Investigation of Hanwoo-specific structural variations using whole-genome sequencing data.
| Title: | Investigation of Hanwoo-specific structural variations using whole-genome sequencing data. |
|---|---|
| Authors: | Park, Jangho, Shin, Wonseok, Mun, Seyoung, Oh, Man Hwan, Lim, Dajeong, Oh, Dong-Yep, Bhak, Youngjune, Bhak, Jong, Park, Yong-Soo, Han, Kyudong |
| Source: | Genes & Genomics; Feb2019, Vol. 41 Issue 2, p233-240, 8p |
| Abstract: | Background: The total length of the cattle genome is approximately ~ 3 billion base pairs. About half of the bovine genome (46.5%) is composed of transposable elements (TEs). The TEs could be a major source of genomic structural variations (SVs) between cattle breeds. These SVs have led to genomic fluidity and rearrangements between interspecies.Objective: TE-mediated insertion and deletion events could have a strong influence on the bovine genome. This study aimed to investigate TE-mediated deletion events that are common to 12 Hanwoo genome resequencing data.Results: We compared 12 Hanwoo genome resequencing data with the cattle reference genome (Bos taurus_UMD_3.1.1) and six other open source data (2 Jersey, 2 Holstein, 2 Angus). By using BreakDancer program, the common SVs to the 12 Hanwoo genomes were detected. A total of 299 Hanwoo-specific SV candidates were detected. Among them, 56 Hanwoo-specific TE-mediated deletion candidate loci were validated by PCR and Sanger sequencing. Finally, we identified one locus, DEL_96, which is an authentic Hanwoo-specific deletion. The DEL_96 event occurred by nonallelic homologous end-joining between LINE (BovB) and unique sequence with 1 bp microhomology. The 370 bp deletion event appeared to be only in the Hanwoo individuals after the divergence of Hanwoo and Holstein lineages.Conclusion: Our study showed that one of the SVs, TE-mediated deletion, could be utilized as a molecular maker to distinguish between Hanwoo and Holstein. [ABSTRACT FROM AUTHOR] |
| Copyright of Genes & Genomics is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Complementary Index |
| FullText | Text: Availability: 0 CustomLinks: – Url: https://resolver.ebsco.com/c/xy5jbn/result?sid=EBSCO:edb&genre=article&issn=19769571&ISBN=&volume=41&issue=2&date=20190201&spage=233&pages=233-240&title=Genes & Genomics&atitle=Investigation%20of%20Hanwoo-specific%20structural%20variations%20using%20whole-genome%20sequencing%20data.&aulast=Park%2C%20Jangho&id=DOI:10.1007/s13258-018-0772-3 Name: Full Text Finder (for New FTF UI) (s8985755) Category: fullText Text: Find It @ SCU Libraries MouseOverText: Find It @ SCU Libraries |
|---|---|
| Header | DbId: edb DbLabel: Complementary Index An: 134855193 RelevancyScore: 886 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 885.532104492188 |
| IllustrationInfo | |
| Items | – Name: Title Label: Title Group: Ti Data: Investigation of Hanwoo-specific structural variations using whole-genome sequencing data. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Park%2C+Jangho%22">Park, Jangho</searchLink><br /><searchLink fieldCode="AR" term="%22Shin%2C+Wonseok%22">Shin, Wonseok</searchLink><br /><searchLink fieldCode="AR" term="%22Mun%2C+Seyoung%22">Mun, Seyoung</searchLink><br /><searchLink fieldCode="AR" term="%22Oh%2C+Man+Hwan%22">Oh, Man Hwan</searchLink><br /><searchLink fieldCode="AR" term="%22Lim%2C+Dajeong%22">Lim, Dajeong</searchLink><br /><searchLink fieldCode="AR" term="%22Oh%2C+Dong-Yep%22">Oh, Dong-Yep</searchLink><br /><searchLink fieldCode="AR" term="%22Bhak%2C+Youngjune%22">Bhak, Youngjune</searchLink><br /><searchLink fieldCode="AR" term="%22Bhak%2C+Jong%22">Bhak, Jong</searchLink><br /><searchLink fieldCode="AR" term="%22Park%2C+Yong-Soo%22">Park, Yong-Soo</searchLink><br /><searchLink fieldCode="AR" term="%22Han%2C+Kyudong%22">Han, Kyudong</searchLink> – Name: TitleSource Label: Source Group: Src Data: Genes & Genomics; Feb2019, Vol. 41 Issue 2, p233-240, 8p – Name: Abstract Label: Abstract Group: Ab Data: Background: The total length of the cattle genome is approximately ~ 3 billion base pairs. About half of the bovine genome (46.5%) is composed of transposable elements (TEs). The TEs could be a major source of genomic structural variations (SVs) between cattle breeds. These SVs have led to genomic fluidity and rearrangements between interspecies.Objective: TE-mediated insertion and deletion events could have a strong influence on the bovine genome. This study aimed to investigate TE-mediated deletion events that are common to 12 Hanwoo genome resequencing data.Results: We compared 12 Hanwoo genome resequencing data with the cattle reference genome (Bos taurus_UMD_3.1.1) and six other open source data (2 Jersey, 2 Holstein, 2 Angus). By using BreakDancer program, the common SVs to the 12 Hanwoo genomes were detected. A total of 299 Hanwoo-specific SV candidates were detected. Among them, 56 Hanwoo-specific TE-mediated deletion candidate loci were validated by PCR and Sanger sequencing. Finally, we identified one locus, DEL_96, which is an authentic Hanwoo-specific deletion. The DEL_96 event occurred by nonallelic homologous end-joining between LINE (BovB) and unique sequence with 1 bp microhomology. The 370 bp deletion event appeared to be only in the Hanwoo individuals after the divergence of Hanwoo and Holstein lineages.Conclusion: Our study showed that one of the SVs, TE-mediated deletion, could be utilized as a molecular maker to distinguish between Hanwoo and Holstein. [ABSTRACT FROM AUTHOR] – Name: Abstract Label: Group: Ab Data: <i>Copyright of Genes & Genomics is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
| PLink | https://login.libproxy.scu.edu/login?url=https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&scope=site&db=edb&AN=134855193 |
| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1007/s13258-018-0772-3 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 8 StartPage: 233 Titles: – TitleFull: Investigation of Hanwoo-specific structural variations using whole-genome sequencing data. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Park, Jangho – PersonEntity: Name: NameFull: Shin, Wonseok – PersonEntity: Name: NameFull: Mun, Seyoung – PersonEntity: Name: NameFull: Oh, Man Hwan – PersonEntity: Name: NameFull: Lim, Dajeong – PersonEntity: Name: NameFull: Oh, Dong-Yep – PersonEntity: Name: NameFull: Bhak, Youngjune – PersonEntity: Name: NameFull: Bhak, Jong – PersonEntity: Name: NameFull: Park, Yong-Soo – PersonEntity: Name: NameFull: Han, Kyudong IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 02 Text: Feb2019 Type: published Y: 2019 Identifiers: – Type: issn-print Value: 19769571 Numbering: – Type: volume Value: 41 – Type: issue Value: 2 Titles: – TitleFull: Genes & Genomics Type: main |
| ResultId | 1 |