{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,1,31]],"date-time":"2024-01-31T17:05:32Z","timestamp":1706720732483},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,11,15]],"date-time":"2016-11-15T00:00:00Z","timestamp":1479168000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"DFG","award":["234585441"],"award-info":[{"award-number":["234585441"]}]},{"name":"BMBF","award":["0315964"],"award-info":[{"award-number":["0315964"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Genome structure rearrangements are a common phenomenon in allopolyploid species. Deletions, duplications and homeologous non-reciprocal translocations (HNRT) between the highly similar subgenomes can be observed, which are known to have a large impact on phenotypic traits. Current research is limited because these rearrangements can be located genome wide only by cost intensive sequencing approaches and not reliably in high-density array genotyping data. We developed gsrc, an R-package to detect genome structure rearrangements from genotyping data in allopolyploid species including exchanges between subgenomes. We exemplarily apply gsrc to a publicly available Brassica napus dataset.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The compiled R-package and source code are available at http:\/\/cran.r-project.org\/web\/packages\/gsrc\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw648","type":"journal-article","created":{"date-parts":[[2016,10,11]],"date-time":"2016-10-11T14:19:40Z","timestamp":1476195580000},"page":"545-546","source":"Crossref","is-referenced-by-count":12,"title":["gsrc: an R package for genome structure rearrangement calling"],"prefix":"10.1093","volume":"33","author":[{"given":"Fabian","family":"Grandke","sequence":"first","affiliation":[{"name":"Department of Plant Breeding, IFZ Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rod","family":"Snowdon","sequence":"additional","affiliation":[{"name":"Department of Plant Breeding, IFZ Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Birgit","family":"Samans","sequence":"additional","affiliation":[{"name":"Department of Plant Breeding, IFZ Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,11,15]]},"reference":[{"key":"2023020204420084800_btw648-B1","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.dib.2015.01.004","article-title":"Collinearity analysis of Brassica A and C genomes based on an updated inferred unigene order","volume":"3","author":"Bancroft","year":"2015","journal-title":"Data Brief"},{"key":"2023020204420084800_btw648-B2","doi-asserted-by":"crossref","first-page":"e109910.","DOI":"10.1371\/journal.pone.0109910","article-title":"A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic map","volume":"9","author":"Cai","year":"2014","journal-title":"PLOS One"},{"key":"2023020204420084800_btw648-B3","first-page":"242","article-title":"Quantifying uncertainty in genotype calls","volume":"26","author":"Carvalho","year":"2010","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023020204420084800_btw648-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00122-012-1964-x","article-title":"Accessing complex crop genomes with next-generation sequencing","volume":"126","author":"Edwards","year":"2013","journal-title":"TAG Theor. 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Genet"},{"key":"2023020204420084800_btw648-B7","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1093\/biostatistics\/kxh008","article-title":"Circular binary segmentation for the analysis of array-based DNA copy number data","volume":"5","author":"Olshen","year":"2004","journal-title":"Biostatistics (Oxford, England)"},{"key":"2023020204420084800_btw648-B8","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.1101\/gr.5402306","article-title":"High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping","volume":"16","author":"Peiffer","year":"2006","journal-title":"Genome Res"},{"key":"2023020204420084800_btw648-B9","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Core Team","year":"2015"},{"key":"2023020204420084800_btw648-B10","doi-asserted-by":"crossref","first-page":"68.","DOI":"10.1186\/1471-2105-12-68","article-title":"Comparing genotyping algorithms for Illumina\u2019s Infinium whole-genome SNP BeadChips","volume":"12","author":"Ritchie","year":"2011","journal-title":"BMC Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/4\/545\/49037547\/bioinformatics_33_4_545.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/4\/545\/49037547\/bioinformatics_33_4_545.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:46:39Z","timestamp":1675313199000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/4\/545\/2593902"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,11,15]]},"references-count":10,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2017,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw648","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,2,15]]},"published":{"date-parts":[[2016,11,15]]}}}