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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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Graphic representation of the alignments of CFN42 (top)-Mim1 (bottom) replicons. A) pRetMim1a-pRetCFN42b, B) pRetMim1b-pRetCFN42c, C) pRetMim1d-pRetCFN42e, D) pRetMim1e-pRetCFN42d, E) pRetMim1f-pRetCFN42f. ORFs of each replicon are depicted with light blue arrows in their corresponding reading frame. Syntenic segments oriented in the same or opposite direction are joined by red and blue regions, respectively.
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Fig4: Graphic representation of the alignments of CFN42 (top)-Mim1 (bottom) replicons. A) pRetMim1a-pRetCFN42b, B) pRetMim1b-pRetCFN42c, C) pRetMim1d-pRetCFN42e, D) pRetMim1e-pRetCFN42d, E) pRetMim1f-pRetCFN42f. ORFs of each replicon are depicted with light blue arrows in their corresponding reading frame. Syntenic segments oriented in the same or opposite direction are joined by red and blue regions, respectively.

Mentions: The conserved genome in R. etli strains Mim1 and CFN42 includes not only the chromosome but two extrachromosomal replicons (pRetMim1a-pRetCFN42b and pRetMim1d-pRetCFN42e) that have been designated as chromids in CFN42 [42] and one plasmid (pRetMim1b-pRetCFN42c) (Figure 3). Each of the chromids had less than 20 unique genes and the chromid pairs had an ANI around 99% (Table 1). The small replicons pReCFN42a and pRetMim1c were partially conserved and large genomic differences were found in the symbiotic plasmids (Figures 1 and 4, Table 1).Figure 3


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)

Graphic representation of the alignments of CFN42 (top)-Mim1 (bottom) replicons. A) pRetMim1a-pRetCFN42b, B) pRetMim1b-pRetCFN42c, C) pRetMim1d-pRetCFN42e, D) pRetMim1e-pRetCFN42d, E) pRetMim1f-pRetCFN42f. ORFs of each replicon are depicted with light blue arrows in their corresponding reading frame. Syntenic segments oriented in the same or opposite direction are joined by red and blue regions, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Graphic representation of the alignments of CFN42 (top)-Mim1 (bottom) replicons. A) pRetMim1a-pRetCFN42b, B) pRetMim1b-pRetCFN42c, C) pRetMim1d-pRetCFN42e, D) pRetMim1e-pRetCFN42d, E) pRetMim1f-pRetCFN42f. ORFs of each replicon are depicted with light blue arrows in their corresponding reading frame. Syntenic segments oriented in the same or opposite direction are joined by red and blue regions, respectively.
Mentions: The conserved genome in R. etli strains Mim1 and CFN42 includes not only the chromosome but two extrachromosomal replicons (pRetMim1a-pRetCFN42b and pRetMim1d-pRetCFN42e) that have been designated as chromids in CFN42 [42] and one plasmid (pRetMim1b-pRetCFN42c) (Figure 3). Each of the chromids had less than 20 unique genes and the chromid pairs had an ANI around 99% (Table 1). The small replicons pReCFN42a and pRetMim1c were partially conserved and large genomic differences were found in the symbiotic plasmids (Figures 1 and 4, Table 1).Figure 3

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