Bradybase: a comprehensive genomics database for soybean root-nodulating Bradyrhizobium species
| Author(s) | Sharma, Menolin | |
| Date Accessioned | 2022-02-25T14:15:16Z | |
| Date Available | 2022-02-25T14:15:16Z | |
| Publication Date | 2021 | |
| SWORD Update | 2022-01-21T20:02:39Z | |
| Abstract | The symbiotic relationship formed between soybean legumes and root-nodulating Bradyrhizobium spp. provides a sustainable and a ordable source of nitrogen (N) to soybean plants via biological nitrogen fixation (BNF). During this process, Bradyrhizobium spp. form and perform nitrogen fixation inside root nodules with the help of nodulation (nod) and nitrogen fixation (nif and fix) genes located together in symbiosis islands in the bacterial genome. Commonly reported soybean root-nodulating Bradyrhizobium spp. in the US include B. diazoefficiens, B. elkanii, and B. japonicum, which are also used as commercial inoculants due to observed increases in soybean yield which varies based on phenotypic traits such as symbiotic e ectiveness (nodulation and nitrogen fixation abilities) and competitiveness with indigenous Bradyrhizobium spp. Genomic analyses, including gene and symbiosis island composition, potentially provide a readily available and cost efficient approach to the prediction of phenotypic traits. However, only 21 complete genomes for these three species are available in NCBI GenBank and RefSeq, and no comprehensive resource is available to gather data about Bradyrhizobium, a genus critical to sustainable soybean production that will facilitate food security for a global population expected to reach 9.9 billion by 2050. Bradybase, an organism-specific database for soybean root-nodulating Bradyrhizobium spp., was developed as a publicly available web resource for bradyrhizobia researchers and stakeholders. Bradybase integrates genomes and phenomic data from NCBI RefSeq and the University of Delaware Bradyrhizobium Culture Collection (UDBCC), which consists of 352 Bradyrhizobium accessions (340 field isolates and 12 USDA reference strains) established to genotypically and phenotypically characterize the indigenous soybean root-nodulating Bradyrhizobium spp. in the state of Delaware. In this study, 21 UDBCC accessions were selected based on phenotypic diversity and assembled to complete or near complete genomes using long reads generated from Pacific Biosciences (PacBio) RSII Single Molecule Real Time (SMRT) technology. A novel pipeline corrected frameshifted genes, often a result of the high PacBio RSII error rate (13-15%), using reference RefSeq genes. Genome assembly and annotation highlighted the importance of the often overlooked manual assessment and correction of completely assembled microbial genomes, particularly those assembled from PacBio subreads alone, before depositing the genomes into large scale databases like NCBI. Bradybase presents a platform for the integration of tools, analyses, data, and collaboration forums specific to soybean-bradyrhizobia symbiosis research studies benefitting the research and agricultural communities. | en_US |
| Advisor | Polson, Shawn W. | |
| Degree | M.S. | |
| Department | University of Delaware, Center for Bioinformatics and Computational Biology | |
| DOI | https://doi.org/10.58088/rc71-0z52 | |
| Unique Identifier | 1299307832 | |
| URL | https://udspace.udel.edu/handle/19716/30565 | |
| Language | en | |
| Publisher | University of Delaware | en_US |
| URI | https://login.udel.idm.oclc.org/login?url=https://www.proquest.com/dissertations-theses/bradybase-comprehensive-genomics-database-soybean/docview/2622296470/se-2?accountid=10457 | |
| Keywords | Bradyrhizobia | |
| Keywords | Genomic analysis | |
| Keywords | PacBio | |
| Keywords | Root-nodulating | |
| Keywords | Soybean | |
| Title | Bradybase: a comprehensive genomics database for soybean root-nodulating Bradyrhizobium species | en_US |
| Type | Thesis | en_US |