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Genomic basis of symbiovar mimosae in Rhizobium etli.

Rogel MA, Bustos P, Santamaría RI, González V, Romero D, Cevallos MÁ, Lozano L, Castro-Mondragón J, Martínez-Romero J, Ormeño-Orrillo E, Martínez-Romero E - BMC Genomics (2014)

Bottom Line: Differences were found in plasmids especially in the symbiosis plasmid, not only in nod gene sequences but in nod gene content.Genes involved in P. vulgaris exudate uptake were not found in symbiovar mimosae but hup genes (involved in hydrogen uptake) were found.Plasmid pRetCFN42a was partially contained in Mim1 and a plasmid (pRetMim1c) was found only in Mim1.

View Article: PubMed Central - PubMed

Affiliation: Ecological Genomics programs, Genomics Science Center, CCG, Cuernavaca, Morelos, Mexico. esperanzaeriksson@yahoo.com.mx.

ABSTRACT

Background: Symbiosis genes (nod and nif) involved in nodulation and nitrogen fixation in legumes are plasmid-borne in Rhizobium. Rhizobial symbiotic variants (symbiovars) with distinct host specificity would depend on the type of symbiosis plasmid. In Rhizobium etli or in Rhizobium phaseoli, symbiovar phaseoli strains have the capacity to form nodules in Phaseolus vulgaris while symbiovar mimosae confers a broad host range including different mimosa trees.

Results: We report on the genome of R. etli symbiovar mimosae strain Mim1 and its comparison to that from R. etli symbiovar phaseoli strain CFN42. Differences were found in plasmids especially in the symbiosis plasmid, not only in nod gene sequences but in nod gene content. Differences in Nod factors deduced from the presence of nod genes, in secretion systems or ACC-deaminase could help explain the distinct host specificity. Genes involved in P. vulgaris exudate uptake were not found in symbiovar mimosae but hup genes (involved in hydrogen uptake) were found. Plasmid pRetCFN42a was partially contained in Mim1 and a plasmid (pRetMim1c) was found only in Mim1. Chromids were well conserved.

Conclusions: The genomic differences between the two symbiovars, mimosae and phaseoli may explain different host specificity. With the genomic analysis presented, the term symbiovar is validated. Furthermore, our data support that the generalist symbiovar mimosae may be older than the specialist symbiovar phaseoli.

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Representation ofR. etliMim1 chromosome. Circles from outermost to innermost indicate: genomic islands of Mim1 (in blue), ORFs in the leading strand, ORFs in the lagging strand, BLAST matches against CFN42 chromosome, genomic islands of CFN42 (in red), GC content, GC skew, coordinates.
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Fig2: Representation ofR. etliMim1 chromosome. Circles from outermost to innermost indicate: genomic islands of Mim1 (in blue), ORFs in the leading strand, ORFs in the lagging strand, BLAST matches against CFN42 chromosome, genomic islands of CFN42 (in red), GC content, GC skew, coordinates.

Mentions: There were more than twice as many unique genes in Mim1 than in CFN42, mainly in plasmids. The respective chromosomes of each strain had around 260 unique genes. In chromosomes, 35 genomic islands were identified only in Mim1 and 17 only in CFN42. (Figure 2); genes found in Mim1 genomic islands are shown in Additional file 1: Table S1. Examples of unique genes found in Mim1 and not in CFN42 are those encoding cytochrome oxidases, some chaperonins, dipeptide transporters, lactate dehydrogenase, a PHB depolymerase, a ferritin–like protein, exopolysaccharide biosynthesis genes, a type VI secretion system and menaquinone biosynthesis as well as many hypothetical genes.Figure 2


Genomic basis of symbiovar mimosae in Rhizobium etli.

Rogel MA, Bustos P, Santamaría RI, González V, Romero D, Cevallos MÁ, Lozano L, Castro-Mondragón J, Martínez-Romero J, Ormeño-Orrillo E, Martínez-Romero E - BMC Genomics (2014)

Representation ofR. etliMim1 chromosome. Circles from outermost to innermost indicate: genomic islands of Mim1 (in blue), ORFs in the leading strand, ORFs in the lagging strand, BLAST matches against CFN42 chromosome, genomic islands of CFN42 (in red), GC content, GC skew, coordinates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4125696&req=5

Fig2: Representation ofR. etliMim1 chromosome. Circles from outermost to innermost indicate: genomic islands of Mim1 (in blue), ORFs in the leading strand, ORFs in the lagging strand, BLAST matches against CFN42 chromosome, genomic islands of CFN42 (in red), GC content, GC skew, coordinates.
Mentions: There were more than twice as many unique genes in Mim1 than in CFN42, mainly in plasmids. The respective chromosomes of each strain had around 260 unique genes. In chromosomes, 35 genomic islands were identified only in Mim1 and 17 only in CFN42. (Figure 2); genes found in Mim1 genomic islands are shown in Additional file 1: Table S1. Examples of unique genes found in Mim1 and not in CFN42 are those encoding cytochrome oxidases, some chaperonins, dipeptide transporters, lactate dehydrogenase, a PHB depolymerase, a ferritin–like protein, exopolysaccharide biosynthesis genes, a type VI secretion system and menaquinone biosynthesis as well as many hypothetical genes.Figure 2

Bottom Line: Differences were found in plasmids especially in the symbiosis plasmid, not only in nod gene sequences but in nod gene content.Genes involved in P. vulgaris exudate uptake were not found in symbiovar mimosae but hup genes (involved in hydrogen uptake) were found.Plasmid pRetCFN42a was partially contained in Mim1 and a plasmid (pRetMim1c) was found only in Mim1.

View Article: PubMed Central - PubMed

Affiliation: Ecological Genomics programs, Genomics Science Center, CCG, Cuernavaca, Morelos, Mexico. esperanzaeriksson@yahoo.com.mx.

ABSTRACT

Background: Symbiosis genes (nod and nif) involved in nodulation and nitrogen fixation in legumes are plasmid-borne in Rhizobium. Rhizobial symbiotic variants (symbiovars) with distinct host specificity would depend on the type of symbiosis plasmid. In Rhizobium etli or in Rhizobium phaseoli, symbiovar phaseoli strains have the capacity to form nodules in Phaseolus vulgaris while symbiovar mimosae confers a broad host range including different mimosa trees.

Results: We report on the genome of R. etli symbiovar mimosae strain Mim1 and its comparison to that from R. etli symbiovar phaseoli strain CFN42. Differences were found in plasmids especially in the symbiosis plasmid, not only in nod gene sequences but in nod gene content. Differences in Nod factors deduced from the presence of nod genes, in secretion systems or ACC-deaminase could help explain the distinct host specificity. Genes involved in P. vulgaris exudate uptake were not found in symbiovar mimosae but hup genes (involved in hydrogen uptake) were found. Plasmid pRetCFN42a was partially contained in Mim1 and a plasmid (pRetMim1c) was found only in Mim1. Chromids were well conserved.

Conclusions: The genomic differences between the two symbiovars, mimosae and phaseoli may explain different host specificity. With the genomic analysis presented, the term symbiovar is validated. Furthermore, our data support that the generalist symbiovar mimosae may be older than the specialist symbiovar phaseoli.

Show MeSH
Related in: MedlinePlus