Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population
Copy number variations (CNVs) are important structural variations that can cause significant phenotypic diversity. Reliable CNVs mapping can be achieved by identification of CNVs from different genetic backgrounds. Investigations on the characteristics of overlapping between CNV regions (CNVRs) and...
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Frontiers Media S.A.
2021-10-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.753748/full |
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| author | Zhipeng Wang Zhipeng Wang Yuanyuan Guo Yuanyuan Guo Shengwei Liu Shengwei Liu Qingli Meng |
| author_facet | Zhipeng Wang Zhipeng Wang Yuanyuan Guo Yuanyuan Guo Shengwei Liu Shengwei Liu Qingli Meng |
| author_sort | Zhipeng Wang |
| collection | DOAJ |
| description | Copy number variations (CNVs) are important structural variations that can cause significant phenotypic diversity. Reliable CNVs mapping can be achieved by identification of CNVs from different genetic backgrounds. Investigations on the characteristics of overlapping between CNV regions (CNVRs) and protein-coding genes (CNV genes) or miRNAs (CNV-miRNAs) can reveal the potential mechanisms of their regulation. In this study, we used 50 K SNP arrays to detect CNVs in Duroc purebred pig. A total number of 211 CNVRs were detected with a total length of 118.48 Mb, accounting for 5.23% of the autosomal genome sequence. Of these CNVRs, 32 were gains, 175 losses, and four contained both types (loss and gain within the same region). The CNVRs we detected were non-randomly distributed in the swine genome and were significantly enriched in the segmental duplication and gene density region. Additionally, these CNVRs were overlapping with 1,096 protein-coding genes (CNV-genes), and 39 miRNAs (CNV-miRNAs), respectively. The CNV-genes were enriched in terms of dosage-sensitive gene list. The expression of the CNV genes was significantly higher than that of the non-CNV genes in the adult Duroc prostate. Of all detected CNV genes, 22.99% genes were tissue-specific (TSI > 0.9). Strong negative selection had been underway in the CNV-genes as the ones that were located entirely within the loss CNVRs appeared to be evolving rapidly as determined by the median dN plus dS values. Non-CNV genes tended to be miRNA target than CNV-genes. Furthermore, CNV-miRNAs tended to target more genes compared to non-CNV-miRNAs, and a combination of two CNV-miRNAs preferentially synergistically regulated the same target genes. We also focused our efforts on examining CNV genes and CNV-miRNAs functions, which were also involved in the lipid metabolism, including DGAT1, DGAT2, MOGAT2, miR143, miR335, and miRLET7. Further molecular experiments and independent large studies are needed to confirm our findings. |
| first_indexed | 2024-12-20T00:20:03Z |
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| id | doaj.art-8448432e6f794039921a6e120a2d57a1 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-20T00:20:03Z |
| publishDate | 2021-10-01 |
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| spelling | doaj.art-8448432e6f794039921a6e120a2d57a12022-12-21T20:00:13ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-10-011210.3389/fgene.2021.753748753748Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred PopulationZhipeng Wang0Zhipeng Wang1Yuanyuan Guo2Yuanyuan Guo3Shengwei Liu4Shengwei Liu5Qingli Meng6College of Animal Science and Technology, Northeast Agricultural University, Harbin, ChinaBioinformatics Center, Northeast Agricultural University, Harbin, ChinaCollege of Animal Science and Technology, Northeast Agricultural University, Harbin, ChinaBioinformatics Center, Northeast Agricultural University, Harbin, ChinaCollege of Animal Science and Technology, Northeast Agricultural University, Harbin, ChinaBioinformatics Center, Northeast Agricultural University, Harbin, ChinaBeijing Breeding Swine Center, Beijing, ChinaCopy number variations (CNVs) are important structural variations that can cause significant phenotypic diversity. Reliable CNVs mapping can be achieved by identification of CNVs from different genetic backgrounds. Investigations on the characteristics of overlapping between CNV regions (CNVRs) and protein-coding genes (CNV genes) or miRNAs (CNV-miRNAs) can reveal the potential mechanisms of their regulation. In this study, we used 50 K SNP arrays to detect CNVs in Duroc purebred pig. A total number of 211 CNVRs were detected with a total length of 118.48 Mb, accounting for 5.23% of the autosomal genome sequence. Of these CNVRs, 32 were gains, 175 losses, and four contained both types (loss and gain within the same region). The CNVRs we detected were non-randomly distributed in the swine genome and were significantly enriched in the segmental duplication and gene density region. Additionally, these CNVRs were overlapping with 1,096 protein-coding genes (CNV-genes), and 39 miRNAs (CNV-miRNAs), respectively. The CNV-genes were enriched in terms of dosage-sensitive gene list. The expression of the CNV genes was significantly higher than that of the non-CNV genes in the adult Duroc prostate. Of all detected CNV genes, 22.99% genes were tissue-specific (TSI > 0.9). Strong negative selection had been underway in the CNV-genes as the ones that were located entirely within the loss CNVRs appeared to be evolving rapidly as determined by the median dN plus dS values. Non-CNV genes tended to be miRNA target than CNV-genes. Furthermore, CNV-miRNAs tended to target more genes compared to non-CNV-miRNAs, and a combination of two CNV-miRNAs preferentially synergistically regulated the same target genes. We also focused our efforts on examining CNV genes and CNV-miRNAs functions, which were also involved in the lipid metabolism, including DGAT1, DGAT2, MOGAT2, miR143, miR335, and miRLET7. Further molecular experiments and independent large studies are needed to confirm our findings.https://www.frontiersin.org/articles/10.3389/fgene.2021.753748/fullcopy number variationsduroc purebred pigCNV-miRNAsCNV-genesgenome-wide assessment |
| spellingShingle | Zhipeng Wang Zhipeng Wang Yuanyuan Guo Yuanyuan Guo Shengwei Liu Shengwei Liu Qingli Meng Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population Frontiers in Genetics copy number variations duroc purebred pig CNV-miRNAs CNV-genes genome-wide assessment |
| title | Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population |
| title_full | Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population |
| title_fullStr | Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population |
| title_full_unstemmed | Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population |
| title_short | Genome-Wide Assessment Characteristics of Genes Overlapping Copy Number Variation Regions in Duroc Purebred Population |
| title_sort | genome wide assessment characteristics of genes overlapping copy number variation regions in duroc purebred population |
| topic | copy number variations duroc purebred pig CNV-miRNAs CNV-genes genome-wide assessment |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.753748/full |
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