Carp Genomes Uncover Speciation and Chromosome Evolution of Fishes

Carps jumping out of water (Credit:IHB)

The bighead carp (Hypophthalmichthys nobilis), one of the most popular edible fish species in China, are wreaking havoc in the United States since its introduction with the silver carp (Hypophthalmichthys molitrix) in the 1970s to clear up the weeds and parasites in the waters. These typical clade of endemic East Asian Cyprinidae are now considered by the US as the most invasive alien species since they are not served as edible fish and have no natural predators.   

A research team led by Prof. HE Shunping from Institute of Hydrobiology of the Chinese Academy of Sciences (IHB), in collaboration with BGI and others, revealed the evolutionary history of the East Asian cyprinids, and further explored the evolution and speciation of the silver carp and bighead carp, as well as genomic differentiation between the populations. The results were published online in Molecular Ecology Resources.  

By integrating short-read sequencing and genetic maps, He’s team presented chromosomal-level genome assemblies with high quality and contiguity for the silver carp and the bighead carp. Simultaneously, they sampled 20 silver carp (seven from the Pearl River, four from the Amur River and nine from Yangtze River) and 22 bighead carp (eight from the Pearl River, four from the Amur River and 10 from Yangtze River) for re-sequencing.    

They found that an East Asian cyprinid genome-specific chromosome fusion took place ~9.2 million years after this clade diverged from the clade containing the common carp and Sinocyclocheilus, suggesting that the East Asian cyprinids may possess only 24 pairs of chromosomes due to the fusion of two ancestral chromosomes.   

Besides, phylogenetic analysis showed that the bighead carp formed a clade with the silver carp, with an estimated divergence time of 3.6 million years ago. Population genetics and introgression indicated that silver carp and bighead carp were highly divergent, yet introgression between these species was detected in population analysis.    

The researchers additionally identified the regions which might be associated with divergence or speciation. Genes associated with the divergent regions were revealed to be associated with reproductive system development and the development of primary female sexual characteristics, and the divergent regions might have influence on early speciation, reproductive isolation and environmental adaptations between the two species.   

“These genomic data are important resource for further studies of these East Asian cyprinids on their evolution, conservation and commercial breeding,” said YANG Liandong, a member of Prof. He’s team and one of the authors of the paper.     

This research was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31000000), the National Natural Science Foundation of China (31702016 and 31972866) and Youth Innovation Promotion Association, Chinese Academy of Sciences.