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

Plant Direct
Morgan O HammR Clay Wright

Abstract

Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of these data remain 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, su...Continue Reading

References

Oct 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·M Nei, W H Li
Jun 10, 1977·Science·F Jacob
Dec 29, 2000·Nature·UNKNOWN Arabidopsis Genome Initiative
Sep 27, 2001·Proceedings of the National Academy of Sciences of the United States of America·N ZenserJ Callis
Feb 5, 2003·The Plant Cell·Shiv B TiwariTom Guilfoyle
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Jan 27, 2004·The Plant Cell·Shiv B TiwariTom J Guilfoyle
Jul 13, 2004·Plant Physiology·David L RemingtonJason W Reed
Mar 9, 2005·Current Opinion in Plant Biology·Richard C Moore, Michael D Purugganan
May 24, 2005·PLoS Biology·Magnus NordborgJoy Bergelson
Jul 5, 2005·Developmental Cell·Nihal DharmasiriMark Estelle
Jun 10, 2006·Science·Jeff A LongElliot M Meyerowitz
Jul 14, 2007·Proceedings of the National Academy of Sciences of the United States of America·Justin O BorevitzJoseph R Ecker
Sep 29, 2007·Current Opinion in Plant Biology·Tom J Guilfoyle, Gretchen Hagen
Jun 13, 2009·Genome Biology·Detlef Weigel, Richard Mott
Dec 19, 2009·Proceedings of the National Academy of Sciences of the United States of America·G ParryM Estelle
Feb 16, 2011·Biochimica Et Biophysica Acta·Conrad A Nieduszynski, Gianni Liti
Dec 21, 2011·Methods in Molecular Biology·Angela WilkinsOlivier Lichtarge
Jan 24, 2012·Developmental Cell·Eike H RademacherDolf Weijers
Apr 3, 2012·Nature Chemical Biology·Luz Irina A Calderón VillalobosMark Estelle
May 23, 2012·Plant Science : an International Journal of Experimental Plant Biology·Tom J Guilfoyle, Gretchen Hagen
Jul 31, 2012·Plant Physiology·Kyle A HavensJennifer L Nemhauser
Dec 12, 2012·The Plant Journal : for Cell and Molecular Biology·Ya-Long Guo
Jun 12, 2013·Nucleic Acids Research·Elad Firnberg, Marc Ostermeier
Apr 8, 2014·Proceedings of the National Academy of Sciences of the United States of America·David A KorasickLucia C Strader
Apr 9, 2014·Nature Communications·Max H NanaoRenaud Dumas
Aug 13, 2014·The Journal of Antimicrobial Chemotherapy·Eliane Siebor, Catherine Neuwirth
Sep 4, 2014·Trends in Genetics : TIG·Maximilian O PressChristine Queitsch
Jan 31, 2015·Development·Jessica M GusemanJennifer L Nemhauser

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Citations

Aug 11, 2020·Plant Direct·Geraint ParryUNKNOWN Multinational Arabidopsis Steering Committee
Mar 14, 2021·Development·Román Ramos Báez, Jennifer L Nemhauser
Jun 2, 2020·Current Opinion in Plant Biology·Amy Lanctot, Jennifer L Nemhauser

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Methods Mentioned

BETA
ubiquitination

Software Mentioned

ViVa Alignment
R
vcfR
ViVa R
ViVa webtool
Decipher
Gene
biomaRt R
ViVa
ePlant browser

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