Abstract
Rhizobium etli is a Gram-negative soil-dwelling alphaproteobacterium that carries out symbiotic biological nitrogen fixation in close association with legume hosts. R. etli strains exhibit high sequence divergence and are geographically structured, with a potentially dramatic influence on the outcome of symbiosis. Here, we present the genome sequence of R. etli CNPAF512, a Brazilian isolate from bean nodules. We anticipate that the availability of genome sequences of R. etli strains from distinctly different areas will provide valuable new insights into the geographic mosaic of the R. etli pangenome and the evolutionary dynamics that shape it.
TEXT
Rhizobium etli is a soil-dwelling alphaproteobacterium that belongs to the Rhizobium/Agrobacterium group of the Rhizobiaceae (11). Rhizobia are known to establish a nitrogen-fixing symbiotic interaction with leguminous host plants (2, 8). R. etli is the natural microsymbiont of Phaseolus vulgaris L., the common bean. In addition, R. etli has been shown to nodulate at least 20 genera of legumes and to form nitrogen-fixing nodules on half of these (5, 12, 13). Given the strong integration of beans into the diet of Latin America, it is unsurprising that R. etli strains have been isolated from diverse geographical regions across the continent. Previously, the genome sequences of two R. etli strains were published, namely, R. etli CFN42, originating from Mexico (4), and R. etli CIAT652, originating from Costa Rica (3). Comparative analysis revealed an unexpectedly high degree of sequence divergence between the two strains. Furthermore, a genetic marker-based study suggests that R. etli populations are geographically structured (7). We therefore anticipate that the availability of additional, high-quality genome sequences of R. etli strains isolated from distinctly different areas will provide valuable new insights into the geographic mosaic of the R. etli pangenome and the evolutionary dynamics that shape it. Here, we present the genome sequence of R. etli CNPAF512, a Brazilian isolate from P. vulgaris nodules (9).
Highly pure genomic DNA of R. etli CNPAF512 was subjected to Solexa sequencing on the Illumina GAIIx platform, resulting in 12,360,096 paired-end reads of 50 bp each and a median coverage depth of 35-fold. Sequences were assembled de novo using Velvet (14) as well as being mapped to the R. etli CIAT652 genome by the MAQ assembler (6). Both assemblies were integrated by MAIA (10), resulting in a total of 489 contigs (13,764-bp average length). Protein-coding genes were predicted using the Softberry FgenesB algorithm (http://linux1.softberry.com/all.htm). Functional annotation was performed by BLAST searches against the GenBank database.
The genome sequence of R. etli CNPAF512 totals 6.7 Mbp with a G+C content of 62%. It contains 7,792 predicted open reading frames (ORFs), located on a chromosome and four megaplasmids. Of the predicted ORFs, 4,162 are similar to genes found in R. etli CFN42 or CIAT652, 1,393 are similar to genes of other fully sequenced genomes, and the remaining 2,291 are unique to R. etli CNPAF512.
Several features distinguish the R. etli CNPAF512 genome from that of other sequenced R. etli strains. Most markedly, we identified genes putatively involved in acetoin metabolism, capsular heptose biosynthesis, DNA phosphorothioation, N-linked protein glycosylation, noninheritable multidrug tolerance, and taurine utilization that are absent from the genomes of both R. etli CFN42 and CIAT652. In addition, the CNPAF512 genome is significantly enriched in genes that are predicted to play a role in amino acid metabolism and inositol catabolism, providing added metabolic versatility. Possible determinants of host specificity include type III and type VI protein secretion systems (1).
Nucleotide sequence accession number.
The draft genome sequence obtained in this work has been deposited at DDBJ/EMBL/GenBank under the accession number AEYZ00000000.
Acknowledgments
This work was supported by grants from the Research Council of the K.U. Leuven (GOA/011/2008 and PF/2010/07) and from the Fund for Scientific Research-Flanders (G.0412.10).
Footnotes
Published ahead of print on 22 April 2011.
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