Draft genome sequence of type strain HBR26Tand description ofRhizobium aethiopicumsp. nov.
Rhizobium aethiopicumsp. nov. is a newly proposed species within the genusRhizobium. This species includes six rhizobial strains; which were isolated from root nodules of the legume plantPhaseolus vulgarisgrowing in soils of Ethiopia. The species fixes nitrogen effectively in symbiosis with the host plantP. vulgaris,and is composed of aerobic, Gram-negative staining, rod-shaped bacteria. The genome of type strain HBR26TofR. aethiopicumsp. nov. was one of the rhizobial genomes sequenced as a part of the DOE JGI 2014 Genomic Encyclopedia project designed for soil and plant-associated and newly described type strains. The genome sequence is arranged in 62 scaffolds and consists of 6,557,588 bp length, with a 61% G + C content and 6221 protein-coding and 86 RNAs genes. The genome of HBR26TcontainsrepABCgenes (plasmid replication genes) homologous to the genes found in five differentRhizobium etliCFN42Tplasmids, suggesting that HBR26Tmay have five additional replicons other than the chromosome. In the genome of HBR26T, the nodulation genesnodB, nodC, nodS, nodI, nodJandnodDare located in the same module, and organized in a similar way asnodgenes found in the genome of other known common bean-nodulating rhizobial species.nodAgene is found in a different scaffold, but it is also very similar tonodAgenes of other bean-nodulating rhizobial strains. Though HBR26Tis distinct on the phylogenetic tree and based on ANI analysis (the highest value 90.2% ANI with CFN42T) from other bean-nodulating species, thesenodgenes and most nitrogen-fixing genes found in the genome of HBR26Tshare high identity with the corresponding genes of known bean-nodulating rhizobial species (96-100% identity). This suggests that symbiotic genes might be shared between bean-nodulating rhizobia through horizontal gene transfer.R. aethiopicumsp. nov. was grouped into the genusRhizobiumbut was distinct from all recognized species of that genus by phylogenetic analyses of combined sequences of the housekeeping genesrecAandglnII. The closest reference type strains for HBR26TwereR. etliCFN42T(94% similarity of the combinedrecAandglnIIsequences) andRhizobium bangladeshenseBLR175T(93%). Genomic ANI calculation based on protein-coding genes also revealed that the closest reference strains wereR. bangladeshenseBLR175TandR. etliCFN42Twith ANI values 91.8 and 90.2%, respectively. Nevertheless, the ANI values between HBR26Tand BLR175Tor CFN42Tare far lower than the cutoff value of ANI (> = 96%) between strains in the same species, confirming that HBR26Tbelongs to a novel species. Thus, on the basis of phylogenetic, comparative genomic analyses and ANI results, we formally propose the creation ofR. aethiopicumsp. nov. with strain HBR26T(=HAMBI 3550T=LMG 29711T) as the type strain. The genome assembly and annotation data is deposited in the DOE JGI portal and also available at European Nucleotide Archive under accession numbers FMAJ01000001-FMAJ01000062.
Department of Environmental Sciences, University of Helsinki, Viikinkaari 2a, Helsinki, Finland.
Aregu Amsalu
AA
Aserse
DOE Joint Genome Institute, Walnut Creek, USA.
Tanja
T
Woyke
DOE Joint Genome Institute, Walnut Creek, USA.
Nikos C
NC
Kyrpides
Department of Microbiology, University of Georgia, Biological Sciences Building, Athens, USA.
William B
WB
Whitman
Department of Environmental Sciences, University of Helsinki, Viikinkaari 2a, Helsinki, Finland.
Kristina
K
Lindström
Average Nucleotide Identity; Common bean; Ethiopia; Genome; Rhizobium aethiopicum; Symbiotic