1
|
Waldbieser GC, Liu S, Yuan Z, Older CE, Gao D, Shi C, Bosworth BG, Li N, Bao L, Kirby MA, Jin Y, Wood ML, Scheffler B, Simpson S, Youngblood RC, Duke MV, Ballard L, Phillippy A, Koren S, Liu Z. Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions. BMC Biol 2023; 21:67. [PMID: 37013528 PMCID: PMC10071708 DOI: 10.1186/s12915-023-01556-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/08/2023] [Indexed: 04/05/2023] Open
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.
Collapse
Affiliation(s)
- Geoffrey C Waldbieser
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experiment Station Road, P.O. Box 38, Stoneville, MS, 38776, USA
| | - Shikai Liu
- MOE Key Laboratory of Mariculture and College of Fisheries, Ocean University of China, Qingdao, 266003, China
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture, and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - 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, Auburn, AL, 36849, USA
| | - Caitlin E Older
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experiment Station Road, P.O. Box 38, Stoneville, MS, 38776, USA
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, 13244, USA
| | - Chenyu Shi
- MOE Key Laboratory of Mariculture and College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Brian G Bosworth
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experiment Station Road, P.O. Box 38, Stoneville, MS, 38776, USA
| | - 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, Auburn, AL, 36849, USA
| | - 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, Auburn, AL, 36849, USA
| | - Mona A Kirby
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experiment Station Road, P.O. Box 38, Stoneville, MS, 38776, USA
| | - 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, Auburn, AL, 36849, USA
| | - Monica L Wood
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experiment Station Road, P.O. Box 38, Stoneville, MS, 38776, USA
| | - Brian Scheffler
- US Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit, Stoneville, MS, USA
| | - Sheron Simpson
- US Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit, Stoneville, MS, USA
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Starkville, MS, 39762, USA
| | - Mary V Duke
- US Department of Agriculture, Agricultural Research Service, Genomics and Bioinformatics Research Unit, Stoneville, MS, USA
| | - Linda Ballard
- USDA-ARS Warmwater Aquaculture Research Unit, 141 Experiment Station Road, P.O. Box 38, Stoneville, MS, 38776, USA
| | - Adam Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, 13244, USA.
| |
Collapse
|
2
|
Dai P, Sun G, Jia Y, Pan Z, Tian Y, Peng Z, Li H, He S, Du X. Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton (Gossypium hirsutum). Theor Appl Genet 2020; 133:3273-3285. [PMID: 32844253 DOI: 10.1007/s00122-020-03668-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/08/2020] [Indexed: 05/06/2023]
Abstract
Three extensive eco-haplotypes associated with population differentiation and environmental adaptability in Upland cotton were identified, with A06_85658585, A08_43734499 and A06_113104285 considered the eco-loci for environmental adaptability. Population divergence is suggested to be the primary force driving the evolution of environmental adaptability in various species. Chromosome inversion increases reproductive isolation between subspecies and accelerates population divergence to adapt to new environments. Although modern cultivated Upland cotton (Gossypium hirsutum L.) has spread worldwide, the noticeable phenotypic differences still existed among cultivars grown in different areas. In recent years, the long-distance migration of cotton cultivation areas throughout China has demanded that breeders better understand the genetic basis of environmental adaptability in Upland cotton. Here, we integrated the genotypes of 419 diverse accessions, long-term environment-associated variables (EAVs) and environment-associated traits (EATs) to evaluate subgroup differentiation and identify adaptive loci in Upland cotton. Two highly divergent genomic regions were found on chromosomes A06 and A08, which likely caused by extensive chromosome inversions. The subgroups could be geographically classified based on distinct haplotypes in the divergent regions. A genome-wide association study (GWAS) also confirmed that loci located in these regions were significantly associated with environmental adaptability in Upland cotton. Our study first revealed the cause of population divergence in Upland cotton, as well as the consequences of variation in its environmental adaptability. These findings provide new insights into the genetic basis of environmental adaptability in Upland cotton, which could accelerate the development of molecular markers for adaptation to climate change in future cotton breeding.
Collapse
Affiliation(s)
- Panhong Dai
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Agricultural College, Yangtze University, Jingzhou, 434000, China
| | - Gaofei Sun
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- School of Computer Science & Information Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Yinhua Jia
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhaoe Pan
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yingbing Tian
- Agricultural College, Yangtze University, Jingzhou, 434000, China
| | - Zhen Peng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Hongge Li
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Shoupu He
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
| | - Xiongming Du
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
| |
Collapse
|
3
|
Wright AE, Harrison PW, Montgomery SH, Pointer MA, Mank JE. Independent stratum formation on the avian sex chromosomes reveals inter-chromosomal gene conversion and predominance of purifying selection on the W chromosome. Evolution 2014; 68:3281-95. [PMID: 25066800 PMCID: PMC4278454 DOI: 10.1111/evo.12493] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 07/15/2014] [Indexed: 12/27/2022]
Abstract
We used a comparative approach spanning three species and 90 million years to study the evolutionary history of the avian sex chromosomes. Using whole transcriptomes, we assembled the largest cross-species dataset of W-linked coding content to date. Our results show that recombination suppression in large portions of the avian sex chromosomes has evolved independently, and that long-term sex chromosome divergence is consistent with repeated and independent inversions spreading progressively to restrict recombination. In contrast, over short-term periods we observe heterogeneous and locus-specific divergence. We also uncover four instances of gene conversion between both highly diverged and recently evolved gametologs, suggesting a complex mosaic of recombination suppression across the sex chromosomes. Lastly, evidence from 16 gametologs reveal that the W chromosome is evolving with a significant contribution of purifying selection, consistent with previous findings that W-linked genes play an important role in encoding sex-specific fitness.
Collapse
Affiliation(s)
- Alison E Wright
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, OX1 3PS, United Kingdom; Department of Genetics, Evolution and Environment, University College, London, London, WC1E 6BT, United Kingdom.
| | | | | | | | | |
Collapse
|
4
|
Herrera P, Taylor ML, Skeats A, Price TAR, Wedell N. Can patterns of chromosome inversions in Drosophila pseudoobscura predict polyandry across a geographical cline? Ecol Evol 2014; 4:3072-81. [PMID: 25247064 PMCID: PMC4161180 DOI: 10.1002/ece3.1165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/09/2014] [Accepted: 06/19/2014] [Indexed: 11/17/2022] Open
Abstract
Female multiple mating, known as polyandry, is ubiquitous and occurs in a wide variety of taxa. Polyandry varies greatly from species in which females mate with one or two males in their lifetime to species in which females may mate with several different males on the same day. As multiple mating by females is associated with costs, numerous hypotheses attempt to explain this phenomenon. One hypothesis not extensively explored is the possibility that polyandrous behavior is captured and "fixed" in populations via genetic processes that preserve the behavior independently of any adaptive benefit of polyandry. Here, we use female isolines derived from populations of Drosophila pseudoobscura from three locations in North America to examine whether different female remating levels are associated with patterns of chromosome inversions, which may explain patterns of polyandry across the geographic range. Populations differed with respect to the frequency of polyandry and the presence of inversion polymorphisms on the third chromosome. The population with the lowest level of female remating was the only one that was entirely comprised of homokaryotypic lines, but the small number of populations prevented us investigating this relationship further at a population level. However, we found no strong relationship between female remating levels and specific karyotypes of the various isolines.
Collapse
Affiliation(s)
- Paul Herrera
- Biosciences, University of ExeterCornwall Campus, Penryn, TR10 9FE, U.K
| | - Michelle L Taylor
- Biosciences, University of ExeterCornwall Campus, Penryn, TR10 9FE, U.K
| | - Alison Skeats
- Biosciences, University of ExeterCornwall Campus, Penryn, TR10 9FE, U.K
| | - Tom A R Price
- Institute of Integrative Biology, University of LiverpoolLiverpool, L69 7ZB, U.K
| | - Nina Wedell
- Biosciences, University of ExeterCornwall Campus, Penryn, TR10 9FE, U.K
| |
Collapse
|