Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions
Geoffrey C. Waldbieser,
Shikai Liu,
Zihao Yuan,
Caitlin E. Older,
Dongya Gao,
Chenyu Shi,
Brian G. Bosworth,
Ning Li,
Lisui Bao,
Mona A. Kirby,
Yulin Jin,
Monica L. Wood,
Brian Scheffler,
Sheron Simpson,
Ramey C. Youngblood,
Mary V. Duke,
Linda Ballard,
Adam Phillippy,
Sergey Koren,
Zhanjiang Liu
Affiliations
Geoffrey C. Waldbieser
USDA-ARS Warmwater Aquaculture Research Unit
Shikai Liu
MOE Key Laboratory of Mariculture and College of Fisheries, Ocean University of China
Zihao Yuan
The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Caitlin E. Older
USDA-ARS Warmwater Aquaculture Research Unit
Dongya Gao
Department of Biology, College of Arts and Sciences, Syracuse University
Chenyu Shi
MOE Key Laboratory of Mariculture and College of Fisheries, Ocean University of China
Brian G. Bosworth
USDA-ARS Warmwater Aquaculture Research Unit
Ning Li
The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Lisui Bao
The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Mona A. Kirby
USDA-ARS Warmwater Aquaculture Research Unit
Yulin Jin
The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University
Monica L. Wood
USDA-ARS Warmwater Aquaculture Research Unit
Brian Scheffler
US Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit
Sheron Simpson
US Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit
Ramey C. Youngblood
Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
Mary V. Duke
US Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit
Linda Ballard
USDA-ARS Warmwater Aquaculture Research Unit
Adam Phillippy
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health
Sergey Koren
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health
Zhanjiang Liu
Department of Biology, College of Arts and Sciences, Syracuse University
Abstract Background 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. Results 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 × F1 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. Conclusions 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.
