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Population genomics reveals possible genetic evidence for parallel evolution of Sebastiscus marmoratus in the northwestern Pacific Ocean.

ABSTRACT: Understanding patterns of population diversity and structuring among marine populations is of great importance for evolutionary biology, and can also directly inform fisheries management and conservation. In this study, genotyping-by-sequencing was used to assess population genetic diversity and connectivity of Sebastiscus marmoratus. Based on 130 individuals sampled from 10 locations in the northwestern Pacific Ocean, we identified and genotyped 17 653 single-nucleotide polymorphisms. The patterns of genetic diversity and population differentiation suggested that the Okinawa Trough might be the ancestral centre of S. marmoratus after the Last Glacial Maximum. A shallow genetic structure was observed among sampled populations based on the implemented structuring approaches. Surprisingly, we detected genetic homogeneity in two population pairs (i.e. Xiamen-Niigata and Zhuhai-Iki Island), in which populations have large geographical and latitudinal intervals. Population structure and allele frequency distribution based on outlier loci also mirrored the observed genetic homogeneity in the above-mentioned population pairs. Integrated with biological, environmental and genomic data, our results provide possible genetic evidence for parallel evolution. Our study also provides new perspectives on the population structure of S. marmoratus, which could have important implications for sound management and conservation of this fishery species.

SUBMITTER: Xu S

PROVIDER: S-EPMC6769290 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Population genomics reveals possible genetic evidence for parallel evolution of Sebastiscus marmoratus in the northwestern Pacific Ocean.

Xu Shengyong S Yanagimoto Takashi T Song Na N Cai Shanshan S Gao Tianxiang T Zhang Xiumei X

Open biology 20190904 9

Understanding patterns of population diversity and structuring among marine populations is of great importance for evolutionary biology, and can also directly inform fisheries management and conservation. In this study, genotyping-by-sequencing was used to assess population genetic diversity and connectivity of Sebastiscus marmoratus. Based on 130 individuals sampled from 10 locations in the northwestern Pacific Ocean, we identified and genotyped 17 653 single-nucleotide polymorphisms. The patte ...[more]

PMID: 31480992

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Project description:Simple Summary Changes in salinity can have an impact on the physiological processes of fish. In this study, RNA-seq sequencing was used to detect and analyze the differential gene expression of Sebastiscus marmoratus in salinity fluctuations and to explore the genes and pathways related to salinity stress. The results demonstrated that pik3r6b, cPLA2γ-like, and WSB1 were differentially expressed in all three groups. All three genes were highly expressed in the high-salt group, with wsb1 being more expressed than pik3r6b and cPLA2γ-like. The results of this study provide some basic theoretical references for the salinity adaptation mechanism of Sebastiscus marmoratus. Abstract The marbled rockfish, Sebastiscus marmoratus, belongs to the euryhaline fish and is an oviparous scleractinian fish. There are few studies on the adaptation mechanism, functional genes, and related pathways of S. marmoratus and salinity. The results showed that a total of 72.1 GB of clean reads were obtained and all clean reads annotated a total of 25,278 Unigenes, of which 2,160 were novel genes. Compared to 20‰, 479 and 520 differential genes were obtained for 35‰ and 10‰, respectively. Gene ontology (GO) enrichment analysis revealed significant enrichment in protein binding, ion binding, ATP binding, and catalytic activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that differentially expressed genes significantly expressed under salinity stress were mainly involved in the pathways of the cytochrome P450 metabolism of xenobiotics, tryptophan metabolism, cellular senescence, and calcium signaling pathways. Among them, pik3r6b, cPLA2γ-like, and WSB1 were differentially expressed in all three groups, and they were associated with apoptosis, inflammation, DNA damage, immune regulation, and other physiological processes. Six differentially expressed genes were randomly selected for qRT-PCR validation, and the results showed that the transcriptomic data were of high confidence.

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Population genomics reveals possible genetic evidence for parallel evolution of Sebastiscus marmoratus in the northwestern Pacific Ocean.

Publications

Population genomics reveals possible genetic evidence for parallel evolution of Sebastiscus marmoratus in the northwestern Pacific Ocean.

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