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dc.contributor.authorFuentes, Roven Rommel
dc.contributor.authorChebotarov, Dmytro
dc.contributor.authorDuitama, Jorge
dc.contributor.authorSmith, Sean
dc.contributor.authorDe la Hoz, Juan Fernando
dc.contributor.authorMohiyuddin, Marghoob
dc.contributor.authorWing, Rod Anthony
dc.contributor.authorMcNally, Kenneth L.
dc.contributor.authorTatarinova, Tatiana
dc.contributor.authorGrigoriev, Andrey
dc.contributor.authorMauleon, Ramil
dc.contributor.authorAlexandrov, Nickolai
dc.date.accessioned2019-05-20T08:58:34Z
dc.date.available2019-05-20T08:58:34Z
dc.date.issued2019-04-16
dc.identifier.citationFuentes RR, Chebotarov D, Duitama J, Smith S, De la Hoz JF, et al. (2019) Structural variants in 3000 rice genomes. Genome Research 29: 870–880. Available: http://dx.doi.org/10.1101/gr.241240.118.
dc.identifier.issn1088-9051
dc.identifier.issn1549-5469
dc.identifier.doi10.1101/gr.241240.118
dc.identifier.urihttp://hdl.handle.net/10754/652911
dc.description.abstractInvestigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences in highly repetitive genomes. Combining different bioinformatic approaches for SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 million individual SV calls that grouped into 1.5 million allelic variants. We found enrichment of long SVs in promoters and an excess of shorter variants in 5' UTRs. Across the rice genomes, we identified regions of high SV frequency enriched in stress response genes. We demonstrated how SVs may help in finding causative variants in genome-wide association analysis. These new insights into rice genome biology are valuable for understanding the effects SVs have on gene function, with the prospect of identifying novel agronomically important alleles that can be utilized to improve cultivated rice.
dc.description.sponsorshipWork in the Grigoriev laboratory is supported by awards from the National Science Foundation (DBI-1458202, ACI-1548562), National Institute of Health (R15CA220059), and New Jersey Health Foundation (PC77-17). We thank XSEDE (MCB150014), PRAGMA, Universidad de los Andes, and the Department of Science and Technology, Advanced Science and Technology Institute of the Philippines for computing resources. We thank the Bill and Melinda Gates Foundation for support to the 3K RG via the GSR Phase 2 award OPPGD1393.
dc.publisherCold Spring Harbor Laboratory
dc.relation.urlhttps://genome.cshlp.org/content/29/5/870
dc.rightsThis article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.titleStructural variants in 3000 rice genomes
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentPlant Science
dc.identifier.journalGenome Research
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionBioinformatics Group, Wageningen University and Research, PB Wageningen, 6708, , Netherlands
dc.contributor.institutionInternational Rice Research Institute, Laguna, 4031, , Philippines
dc.contributor.institutionAgrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, 6713, , Colombia
dc.contributor.institutionSystems and Computing Engineering Department, Universidad de Los Andes, Bogotá 111711, , Colombia
dc.contributor.institutionBiology Department, Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08102, , United States
dc.contributor.institutionRoche Sequencing Solutions, Belmont, CA, 94002, , United States
dc.contributor.institutionArizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, , United States
dc.contributor.institutionLaboratory of Forest Genomics, Siberian Federal University, Krasnoyarsk, 660041, , Russian Federation
dc.contributor.institutionA.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, , , Russian Federation
dc.contributor.institutionVavilov Institute of General Genetics, Moscow, 119333, , Russian Federation
dc.contributor.institutionDepartment of Biology, University of La Verne, La Verne, CA, 91750, , United States
kaust.personWing, Rod Anthony
refterms.dateFOA2019-05-20T13:22:39Z
dc.date.published-online2019-04-16
dc.date.published-print2019-05


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This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
Except where otherwise noted, this item's license is described as This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.