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

Channel catfish and blue catfish are the most important aquacultured species in the USA. The species do not readily intermate naturally but F hybrids can be produced through artificial spawning. F hybrids produced by mating channel catfish female with blue catfish male exhibit heterosis and provide...

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Bibliographic Details
Published in:	BMC biology Vol. 21; no. 1; p. 67
Main Authors:	Waldbieser, Geoffrey C, Liu, Shikai, Yuan, Zihao, Older, Caitlin E, Gao, Dongya, Shi, Chenyu, Bosworth, Brian G, Li, Ning, Bao, Lisui, Kirby, Mona A, Jin, Yulin, Wood, Monica L, Scheffler, Brian, Simpson, Sheron, Youngblood, Ramey C, Duke, Mary V, Ballard, Linda, Phillippy, Adam, Koren, Sergey, Liu, Zhanjiang
Format:	Journal Article
Language:	English
Published:	England BioMed Central Ltd 03-04-2023 BioMed Central BMC
Subjects:	Animals Aquaculture Blue catfish Catfish Catfishes Chromosome Inversion Chromosome Mapping Chromosomes Comparative analysis Environmental aspects Female Females Fish Fish-culture Gene mapping Gene sequencing Genes Genetic analysis Genetic aspects Genetic Linkage Genome Genomes Genomics Growth Heterosis Humans Hybrid vigor Hybridization Hybrids Hypotheses Ictaluridae - genetics Ictalurus furcatus Identification and classification Inversion Inversions Linkage analysis Male Males Management Mapping Methods Recombinants Recombination Reference genome Reproductive isolation Satellite DNA Sequence analysis Spawning Teleost Teleostei United States United States > US Teleost Sequence assembly Channel catfish Reference genome Blue catfish Fish Genome Speciation Aquaculture Chromosome inversion
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Summary:	Channel catfish and blue catfish are the most important aquacultured species in the USA. The species do not readily intermate naturally but F hybrids can be produced through artificial spawning. F 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. We present high-quality reference genome sequences for both channel catfish and blue catfish, containing only 67 and 139 total gaps, respectively. We also report three pericentric chromosome inversions between the two genomes, as evidenced by long reads across the inversion junctions from distinct individuals, genetic linkage mapping, and PCR amplicons across the inversion junctions. Recombination rates within the inversional segments, detected as double crossovers, are extremely low among backcross progenies (progenies of channel catfish female × F hybrid male), suggesting that the pericentric inversions interrupt postzygotic recombination or survival of recombinants. Identification of channel catfish- and blue catfish-specific genes, along with expansions of immunoglobulin genes and centromeric Xba elements, provides insights into genomic hallmarks of these species. We generated high-quality reference genome sequences for both blue catfish and channel catfish and identified major chromosomal inversions on chromosomes 6, 11, and 24. These perimetric inversions were validated by additional sequencing analysis, genetic linkage mapping, and PCR analysis across the inversion junctions. The reference genome sequences, as well as the contrasted chromosomal architecture should provide guidance for the interspecific breeding programs.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1741-7007 1741-7007
DOI:	10.1186/s12915-023-01556-8