About BradyBase

A database dedicated to soybean root-nodulating bradyrhizobia species can benefit the community of researchers working in these species. While genes and genome assemblies are available in large scale databases like the National Center for Biotechnology Information (NCBI), the European Molecular Biological Laboratory (EMBL), and the DNA Databank of Japan (DDBJ), they do not provide background information, experimental protocols, and phenotypic data for the Bradyrhizobium spp. As of July 31st 2021, 126 genome assemblies were hosted in NCBI along with their genes and annotations for Bradyrhizobium species: B. diazoefficiens, B. daqingense, B. elkanii, B. huanghuaihaiense, B. liaoningense, B. ottawaense, B. yuanmingense, and B. diazoefficiens. Aggregating and analyzing the available information including taxonomy, genome assemblies, genes, proteins and annotations can be time consuming and error prone. A database for soybean-root nodulating bradyrhizobia can expedite this by compiling data from multiple resources and providing necessary data analysis tools.

Here, we have developed BradyBase (http://bradybase.dbi.udel.edu) to address the need for a database focused on soybean root-nodulating Bradyrhizobium spp.. The Tripal-based web interface hosts the latest available genome assemblies, genes, nucleotide sequences, gene functional annotations, and gene ontology for the soybean root-nodulating Bradyrhizobium spp. Included are Bradyrhizobium spp. available in NCBI and the University of Delaware Bradyrhizobium Culture Collection (UDBCC), including available phenotypic features, taxonomy, and metadata for genome assemblies including sequencing technology, level of assembly, and number of contigs. Phylogenetic trees and a genome browser feature help to visualize the genomic and genotypic data. BradyBase can be extended to include field experimental results for symbiotic effectiveness of Bradyrhizobium spp. on soybean plants, experiment protocols, culture stocks information, comparative genomics information, bioinformatically predicted phages on each genome, and so on to provide a complete reference site for the soybean root-nodulating Bradyrhizobium species.

University of Delaware Bradyrhizobium Culture Collection (UDBCC)

The University of Delaware Bradyrhizobium Culture Collection (UDBCC) was established with an aim to study the diversity of soybean bradyrhizobia in the state of Delaware and its impact in soybean agriculture. It consists of 352 (initially 382) soybean root-nodulating bradyrhizobia accessions which includes 340 isolates collected from 31 soybean farms spread across the state and 12 reference USDA strains (USDA 31, 38, 46, 62, 76, 94, 110, 122, 123, 130, 135, and 138). Field isolates were collected from several soybean cultivars of growth stages V3 to R5.