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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 A
dc.contributor.authorMcNally, Kenneth L
dc.contributor.authorTatarinova, Tatiana
dc.contributor.authorGrigoriev, Andrey
dc.contributor.authorMauleon, Ramil
dc.contributor.authorAlexandrov, Nickolai
dc.date.accessioned2019-08-19T22:49:58Z
dc.date.available2019-08-19T22:49:58Z
dc.date.issued2019-04-16
dc.identifier.citationFuentes, R. R., Chebotarov, D., Duitama, J., Smith, S., De la Hoz, J. F., Mohiyuddin, M., ... & Mauleon, R. (2019). Structural variants in 3000 rice genomes. Genome research, 29(5), 870-880.en_US
dc.identifier.issn1088-9051
dc.identifier.pmid30992303
dc.identifier.doi10.1101/gr.241240.118
dc.identifier.urihttp://hdl.handle.net/10150/633880
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 into1.5 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.en_US
dc.description.sponsorshipNational Science Foundation [DBI-1458202, ACI-1548562]; National Institute of Health [R15CA220059]; New Jersey Health Foundation [PC77-17]; Bill and Melinda Gates Foundation [OPPGD1393]; XSEDE, PRAGMA, Universidad de los Andes [MCB150014]en_US
dc.language.isoenen_US
dc.publisherCOLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPTen_US
dc.rightsCopyright © 2019 Fuentes et al.; Published by Cold Spring Harbor Laboratory Press.en_US
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/
dc.titleStructural variants in 3000 rice genomesen_US
dc.typeArticleen_US
dc.contributor.departmentUniv Arizona, Arizona Genom Insten_US
dc.identifier.journalGENOME RESEARCHen_US
dc.description.note6 month embargo; published online: 16 April 2019en_US
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.en_US
dc.eprint.versionFinal published versionen_US
dc.source.journaltitleGenome research


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