Comparative genomics as a tool for rapid identification of elite indigenous soybean nodulating Rhizobia in South Kivu, D.R. Congo

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Bintu Nabintu Ndusha
Shellemia Okoth Keya
Richard Ndemo Onwonga
Leon Nsharwasi Nabahungu
Gustave Mushagalusa Nachigera
Leah Kago
Collins Mutai
Sita Ghimire


The use of indigenous rhizobia as inoculants is the best option for improving soybeans productivity and Biological Nitrogen Fixation (BNF). The selection method to date of effective rhizobia nodulating legumes among indigenous population to be included in inoculants formula is time consuming. We sequenced 24 genomes of indigenous Soybean nodulating rhizobia (SNR) isolated from soybean’s root nodules grown in South Kivu province of DRC in order to identify rapidly candidate elite strains. Full genomes sequences of 24 indigenous rhizobia were obtained on Miseq, libraries prepared using Nextera xt protocols and compared with genome of the commercial strain Bradyrhizobium japonicum USDA 110 (accession number CP011360.1). The genomic features were determined and the presence of nitrogen fixation genes detected. Out of 24 samples, we obtained 14 high quality genomes of indigenous SNR, of mean size of 8.383 Mb ±0.762 bp with mean GC content of 62%. These SNR belonged mostly to Bradyrhizobium (64%) genus and few to Rhizobium, Microvirga and Kosakonia. Their chromosomes comprised a mean of 8063±975 genes and 99% of these were protein-coding genes. The full set of nodulation genes (nod and nif) were detected in 11 out of 14 indigenous strains and eight genomes of indigenous strains (NAC53, NAC46, NAC22, NAC76, NAC37, NAC17, NAC28 and NAC42) were close to the commercial strains USDA110 and can be considered as candidate elite strains. We conclude that comparative genomics can be used is a tool for rapid identification of elite strains.

Key words: Genomics, Glycine max, indigenous rhizobia, rhizobia selection, South Kivu

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