA sequence assemblies that accurately represent the channel and blue catfish genomes. The new channel catfish genome assembly is a marked improvement over the existing reference assembly, while the blue catfish genome assembly is novel. Three chromosomes contained large structural changes which likely lead to the lowered fertility observed in channel x blue hybrid F1 offspring. The research also revealed sets of genes that are unique within each species, and also genes unique to both species but different from other fish. The new genome assemblies will support genomic selection and selective breeding in both species toward improvement of U.S. catfish production.

Technical Abstract: Channel catfish and blue catfish are the most important aquacultured species in the USA. The species do not readily intermate naturally but F1 hybrids can be produced through artificial spawning. F1 hybrids produced by mating channel catfish female with blue catfish male exhibit heterosis and provide an ideal system to study reproductive isolation and hybrid vigor. The purpose of the study was to generate high-quality chromosome level reference genome sequences and to determine their genomic similarities and differences.