Accelerating structure-function mapping using the ViVa webtool to mine natural variation

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dc.contributor.authorHamm, Morganen
dc.contributor.authorMoss, Britneyen
dc.contributor.authorLeydon, Alexanderen
dc.contributor.authorGala, Hardiken
dc.contributor.authorLanctot, Amyen
dc.contributor.authorRamos, Románen
dc.contributor.authorKlaeser, Hannahen
dc.contributor.authorLemmex, Andrewen
dc.contributor.authorZahler, Mollyeen
dc.contributor.authorNemhauser, Jennifer L.en
dc.contributor.authorWright, R. Clayen
dc.contributor.departmentBiological Systems Engineeringen
dc.date.accessioned2019-01-21T18:02:02Zen
dc.date.available2019-01-21T18:02:02Zen
dc.date.issued2018-12-05en
dc.date.updated2019-01-21T18:01:42Zen
dc.description.abstractThousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of this data remains inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well-studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project (http://snp-seek.irri.org/) and human genetic variation (https://www.ncbi.nlm.nih.gov/clinvar/).en
dc.description.versionSubmitted versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1101/488395en
dc.identifier.issn2475-4455en
dc.identifier.orcidWright, Robert [0000-0001-7125-3943]en
dc.identifier.urihttp://hdl.handle.net/10919/86814en
dc.language.isoenen
dc.publisherWileyen
dc.relation.urihttps://doi.org/10.1101/488395en
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.titleAccelerating structure-function mapping using the ViVa webtool to mine natural variationen
dc.title.serialPlant Directen
dc.typeArticleen
dc.type.dcmitypeTexten
dc.type.otherArticleen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Biological Systems Engineeringen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen

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