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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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Schematic representation of plasmid patterns ofRhizobium etlisymbiovars phaseoli and mimosae andR. leguminosarum. Equivalent replicons are indicated with the same color. *indicates the symbiotic plasmid. C indicates chromids.
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Fig1: Schematic representation of plasmid patterns ofRhizobium etlisymbiovars phaseoli and mimosae andR. leguminosarum. Equivalent replicons are indicated with the same color. *indicates the symbiotic plasmid. C indicates chromids.

Mentions: The final assembly of the R. etli sv. mimosae Mim1 genome rendered seven circular molecules: one chromosome and six plasmids at 150× coverage on average. The chromosome was 4.8 Mb in size while the plasmids ranged in size from 181 kb to 1.08 Mb (Figure 1). Average Nucleotide Identity (ANI) and the percentage of conserved DNA between Mim1 and CFN42 were 98.6% and 82.4% respectively on a whole genome analysis, confirming that both strains belong to the same species. Lower ANI (less than 90%) was found between Mim1 and strains of other species such as R. phaseoli and R. leguminosarum.Figure 1


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)

Schematic representation of plasmid patterns ofRhizobium etlisymbiovars phaseoli and mimosae andR. leguminosarum. Equivalent replicons are indicated with the same color. *indicates the symbiotic plasmid. C indicates chromids.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Schematic representation of plasmid patterns ofRhizobium etlisymbiovars phaseoli and mimosae andR. leguminosarum. Equivalent replicons are indicated with the same color. *indicates the symbiotic plasmid. C indicates chromids.
Mentions: The final assembly of the R. etli sv. mimosae Mim1 genome rendered seven circular molecules: one chromosome and six plasmids at 150× coverage on average. The chromosome was 4.8 Mb in size while the plasmids ranged in size from 181 kb to 1.08 Mb (Figure 1). Average Nucleotide Identity (ANI) and the percentage of conserved DNA between Mim1 and CFN42 were 98.6% and 82.4% respectively on a whole genome analysis, confirming that both strains belong to the same species. Lower ANI (less than 90%) was found between Mim1 and strains of other species such as R. phaseoli and R. leguminosarum.Figure 1

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