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

Lisa C Crossman, Santiago Castillo-Ramírez, Craig McAnnula, Luis Lozano, Georgios S Vernikos, José L Acosta, Zara F Ghazoui, Ismael Hernández-González, Georgina Meakin, Alan W Walker, Michael F Hynes, J Peter W Young, J Allan Downie, David Romero, Andrew W B Johnston, Guillermo Dávila, Julian Parkhill, Víctor González

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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 languageEnglish
Pages (from-to)e2567
Number of pages9
JournalPloS ONE
Volume3
Issue number7
DOIs
Publication statusPublished - 2 Jul 2008

Fingerprint

nitrogen-fixing bacteria
Bacteria
plasmids
Plasmids
Nitrogen
genomics
Accessories
Rhizobium etli
Genome Components
Rhizobium leguminosarum bv. viciae
Rhizobium leguminosarum
Rhizobium
protein transport
Protein Transport
Chromosomes
Metabolites
Genes
metabolites
chromosomes
genome

Keywords

  • evolution, molecular
  • genome, bacterial
  • models, genetic
  • nitrogen fixation
  • phylogeny
  • plasmids
  • Rhizobium etli
  • Rhizobium leguminosarum
  • symbiosis
  • synteny

Cite this

Crossman, L. C., Castillo-Ramírez, S., McAnnula, C., Lozano, L., Vernikos, G. S., Acosta, J. L., ... González, V. (2008). A common 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

A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria. / Crossman, Lisa C; Castillo-Ramírez, Santiago; McAnnula, Craig; Lozano, Luis; Vernikos, Georgios S; Acosta, José L; Ghazoui, Zara F; Hernández-González, Ismael; Meakin, Georgina; Walker, Alan W; Hynes, Michael F; Young, J Peter W; Downie, J Allan; Romero, David; Johnston, Andrew W B; Dávila, Guillermo; Parkhill, Julian; González, Víctor.

In: PloS ONE, Vol. 3, No. 7, 02.07.2008, p. e2567.

Research output: Contribution to journalArticle

Crossman, LC, Castillo-Ramírez, S, McAnnula, C, Lozano, L, Vernikos, GS, Acosta, JL, Ghazoui, ZF, Hernández-González, I, Meakin, G, Walker, AW, Hynes, MF, Young, JPW, Downie, JA, Romero, D, Johnston, AWB, Dávila, G, Parkhill, J & González, V 2008, 'A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria', PloS ONE, vol. 3, no. 7, pp. e2567. https://doi.org/10.1371/journal.pone.0002567
Crossman LC, Castillo-Ramírez S, McAnnula C, Lozano L, Vernikos GS, Acosta JL et al. A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria. PloS ONE. 2008 Jul 2;3(7):e2567. https://doi.org/10.1371/journal.pone.0002567
Crossman, Lisa C ; Castillo-Ramírez, Santiago ; McAnnula, Craig ; Lozano, Luis ; Vernikos, Georgios S ; Acosta, José L ; Ghazoui, Zara F ; Hernández-González, Ismael ; Meakin, Georgina ; Walker, Alan W ; Hynes, Michael F ; Young, J Peter W ; Downie, J Allan ; Romero, David ; Johnston, Andrew W B ; Dávila, Guillermo ; Parkhill, Julian ; González, Víctor. / A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria. In: PloS ONE. 2008 ; Vol. 3, No. 7. pp. e2567.
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