A comon genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria

Lisa C. Crossman; Santiago Castillo-Ramirez; Craig McAnnula; Luis Lozano; Georgios S. Vernikos; Jose L. Acosta; Zara F. Ghazoui; Ismael Hernandez-Gonzalez; Georgina Meakin; Alan W. Walker; Michael F. Hynes; J. Peter W. Young; J. Allan Downie; David Romero; Andrew W. B. Johnston; Guillermo Davila; Julian Parkhill; Victor Gonzalez

doi:10.1371/journal.pone.0002567

A comon genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria

Lisa C. Crossman, Santiago Castillo-Ramirez, Craig McAnnula, Luis Lozano, Georgios S. Vernikos, Jose L. Acosta, Zara F. Ghazoui, Ismael Hernandez-Gonzalez, Georgina Meakin, Alan W. Walker, Michael F. Hynes, J. Peter W. Young, J. Allan Downie, David Romero, Andrew W. B. Johnston, Guillermo Davila, Julian Parkhill, Victor Gonzalez

Research output: Contribution to journal › Article › peer-review

57 Citations (Scopus)

Abstract

This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.

Original language	English
Article number	e2567
Journal	PLoS One
Volume	3
Issue number	7
DOIs	https://doi.org/10.1371/journal.pone.0002567
Publication status	Published - 2 Jul 2008

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10.1371/journal.pone.0002567Licence: CC BY

http://dx.doi.org/10.1371/journal.pone.0002567Licence: CC BY

Cite this

Crossman, L. C., Castillo-Ramirez, S., McAnnula, C., Lozano, L., Vernikos, G. S., Acosta, J. L., Ghazoui, Z. F., Hernandez-Gonzalez, I., Meakin, G., Walker, A. W., Hynes, M. F., Young, J. P. W., Downie, J. A., Romero, D., Johnston, A. W. B., Davila, G., Parkhill, J., & Gonzalez, V. (2008). A comon genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria. PLoS One, 3(7), [e2567]. https://doi.org/10.1371/journal.pone.0002567

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title = "A comon genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria",

abstract = "This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.",

author = "Crossman, {Lisa C.} and Santiago Castillo-Ramirez and Craig McAnnula and Luis Lozano and Vernikos, {Georgios S.} and Acosta, {Jose L.} and Ghazoui, {Zara F.} and Ismael Hernandez-Gonzalez and Georgina Meakin and Walker, {Alan W.} and Hynes, {Michael F.} and Young, {J. Peter W.} and Downie, {J. Allan} and David Romero and Johnston, {Andrew W. B.} and Guillermo Davila and Julian Parkhill and Victor Gonzalez",

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Crossman, LC, Castillo-Ramirez, S, McAnnula, C, Lozano, L, Vernikos, GS, Acosta, JL, Ghazoui, ZF, Hernandez-Gonzalez, I, Meakin, G, Walker, AW, Hynes, MF, Young, JPW, Downie, JA, Romero, D, Johnston, AWB, Davila, G, Parkhill, J & Gonzalez, V 2008, 'A comon genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria', PLoS One, vol. 3, no. 7, e2567. https://doi.org/10.1371/journal.pone.0002567

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T1 - A comon genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria

AU - Crossman, Lisa C.

AU - Castillo-Ramirez, Santiago

AU - McAnnula, Craig

AU - Lozano, Luis

AU - Vernikos, Georgios S.

AU - Acosta, Jose L.

AU - Ghazoui, Zara F.

AU - Hernandez-Gonzalez, Ismael

AU - Meakin, Georgina

AU - Walker, Alan W.

AU - Hynes, Michael F.

AU - Young, J. Peter W.

AU - Downie, J. Allan

AU - Romero, David

AU - Johnston, Andrew W. B.

AU - Davila, Guillermo

AU - Parkhill, Julian

AU - Gonzalez, Victor

PY - 2008/7/2

Y1 - 2008/7/2

N2 - This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.

AB - This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.

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