Dataset Information

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus.

ABSTRACT: The marbled rockfish Sebastiscus marmoratus is an ecologically and economically important marine fish species distributed along the northwestern Pacific coast from Japan to the Philippines. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for S. marmoratus. The genome size of S. marmoratus was estimated as approximate 800 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.17% and 39.65%, respectively. The preliminary assembled genome was nearly 609 Mb with GC content of 41.3%, and the data were used to develop microsatellite markers. A total of 191,592 microsatellite motifs were identified. The most frequent repeat motif was dinucleotide with a frequency of 76.10%, followed by 19.63% trinucleotide, 3.91% tetranucleotide, and 0.36% pentanucleotide motifs. The AC, GAG, and ATAG repeats were the most abundant motifs of dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. In summary, a wide range of candidate microsatellite markers were identified and characterized in the present study using genome survey analysis. High-quality whole genome sequence based on the "Illumina+PacBio+Hi-C" strategy is warranted for further comparative genomics and evolutionary biology studies in this species.

SUBMITTER: Xu SY

PROVIDER: S-EPMC7040462 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus.

Xu Sheng-Yong SY Song Na N Xiao Shi-Jun SJ Gao Tian-Xiang TX

Bioscience reports 20200201 2

The marbled rockfish Sebastiscus marmoratus is an ecologically and economically important marine fish species distributed along the northwestern Pacific coast from Japan to the Philippines. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for S. marmoratus. The genome size of S. marmoratus was estimated as approximate 800 Mb by using K-mer analyses, and its heterozyg ...[more]

PMID: 32090250

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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.

Dataset Information

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus.

Publications

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus.

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