Investigation of Hanwoo-specific structural variations using whole-genome sequencing data View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2019-02

AUTHORS

Jangho Park, Wonseok Shin, Seyoung Mun, Man Hwan Oh, Dajeong Lim, Dong-Yep Oh, Youngjune Bhak, Jong Bhak, Yong-Soo Park, Kyudong Han

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. More... »

PAGES

233-240

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s13258-018-0772-3

DOI

http://dx.doi.org/10.1007/s13258-018-0772-3

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1110481308

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30535859


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cattle", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome-Wide Association Study", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genomic Structural Variation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Red Meat", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Dankook University", 
          "id": "https://www.grid.ac/institutes/grid.411982.7", 
          "name": [
            "Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, 31116, Cheonan, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Park", 
        "givenName": "Jangho", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Dankook University", 
          "id": "https://www.grid.ac/institutes/grid.411982.7", 
          "name": [
            "Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, 31116, Cheonan, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Shin", 
        "givenName": "Wonseok", 
        "id": "sg:person.0703073026.29", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0703073026.29"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Dankook University", 
          "id": "https://www.grid.ac/institutes/grid.411982.7", 
          "name": [
            "Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, 31116, Cheonan, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mun", 
        "givenName": "Seyoung", 
        "id": "sg:person.01150603416.44", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01150603416.44"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Dankook University", 
          "id": "https://www.grid.ac/institutes/grid.411982.7", 
          "name": [
            "Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, 31116, Cheonan, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Oh", 
        "givenName": "Man Hwan", 
        "id": "sg:person.01136422063.84", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01136422063.84"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Animal Genomics and Bioinformatics Division, 1500, Kongjwipatjwi-ro, Iseo-myeon, 55365, Wanju-gun, Jeollabuk-do, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lim", 
        "givenName": "Dajeong", 
        "id": "sg:person.01065611022.27", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01065611022.27"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Livestock Research Institute, 36052, Yeongju, Gyeongbuk, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Oh", 
        "givenName": "Dong-Yep", 
        "id": "sg:person.012536711642.06", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012536711642.06"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Ulsan National Institute of Science and Technology", 
          "id": "https://www.grid.ac/institutes/grid.42687.3f", 
          "name": [
            "Department of Biomedical Engineering, School of Life sciences, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bhak", 
        "givenName": "Youngjune", 
        "id": "sg:person.016330227623.26", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016330227623.26"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Ulsan National Institute of Science and Technology", 
          "id": "https://www.grid.ac/institutes/grid.42687.3f", 
          "name": [
            "Department of Biomedical Engineering, School of Life sciences, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bhak", 
        "givenName": "Jong", 
        "id": "sg:person.01346324635.36", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01346324635.36"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Department of Equine Industry, Korea National College of Agriculture and Fisheries, 54874, Jeonju, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Park", 
        "givenName": "Yong-Soo", 
        "id": "sg:person.01112562122.52", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01112562122.52"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Dankook University", 
          "id": "https://www.grid.ac/institutes/grid.411982.7", 
          "name": [
            "Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, 31116, Cheonan, Republic of Korea"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Han", 
        "givenName": "Kyudong", 
        "id": "sg:person.01333145216.07", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01333145216.07"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1111/j.1365-2052.2008.01815.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000664037"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-10-178", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001796224", 
          "https://doi.org/10.1186/1471-2164-10-178"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.070409.107", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003295442"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-10-180", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006120907", 
          "https://doi.org/10.1186/1471-2164-10-180"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.gde.2006.10.009", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007381556"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1169588", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008571755"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1167936", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010221272"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00335-013-9449-z", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013128534", 
          "https://doi.org/10.1007/s00335-013-9449-z"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/mss092", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016699065"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0005350", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020552743"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1363", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020581697", 
          "https://doi.org/10.1038/nmeth.1363"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1363", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020581697", 
          "https://doi.org/10.1038/nmeth.1363"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btp352", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023014918"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2009-10-4-r42", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024097093", 
          "https://doi.org/10.1186/gb-2009-10-4-r42"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.14348/molcells.2015.0019", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024727975"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/jbiol137", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025355704", 
          "https://doi.org/10.1186/jbiol137"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.meatsci.2013.03.014", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025660037"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0901282106", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026804396"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.5851/kosfa.2014.34.6.763", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027254214"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/oxfordjournals.molbev.a026194", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028185636"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg2640", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030857078", 
          "https://doi.org/10.1038/nrg2640"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg2640", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030857078", 
          "https://doi.org/10.1038/nrg2640"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.91.7.2757", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033413146"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0101127", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034083065"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btp324", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038266369"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mcb.16.5.2164", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038631591"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/2055-0391-56-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041402293", 
          "https://doi.org/10.1186/2055-0391-56-2"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/mss158", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042670285"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-15-240", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043688115", 
          "https://doi.org/10.1186/1471-2164-15-240"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-14-519", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053560160", 
          "https://doi.org/10.1186/1471-2164-14-519"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13100-016-0085-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1074188139", 
          "https://doi.org/10.1186/s13100-016-0085-5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s13100-016-0085-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1074188139", 
          "https://doi.org/10.1186/s13100-016-0085-5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/oxfordjournals.jhered.a110160", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1079546455"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2019-02", 
    "datePublishedReg": "2019-02-01", 
    "description": "BACKGROUND: The total length of the cattle genome is approximately ~\u20093\u00a0billion 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.\nOBJECTIVE: 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.\nRESULTS: 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\u00a0bp microhomology. The 370\u00a0bp deletion event appeared to be only in the Hanwoo individuals after the divergence of Hanwoo and Holstein lineages.\nCONCLUSION: Our study showed that one of the SVs, TE-mediated deletion, could be utilized as a molecular maker to distinguish between Hanwoo and Holstein.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1007/s13258-018-0772-3", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": false, 
    "isPartOf": [
      {
        "id": "sg:journal.1040407", 
        "issn": [
          "0254-5934", 
          "2092-9293"
        ], 
        "name": "Genes & Genomics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "2", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "41"
      }
    ], 
    "name": "Investigation of Hanwoo-specific structural variations using whole-genome sequencing data", 
    "pagination": "233-240", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "ff997d34edf86ef6a5f60678c50f52dabecb91ae618bb3f7c250cf0a994c33c6"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "30535859"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101481027"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/s13258-018-0772-3"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1110481308"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/s13258-018-0772-3", 
      "https://app.dimensions.ai/details/publication/pub.1110481308"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T13:50", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000371_0000000371/records_130794_00000006.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://link.springer.com/10.1007%2Fs13258-018-0772-3"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/s13258-018-0772-3'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s13258-018-0772-3'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s13258-018-0772-3'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s13258-018-0772-3'


 

This table displays all metadata directly associated to this object as RDF triples.

261 TRIPLES      21 PREDICATES      64 URIs      26 LITERALS      14 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/s13258-018-0772-3 schema:about N31b326ad7a0f4cda80260fcb93e389fe
2 N7ca3d310fae34f9ea48e93bee1783ebf
3 Nbb581ffc6d6c491694e44a60e142b874
4 Nc027a62579e8495cb100bfac48cf1511
5 Nd3e7f604f04b49cfb5c2bfaf31252606
6 anzsrc-for:06
7 anzsrc-for:0604
8 schema:author N35375482fa5d4ea4aec37a92dfcd8c57
9 schema:citation sg:pub.10.1007/s00335-013-9449-z
10 sg:pub.10.1038/nmeth.1363
11 sg:pub.10.1038/nrg2640
12 sg:pub.10.1186/1471-2164-10-178
13 sg:pub.10.1186/1471-2164-10-180
14 sg:pub.10.1186/1471-2164-14-519
15 sg:pub.10.1186/1471-2164-15-240
16 sg:pub.10.1186/2055-0391-56-2
17 sg:pub.10.1186/gb-2009-10-4-r42
18 sg:pub.10.1186/jbiol137
19 sg:pub.10.1186/s13100-016-0085-5
20 https://doi.org/10.1016/j.gde.2006.10.009
21 https://doi.org/10.1016/j.meatsci.2013.03.014
22 https://doi.org/10.1073/pnas.0901282106
23 https://doi.org/10.1073/pnas.91.7.2757
24 https://doi.org/10.1093/bioinformatics/btp324
25 https://doi.org/10.1093/bioinformatics/btp352
26 https://doi.org/10.1093/molbev/mss092
27 https://doi.org/10.1093/molbev/mss158
28 https://doi.org/10.1093/oxfordjournals.jhered.a110160
29 https://doi.org/10.1093/oxfordjournals.molbev.a026194
30 https://doi.org/10.1101/gr.070409.107
31 https://doi.org/10.1111/j.1365-2052.2008.01815.x
32 https://doi.org/10.1126/science.1167936
33 https://doi.org/10.1126/science.1169588
34 https://doi.org/10.1128/mcb.16.5.2164
35 https://doi.org/10.1371/journal.pone.0005350
36 https://doi.org/10.1371/journal.pone.0101127
37 https://doi.org/10.14348/molcells.2015.0019
38 https://doi.org/10.5851/kosfa.2014.34.6.763
39 schema:datePublished 2019-02
40 schema:datePublishedReg 2019-02-01
41 schema:description 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.
42 schema:genre research_article
43 schema:inLanguage en
44 schema:isAccessibleForFree false
45 schema:isPartOf N0af5660666d145ed83b34651e29ffda7
46 Nfe0f90d54106442185ed7ce0b6c075b5
47 sg:journal.1040407
48 schema:name Investigation of Hanwoo-specific structural variations using whole-genome sequencing data
49 schema:pagination 233-240
50 schema:productId N0c9622b635f5442fa3346d27557e52ba
51 N2189eab5365643d8a907cec631f8e0ec
52 N340d0de01ded4be18f05508659cf57ba
53 N65c7acb296aa46de8e88226f8a2e5cf6
54 Nb09a08714cc7439ab05bc36bde4599c8
55 schema:sameAs https://app.dimensions.ai/details/publication/pub.1110481308
56 https://doi.org/10.1007/s13258-018-0772-3
57 schema:sdDatePublished 2019-04-11T13:50
58 schema:sdLicense https://scigraph.springernature.com/explorer/license/
59 schema:sdPublisher Nec1c5f21453243e18607cc9e84fe0be8
60 schema:url https://link.springer.com/10.1007%2Fs13258-018-0772-3
61 sgo:license sg:explorer/license/
62 sgo:sdDataset articles
63 rdf:type schema:ScholarlyArticle
64 N0af5660666d145ed83b34651e29ffda7 schema:issueNumber 2
65 rdf:type schema:PublicationIssue
66 N0c9622b635f5442fa3346d27557e52ba schema:name dimensions_id
67 schema:value pub.1110481308
68 rdf:type schema:PropertyValue
69 N2189eab5365643d8a907cec631f8e0ec schema:name readcube_id
70 schema:value ff997d34edf86ef6a5f60678c50f52dabecb91ae618bb3f7c250cf0a994c33c6
71 rdf:type schema:PropertyValue
72 N222b5279f1084a75922350698453345f rdf:first sg:person.01065611022.27
73 rdf:rest Nda4fdfa99b2a456096bd3abb98b94fc6
74 N31b326ad7a0f4cda80260fcb93e389fe schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
75 schema:name Animals
76 rdf:type schema:DefinedTerm
77 N340d0de01ded4be18f05508659cf57ba schema:name pubmed_id
78 schema:value 30535859
79 rdf:type schema:PropertyValue
80 N35375482fa5d4ea4aec37a92dfcd8c57 rdf:first N8c0b130c24a344ccbfe190f99945ba70
81 rdf:rest N364da540f12d4ec4bcb2230829e1e6cc
82 N364da540f12d4ec4bcb2230829e1e6cc rdf:first sg:person.0703073026.29
83 rdf:rest Nbc5886e1d8434821be0cd3f3ed83db83
84 N48dbd669e5994170a1f9888ed24139d4 rdf:first sg:person.01112562122.52
85 rdf:rest Ncd095e9f7c634c5fa32bc1d26c56dbdd
86 N61771023074547dcacab586a0a8ff475 schema:name Animal Genomics and Bioinformatics Division, 1500, Kongjwipatjwi-ro, Iseo-myeon, 55365, Wanju-gun, Jeollabuk-do, Republic of Korea
87 rdf:type schema:Organization
88 N65c7acb296aa46de8e88226f8a2e5cf6 schema:name nlm_unique_id
89 schema:value 101481027
90 rdf:type schema:PropertyValue
91 N7ca3d310fae34f9ea48e93bee1783ebf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
92 schema:name Genome-Wide Association Study
93 rdf:type schema:DefinedTerm
94 N8c0b130c24a344ccbfe190f99945ba70 schema:affiliation https://www.grid.ac/institutes/grid.411982.7
95 schema:familyName Park
96 schema:givenName Jangho
97 rdf:type schema:Person
98 N9f66d6a43f554d9ab9847018c740860f rdf:first sg:person.01136422063.84
99 rdf:rest N222b5279f1084a75922350698453345f
100 Nb09a08714cc7439ab05bc36bde4599c8 schema:name doi
101 schema:value 10.1007/s13258-018-0772-3
102 rdf:type schema:PropertyValue
103 Nb4f0a2a3fa934098883ec2dd12f4dda5 rdf:first sg:person.016330227623.26
104 rdf:rest Nd91087658f7e4de6a67d2f42357af5ab
105 Nbb581ffc6d6c491694e44a60e142b874 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
106 schema:name Genomic Structural Variation
107 rdf:type schema:DefinedTerm
108 Nbc5886e1d8434821be0cd3f3ed83db83 rdf:first sg:person.01150603416.44
109 rdf:rest N9f66d6a43f554d9ab9847018c740860f
110 Nc027a62579e8495cb100bfac48cf1511 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
111 schema:name Red Meat
112 rdf:type schema:DefinedTerm
113 Ncd095e9f7c634c5fa32bc1d26c56dbdd rdf:first sg:person.01333145216.07
114 rdf:rest rdf:nil
115 Nd3e7f604f04b49cfb5c2bfaf31252606 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
116 schema:name Cattle
117 rdf:type schema:DefinedTerm
118 Nd91087658f7e4de6a67d2f42357af5ab rdf:first sg:person.01346324635.36
119 rdf:rest N48dbd669e5994170a1f9888ed24139d4
120 Nda4fdfa99b2a456096bd3abb98b94fc6 rdf:first sg:person.012536711642.06
121 rdf:rest Nb4f0a2a3fa934098883ec2dd12f4dda5
122 Nebc7761df3414979ab5bcc80edaef753 schema:name Department of Equine Industry, Korea National College of Agriculture and Fisheries, 54874, Jeonju, Republic of Korea
123 rdf:type schema:Organization
124 Nec1c5f21453243e18607cc9e84fe0be8 schema:name Springer Nature - SN SciGraph project
125 rdf:type schema:Organization
126 Nfe0f90d54106442185ed7ce0b6c075b5 schema:volumeNumber 41
127 rdf:type schema:PublicationVolume
128 Nfe79a6b5feb34d46ac4e66061e8aefe9 schema:name Livestock Research Institute, 36052, Yeongju, Gyeongbuk, Republic of Korea
129 rdf:type schema:Organization
130 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
131 schema:name Biological Sciences
132 rdf:type schema:DefinedTerm
133 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
134 schema:name Genetics
135 rdf:type schema:DefinedTerm
136 sg:journal.1040407 schema:issn 0254-5934
137 2092-9293
138 schema:name Genes & Genomics
139 rdf:type schema:Periodical
140 sg:person.01065611022.27 schema:affiliation N61771023074547dcacab586a0a8ff475
141 schema:familyName Lim
142 schema:givenName Dajeong
143 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01065611022.27
144 rdf:type schema:Person
145 sg:person.01112562122.52 schema:affiliation Nebc7761df3414979ab5bcc80edaef753
146 schema:familyName Park
147 schema:givenName Yong-Soo
148 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01112562122.52
149 rdf:type schema:Person
150 sg:person.01136422063.84 schema:affiliation https://www.grid.ac/institutes/grid.411982.7
151 schema:familyName Oh
152 schema:givenName Man Hwan
153 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01136422063.84
154 rdf:type schema:Person
155 sg:person.01150603416.44 schema:affiliation https://www.grid.ac/institutes/grid.411982.7
156 schema:familyName Mun
157 schema:givenName Seyoung
158 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01150603416.44
159 rdf:type schema:Person
160 sg:person.012536711642.06 schema:affiliation Nfe79a6b5feb34d46ac4e66061e8aefe9
161 schema:familyName Oh
162 schema:givenName Dong-Yep
163 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012536711642.06
164 rdf:type schema:Person
165 sg:person.01333145216.07 schema:affiliation https://www.grid.ac/institutes/grid.411982.7
166 schema:familyName Han
167 schema:givenName Kyudong
168 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01333145216.07
169 rdf:type schema:Person
170 sg:person.01346324635.36 schema:affiliation https://www.grid.ac/institutes/grid.42687.3f
171 schema:familyName Bhak
172 schema:givenName Jong
173 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01346324635.36
174 rdf:type schema:Person
175 sg:person.016330227623.26 schema:affiliation https://www.grid.ac/institutes/grid.42687.3f
176 schema:familyName Bhak
177 schema:givenName Youngjune
178 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016330227623.26
179 rdf:type schema:Person
180 sg:person.0703073026.29 schema:affiliation https://www.grid.ac/institutes/grid.411982.7
181 schema:familyName Shin
182 schema:givenName Wonseok
183 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0703073026.29
184 rdf:type schema:Person
185 sg:pub.10.1007/s00335-013-9449-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1013128534
186 https://doi.org/10.1007/s00335-013-9449-z
187 rdf:type schema:CreativeWork
188 sg:pub.10.1038/nmeth.1363 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020581697
189 https://doi.org/10.1038/nmeth.1363
190 rdf:type schema:CreativeWork
191 sg:pub.10.1038/nrg2640 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030857078
192 https://doi.org/10.1038/nrg2640
193 rdf:type schema:CreativeWork
194 sg:pub.10.1186/1471-2164-10-178 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001796224
195 https://doi.org/10.1186/1471-2164-10-178
196 rdf:type schema:CreativeWork
197 sg:pub.10.1186/1471-2164-10-180 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006120907
198 https://doi.org/10.1186/1471-2164-10-180
199 rdf:type schema:CreativeWork
200 sg:pub.10.1186/1471-2164-14-519 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053560160
201 https://doi.org/10.1186/1471-2164-14-519
202 rdf:type schema:CreativeWork
203 sg:pub.10.1186/1471-2164-15-240 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043688115
204 https://doi.org/10.1186/1471-2164-15-240
205 rdf:type schema:CreativeWork
206 sg:pub.10.1186/2055-0391-56-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041402293
207 https://doi.org/10.1186/2055-0391-56-2
208 rdf:type schema:CreativeWork
209 sg:pub.10.1186/gb-2009-10-4-r42 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024097093
210 https://doi.org/10.1186/gb-2009-10-4-r42
211 rdf:type schema:CreativeWork
212 sg:pub.10.1186/jbiol137 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025355704
213 https://doi.org/10.1186/jbiol137
214 rdf:type schema:CreativeWork
215 sg:pub.10.1186/s13100-016-0085-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1074188139
216 https://doi.org/10.1186/s13100-016-0085-5
217 rdf:type schema:CreativeWork
218 https://doi.org/10.1016/j.gde.2006.10.009 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007381556
219 rdf:type schema:CreativeWork
220 https://doi.org/10.1016/j.meatsci.2013.03.014 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025660037
221 rdf:type schema:CreativeWork
222 https://doi.org/10.1073/pnas.0901282106 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026804396
223 rdf:type schema:CreativeWork
224 https://doi.org/10.1073/pnas.91.7.2757 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033413146
225 rdf:type schema:CreativeWork
226 https://doi.org/10.1093/bioinformatics/btp324 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038266369
227 rdf:type schema:CreativeWork
228 https://doi.org/10.1093/bioinformatics/btp352 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023014918
229 rdf:type schema:CreativeWork
230 https://doi.org/10.1093/molbev/mss092 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016699065
231 rdf:type schema:CreativeWork
232 https://doi.org/10.1093/molbev/mss158 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042670285
233 rdf:type schema:CreativeWork
234 https://doi.org/10.1093/oxfordjournals.jhered.a110160 schema:sameAs https://app.dimensions.ai/details/publication/pub.1079546455
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1093/oxfordjournals.molbev.a026194 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028185636
237 rdf:type schema:CreativeWork
238 https://doi.org/10.1101/gr.070409.107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003295442
239 rdf:type schema:CreativeWork
240 https://doi.org/10.1111/j.1365-2052.2008.01815.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1000664037
241 rdf:type schema:CreativeWork
242 https://doi.org/10.1126/science.1167936 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010221272
243 rdf:type schema:CreativeWork
244 https://doi.org/10.1126/science.1169588 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008571755
245 rdf:type schema:CreativeWork
246 https://doi.org/10.1128/mcb.16.5.2164 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038631591
247 rdf:type schema:CreativeWork
248 https://doi.org/10.1371/journal.pone.0005350 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020552743
249 rdf:type schema:CreativeWork
250 https://doi.org/10.1371/journal.pone.0101127 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034083065
251 rdf:type schema:CreativeWork
252 https://doi.org/10.14348/molcells.2015.0019 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024727975
253 rdf:type schema:CreativeWork
254 https://doi.org/10.5851/kosfa.2014.34.6.763 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027254214
255 rdf:type schema:CreativeWork
256 https://www.grid.ac/institutes/grid.411982.7 schema:alternateName Dankook University
257 schema:name Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, 31116, Cheonan, Republic of Korea
258 rdf:type schema:Organization
259 https://www.grid.ac/institutes/grid.42687.3f schema:alternateName Ulsan National Institute of Science and Technology
260 schema:name Department of Biomedical Engineering, School of Life sciences, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea
261 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...