Recombinase A gene of rhizobium bacteria isolated from root nodules of bambara groundnuts [Vigna subterranea L. Verdc.] in Lake Victoria basin.
Description
Recombinase A gene for rhizobium bacteria isolated form root nodules of bambara groundnuts [Vigna subterranea L. Verdc.] in Lake Victoria basin. RecA genes had uniform sizes of about 530 base pairs . The NCBI accession numbers of recA genes of isolates from this study are given (KJ736760 toKJ736764). Partial sequences of recA genes were used to construct a phylogenetic tree. Two groups A and B were obtained with Group A constituting two clades AI and AII. Clade AI had isolates BAMsp2, BAMKar1, BAMsp2 and BAMkis2 all clustered at 100% bootstrap support with Rhizobium sp. strain VIAD13G and PEPSM18. Isolate BAMKbay2 appeared to form a separate sub-clade indicating its slight genetic difference with the former isolates. Isolates BAMKbay1 and BAMKbay9 strongly clustered with Agrobacterium tumefaciens strain 11-17T B5 at 100% bootstrap support. The second sub-clade AII consisted of BAMKis1 and BAMKar2 which clustered with Rhizobium tropici (NCBI HF563598) and Rhizobium sp. strains BICC 651R and NCPPB 4062 at 99% support. This clustering trend indicated the likelihood of the two latter strains being within the species Rhizobium tropici. Group B had isolates BAMKis8 and BAMKis12 which clustered Bradyrhizobium elkanii strain C9 at 98% similarity index. An equal gene length of recA gene sequence of Pseudomonas sp. strain L1-44-08 was used as an out-group to root the phylogenetic tree.
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Steps to reproduce
Pure isolates of rhizobium from bambara groundnuts were genetically characterized using recA gene primers recA-41R CGR ATC TGG TTG ATG AAG ATC ACC AT recA-640F ATC GAG CGG TCG TTC GGC AAG GG at the Segolip Sequencing Unit, BecA-ILRI Hub, by capillary sequencing on a 3730xl DNA Analyzer (Thermo Fisher Scientific Inc. USA). Forward and reverse sequences were assembled and trimmed on CLC Main Workbench (CLC Bio, Version 6.8.3). Assembled sequences were transferred to MEGA Version 6.0 software and aligned using CLUSTAL W according to Tamura et al., (2011).