LIFE SCIENCE

Scientists have made new breakthroughs in the study of landscape genomics of large and small yellow fish


Genome characteristics of small yellow croaker Photo courtesy of the research group

Population structure and population dynamics history of small and large yellow croaker Photo courtesy of the research group

Distribution of genome heterogeneity differentiation of small yellow croaker and large yellow croaker Courtesy of the research group

Recently, the Yellow Sea Fisheries Research Institute of the Chinese Academy of Fishery Sciences, the Temasek Life Science Research Institute in Singapore and Sun Yat-sen University have made important progress in the research of landscape genomics of large yellow croaker and small yellow croaker, which was published in the journal Molecular Ecology of Ecology and Evolutionary Biology.

Large yellow croaker and small yellow croaker are the only two sister species of the yellow fish genus of the totoaba family, which are endemic fishery resources in the Northwest Pacific Ocean, and were once known as “China’s famous four marine products” together with ribbon fish and squid, and occupy an important position in China’s marine fishing industry.

It is understood that the natural distribution areas of large yellow croaker and small yellow croaker are different, large yellow croaker are mainly distributed in the East China Sea and South China Sea, while small yellow croaker are mainly distributed in the Bohai Yellow Sea and East China Sea, and the sister species have overlapping distribution areas in the East China Sea; The two species have very different population biology characteristics such as body size, spawning migration routes and wintering grounds, but overlap with each other’s spawning time, spawning grounds and nursery grounds in the northern East China Sea.

The team’s earlier research demonstrated that the two sister species separated during the Pleistocene glacial period, in two refuges in the East and South China Seas. After the glaciers retreated, both species experienced rapid expansion and partial contact, and adapted to diverse environmental conditions, such as spawning temperature and salinity.

Based on the observation of population mixing of the two species in the overlapping distribution area, the research team proposed that the species of the yellow croaker genus may follow the speciation model hypothesis of secondary contact, and to this end, the allele changes and distribution patterns of the sister species under the influence of evolutionary dynamics are expected to reveal the heterogeneous differentiation landscape and evolutionary mechanism of the genomes of small yellow croaker and large yellow croaker.

The study used the third-generation PacBio and second-generation Illumina platforms to sequence the genome of the small yellow fish, and used the genetic linkage map to assemble the genome to the chromosomal level. The genome size is 653 MB, there are 24,625 protein-coding genes, and the genome integrity is more than 97%. The mapping of high-quality chromosome-level genome maps provides important genetic resources for the study of population genetics and genome breeding of small yellow croakers.

Elucidating genomic heterogeneous differentiation and its mechanism is an important research proposition in evolutionary biology. The team analyzed the evolutionary mechanism of small yellow croaker and large yellow croaker from the perspective of landscape genomics of species differentiation. The results showed that the differentiation of the two species occurred under secondary contact, and differential introgression and linkage selection may be involved in the heterogeneous differentiation of the genome. The recombination rate of genomic islands was low, and the genetic diversity and recombinant landscape between species were relatively well maintained, indicating that the linkage selection of low recombinant regions played a key role in the heterogeneous differentiation of the ancestral lineages of the two species. The differentiation index (Fst) is positively correlated with absolute sequence differentiation (Dxy), and Dxy is elevated in genomic islands, indicating that the differentiation pattern of the genome is not just caused by linked selection. In addition, the study found that limited gene flow in highly differentiated regions may also reshape the pattern of genomic heterogeneous differentiation.

The authors are Wang Le, Liu Shufang, Yang Yang, Meng Zining, Zhuang Zhimeng, from Temasek Life Science Research Institute in Singapore, Yellow Sea Fisheries Research Institute of Chinese Academy of Fishery Sciences, Sun Yat-sen University and other units. This work was supported by the special fund of Qingdao Marine Science and Technology Pilot National Laboratory and the National Natural Science Foundation of China. (Source: China Science News, Liao Yang, Ruan Xiaohong)

Related paper information:https://doi.org/10.1111/mec.16693



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