Genomic variations explorer (GenVarX): a toolset for annotating promoter and CNV regions using genotypic and phenotypic differences

Authors: CHAN, YEN ON - University Of Missouri; BIOVA, JANA - Palacky University; MAHMOOD, ANSER - University Of Missouri; DIETZ, NICHOLAS - University Of Missouri; Bilyeu, Kristin; SKRABISOVA, MARIA - Palacky University; JOSHI, TRUPTI - University Of Missouri

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/27/2023
Publication Date: 10/9/2023
Citation: Chan, Y., Biova, J., Mahmood, A., Dietz, N., Bilyeu, K.D., Skrabisova, M., Joshi, T. 2023. Genomic variations explorer (GenVarX): a toolset for annotating promoter and CNV regions using genotypic and phenotypic differences. Frontiers in Genetics. 14. Article fgene.2023.1251382. https://doi.org/10.3389/fgene.2023.1251382.
DOI: https://doi.org/10.3389/fgene.2023.1251382

Interpretive Summary: Vast amounts of whole genome sequence data can be generated for now thousands of varieties from a single crop species. The ability to generate this data has recently outpaced the analysis capabilities to effectively utilize the data for crop improvement. The objective of this work was to build an accessible online toolset to investigate whole genome sequence data for two special kinds of genomic sequence variations: regulatory elements and copy number variants. The GenVarX toolset was created that enables deeper analysis of whole genome sequence data, and pairs it with publicly available phenotype data. The toolkit currently supports soybean, rice, and Arabidopsis. The impact of this work is a new framework for deep whole genome sequence analysis for researchers to utilize in crop improvement.

Technical Abstract: The rapid growth of sequencing technology and its increasing popularity in biology-related research over the years has made whole-genome re-sequencing (WGRS) data become widely available. A large amount of WGRS data can unlock the knowledge gap between genomics and phenomics through gaining an understanding of the genomic variations that can lead to phenotype changes. These genomic variations are usually comprised of allele and structural changes in DNA, and these changes can affect the regulatory mechanisms causing changes in gene expression and altering the phenotypes of organisms. In this research work, we created the GenVarX toolset that is backed by transcription factor binding sequence data in promoter regions, the copy number variations data, SNPs and Indels data, and phenotypes data which can potentially provide insights about phenotypic differences and solve compelling questions in plant research. Analytics-wise, we have developed strategies to better utilize the WGRS data and mine the data using efficient data processing scripts, libraries, tools, and frameworks to create the interactive and visualization-enhanced GenVarX toolset that encompasses both promoter regions and copy number variation analysis components. The main capabilities of the GenVarX toolset are to provide easy-to-use interfaces for users to perform queries, visualize data, and interact with the data. Based on different input windows on the user interface, users can provide inputs corresponding to each field and submit the information as a query. The data returned on the results page is usually displayed in a tabular fashion. In addition, interactive figures are also included in the toolset to facilitate the visualization of statistical results or tool outputs. Currently, the GenVarX toolset supports soybean, rice, and Arabidopsis. The researchers can access the soybean GenVarX toolset from SoyKB via https://soykb.org/SoybeanGenVarX/, rice GenVarX toolset, and Arabidopsis GenVarX toolset from KBCommons web portal with links https://kbcommons.org/system/tools/GenVarX/Osativa and https://kbcommons.org/system/tools/GenVarX/Athaliana, respectively.