Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays

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dc.creatorSantuari, Lucaen
dc.creatorPradervand, Sylvainen
dc.creatorAmiguet-Vercher, Amelia-Mariaen
dc.creatorThomas, Jeromeen
dc.creatorDorcey, Eavanen
dc.creatorHarshman, Keithen
dc.creatorXenarios, Ioannisen
dc.creatorJuenger, Thomas E.en
dc.creatorHardtke, Christian S.en
dc.date.accessioned2014-12-15T17:10:06Zen
dc.date.available2014-12-15T17:10:06Zen
dc.date.issued2010-01-12en
dc.description1 Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland -- 2 Swiss Institute of Bioinformatics, Genopode Building, CH-1015 Lausanne, Switzerland -- 3 Lausanne DNA Array Facility, Center for Integrative Genomics, University of Lausanne, Genopode Building, CH-1015 Lausanne, Switzerland -- 4 Section of Integrative Biology and Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station C0930, Austin, Texas 78712, USAen
dc.description.abstractIdentification of small polymorphisms from next generation sequencing short read data is relatively easy, but detection of larger deletions is less straightforward. Here, we analyzed four divergent Arabidopsis accessions and found that intersection of absent short read coverage with weak tiling array hybridization signal reliably flags deletions. Interestingly, individual deletions were frequently observed in two or more of the accessions examined, suggesting that variation in gene content partly reflects a common history of deletion events.en
dc.description.catalogingnotechristian.hardtke@unil.chen
dc.description.departmentIntegrative Biologyen
dc.description.departmentInstitute for Cellular and Molecular Biologyen
dc.description.sponsorshipen
dc.identifier.Filenamegb-2010-11-1-r4en
dc.identifier.citationSantuari, Luca, Sylvain Pradervand, Amelia-Maria Amiguet-Vercher, Jerôme Thomas, Eavan Dorcey, Keith Harshman, Ioannis Xenarios, Thomas E. Juenger, and Christian S. Hardtke. “Substantial Deletion Overlap among Divergent Arabidopsis Genomes Revealed by Intersection of Short Reads and Tiling Arrays.” Genome Biology 11, no. 1 (January 12, 2010): R4. doi:10.1186/gb-2010-11-1-r4.en
dc.identifier.doidoi:10.1186/gb-2010-11-1-r4en
dc.identifier.urihttp://hdl.handle.net/2152/27831en
dc.language.isoEnglishen
dc.publisherGenome Biologyen
dc.rightsAdministrative deposit of works to UT Digital Repository: This works author(s) is or was a University faculty member, student or staff member; this article is already available through open access at http://www.biomedcentral.com. The public license is specified as CC-BY: http://creativecommons.org/licenses/by/4.0/. The library makes the deposit as a matter of fair use (for scholarly, educational, and research purposes), and to preserve the work and further secure public access to the works of the University.en
dc.subjectArabidopsis genomesen
dc.subjecttiling arraysen
dc.subjectshort read dataen
dc.subjectpolymorphismsen
dc.titleSubstantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arraysen
dc.typeArticleen

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