The Allele Catalog Tool: a web-based interactive tool for allele discovery and analysis

Abstract

Background The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize. Results The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes. Conclusions The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website (https://soykb.org/SoybeanAlleleCatalogTool/), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website (https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana). Researchers can use this tool to connect variant alleles of genes with meta-information of species.

Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

“…Numerous additional applications may be realized using these tools, particularly by exploiting the publicly available resequencing data resources of soybean (Liu et al, 2020; Torkamaneh et al, 2021; Valliyodan et al, 2021). Alignments of resequenced data to the gapless genomes and be utilized for allele mining (Chan et al, 2023), comparative genomics, diversity analysis, and genome wide association studies.…”

Natural and artificial selection of multiple alleles revealed through genomic analyses

“…Apart from the Python package, a user-friendly and publicly accessible web-based Soybean MADis Tool powered by the Soy1066 dataset ( Chan et al, 2023 ) has also been created. The architecture of the Soybean MADis Tool includes the MySQL database that links the SoyKB web portals ( Joshi et al, 2012 ; Joshi et al 2014 ; Joshi et al 2017 ), back-end processing code in PHP, and front-end user interfaces with interactive components and visualizations developed with HTML, CSS, and JavaScript.…”

“…In this study, we used our Soy1066 dataset ( Chan et al, 2023 ) available at https://soykb.org/public_data.php as a genotype input. This dataset represents diverse soybean accessions with geographical distribution capturing the worldwide soybean population of distinct improvement statuses ( Glycine soja and Glycine max , landraces, elite lines, and North American cultivars).…”

“…For MADis validation using the example cases, the previously known soybean multiple CMs were used. The genotype data from the Soy1066 dataset ( Chan et al, 2023 ) and phenotype data from the USDA Soybean Germplasm Collection (GRIN, Urbana, IL), both publicly available, were used. During the validation, the MADis analysis was performed for the known causative gene, genes in close distance to causative genes, and randomly chosen genes.…”

“…The Allele Catalog Tool ( Chan et al, 2023 ) was used to analyze the allele distribution in L1 and L2 . The output table was downloaded and streamlined to display only the positions identified by MADis.…”