USDA-ARS Warmwater Aquaculture Research Unit, 141 Experiment Station Road, P.O. Box 38, Stoneville, MS, 38776, USA.
MOE Key Laboratory of Mariculture and College of Fisheries, Ocean University of China, Qingdao, 266003, China.
BMC Biol. 2023 Apr 3;21(1):67. doi: 10.1186/s12915-023-01556-8.
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.
斑点叉尾鮰和北美短吻鳄是美国最重要的水产养殖品种。这两个物种自然交配不易，但可以通过人工授精产生 F1 杂种。通过用雌性斑点叉尾鮰与雄性北美短吻鳄交配产生的 F1 杂种表现出杂种优势，并为研究生殖隔离和杂种优势提供了理想的系统。本研究的目的是生成高质量的染色体水平参考基因组序列，并确定它们的基因组相似性和差异。
我们为斑点叉尾鮰和北美短吻鳄提供了高质量的参考基因组序列，每个基因组仅包含 67 和 139 个总缺口。我们还报告了两个基因组之间的三个着丝粒染色体倒位，这一点可以通过来自不同个体的长读跨越倒位交界处、遗传连锁图谱和跨越倒位交界处的 PCR 扩增来证明。在回交后代（雌性斑点叉尾鮰×F1 杂种雄性）中，倒位片段内的重组率（检测为双交叉）极低，这表明着丝粒倒位中断了合子后重组或重组体的存活。鉴定出斑点叉尾鮰和北美短吻鳄特有的基因，以及免疫球蛋白基因和着丝粒 Xba 元件的扩张，为这些物种的基因组特征提供了线索。
我们为斑点叉尾鮰和北美短吻鳄生成了高质量的参考基因组序列，并确定了染色体 6、11 和 24 上的主要染色体倒位。这些外周倒位通过额外的测序分析、遗传连锁图谱和跨越倒位交界处的 PCR 分析得到了验证。参考基因组序列以及对比的染色体结构应该为种间繁殖计划提供指导。
