Viva: Visualizing Variation in the Arabidopsis 1001 Genomes Collection

Thousands of sequenced genomes are now publicly available and represent a large swath of plant evolution; 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 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 with biology and bioinformatics to analyze the natural variation in 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 newly emerging databases of genetic variation, such as the 3,000 Rice Genomes Project (http://snp-seek.irri.org/) to facilitate breeding.