Dataset Information

Whole genome resequencing data for three rockfish species of Sebastes.

ABSTRACT: Here we report Illumina-based whole genome sequencing of three rockfish species of Sebastes in northwest Pacific. The whole genomic DNA was used to prepare 350-bp pair-end libraries and the high-throughput sequencing yielded 128.5, 137.5, and 124.8 million mapped reads corresponding to 38.54, 41.26, and 37.43?Gb sequence data for S. schlegelii, S. koreanus, and S. nudus, respectively. The k-mer analyses revealed genome sizes were 846.4, 832.5, and 813.1?Mb and the sequencing coverages were 45×, 49×, and 46× for three rockfish, respectively. Comparative genomic analyses identified 46,624 genome-wide single nucleotide polymorphisms (SNPs). Phylogenetic analysis revealed closer relationships of the three species, compared to other six rockfish species. Demographic analysis identified contrasting changes between S. schlegelii and other two species, suggesting drastically different response to climate changes. The reported genome data in this study are valuable for further studies on comparative genomics and evolutionary biology of rockfish species.

SUBMITTER: Xu S

PROVIDER: S-EPMC6586840 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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Whole genome resequencing data for three rockfish species of Sebastes.

Xu Shengyong S Zhao Linlin L Xiao Shijun S Gao Tianxiang T

Scientific data 20190620 1

Here we report Illumina-based whole genome sequencing of three rockfish species of Sebastes in northwest Pacific. The whole genomic DNA was used to prepare 350-bp pair-end libraries and the high-throughput sequencing yielded 128.5, 137.5, and 124.8 million mapped reads corresponding to 38.54, 41.26, and 37.43 Gb sequence data for S. schlegelii, S. koreanus, and S. nudus, respectively. The k-mer analyses revealed genome sizes were 846.4, 832.5, and 813.1 Mb and the sequencing coverages were 45×, ...[more]

PMID: 31222011

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Project description:Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptation in Qinghai-Tibetan Plateau. A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal egg counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between Highland-type Tibetan Sheep (HTS) and Valley-type Tibetan sheep (VTS), and RUNX1 and LOC101111988 were significantly differentiated between VTS and Oura-type Tibetan sheep (OTS). The duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in Qinghai-Tibetan Plateau, which deserves further research in detail. In conclusion, for the first time, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep by resequencing, and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.

Dataset Information

Whole genome resequencing data for three rockfish species of Sebastes.

Publications

Whole genome resequencing data for three rockfish species of Sebastes.

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