The genome of Rhizobium leguminosarum has recognizable core and accessory components

J P W Young; L C Crossman; A W B Johnston; N R Thomson; Z F Ghazoui; K H Hull; M Wexler; A R J Curson; J D Todd; P S Poole; T H Mauchline; A K East; M A Quail; C Churcher; C Arrowsmith; I Cherevach; T Chillingworth; K Clarke; A Cronin; P Davis; A Fraser; Z Hance; H Hauser; K Jagels; S Moule; K Mungall; H Norbertczak; E Rabbinowitsch; M Sanders; M Simmonds; S Whitehead; J Parkhill

doi:10.1186/gb-2006-7-4-r34

The genome of Rhizobium leguminosarum has recognizable core and accessory components

J P W Young, L C Crossman, A W B Johnston, N R Thomson, Z F Ghazoui, K H Hull, M Wexler, A R J Curson, J D Todd, P S Poole, T H Mauchline, A K East, M A Quail, C Churcher, C Arrowsmith, I Cherevach, T Chillingworth, K Clarke, A Cronin, P DavisA Fraser, Z Hance, H Hauser, K Jagels, S Moule, K Mungall, H Norbertczak, E Rabbinowitsch, M Sanders, M Simmonds, S Whitehead, J Parkhill

Biology

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

Abstract

Background: Rhizobium leguminosarum is an alpha-proteobacterial N-2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841.

Results: The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes ( Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were overrepresented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens.

Conclusion: Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.

Original language	English
Article number	R34
Pages (from-to)	-
Number of pages	20
Journal	Genome biology
Volume	7
Issue number	4
DOIs	https://doi.org/10.1186/gb-2006-7-4-r34
Publication status	Published - 2006

Bibliographical note

© 2006 Young et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Keywords

AGROBACTERIUM-TUMEFACIENS C58
SYMBIOTIC NITROGEN-FIXATION
3 GROEL HOMOLOGS
BACTERIAL GENOMES
ESCHERICHIA-COLI
BV-VICIAE
BIOVAR VICIAE
FIELD POPULATIONS
EVOLUTIONARY IMPLICATIONS
TRANSFERRED GENES

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gb-2006-7-4-r34.pdf

http://genomebiology.com/2006/7/4/R34

Cite this

Young, J. P. W., Crossman, L. C., Johnston, A. W. B., Thomson, N. R., Ghazoui, Z. F., Hull, K. H., Wexler, M., Curson, A. R. J., Todd, J. D., Poole, P. S., Mauchline, T. H., East, A. K., Quail, M. A., Churcher, C., Arrowsmith, C., Cherevach, I., Chillingworth, T., Clarke, K., Cronin, A., ... Parkhill, J. (2006). The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome biology, 7(4), -. Article R34. https://doi.org/10.1186/gb-2006-7-4-r34

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abstract = "Background: Rhizobium leguminosarum is an alpha-proteobacterial N-2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841.Results: The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes ( Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were overrepresented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens.Conclusion: Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.",

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author = "Young, {J P W} and Crossman, {L C} and Johnston, {A W B} and Thomson, {N R} and Ghazoui, {Z F} and Hull, {K H} and M Wexler and Curson, {A R J} and Todd, {J D} and Poole, {P S} and Mauchline, {T H} and East, {A K} and Quail, {M A} and C Churcher and C Arrowsmith and I Cherevach and T Chillingworth and K Clarke and A Cronin and P Davis and A Fraser and Z Hance and H Hauser and K Jagels and S Moule and K Mungall and H Norbertczak and E Rabbinowitsch and M Sanders and M Simmonds and S Whitehead and J Parkhill",

note = "{\textcopyright} 2006 Young et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.",

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Young, JPW, Crossman, LC, Johnston, AWB, Thomson, NR, Ghazoui, ZF, Hull, KH, Wexler, M, Curson, ARJ, Todd, JD, Poole, PS, Mauchline, TH, East, AK, Quail, MA, Churcher, C, Arrowsmith, C, Cherevach, I, Chillingworth, T, Clarke, K, Cronin, A, Davis, P, Fraser, A, Hance, Z, Hauser, H, Jagels, K, Moule, S, Mungall, K, Norbertczak, H, Rabbinowitsch, E, Sanders, M, Simmonds, M, Whitehead, S & Parkhill, J 2006, 'The genome of Rhizobium leguminosarum has recognizable core and accessory components', Genome biology, vol. 7, no. 4, R34, pp. -. https://doi.org/10.1186/gb-2006-7-4-r34

TY - JOUR

T1 - The genome of Rhizobium leguminosarum has recognizable core and accessory components

AU - Young, J P W

AU - Crossman, L C

AU - Johnston, A W B

AU - Thomson, N R

AU - Ghazoui, Z F

AU - Hull, K H

AU - Wexler, M

AU - Curson, A R J

AU - Todd, J D

AU - Poole, P S

AU - Mauchline, T H

AU - East, A K

AU - Quail, M A

AU - Churcher, C

AU - Arrowsmith, C

AU - Cherevach, I

AU - Chillingworth, T

AU - Clarke, K

AU - Cronin, A

AU - Davis, P

AU - Fraser, A

AU - Hance, Z

AU - Hauser, H

AU - Jagels, K

AU - Moule, S

AU - Mungall, K

AU - Norbertczak, H

AU - Rabbinowitsch, E

AU - Sanders, M

AU - Simmonds, M

AU - Whitehead, S

AU - Parkhill, J

N1 - © 2006 Young et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

PY - 2006

Y1 - 2006

N2 - Background: Rhizobium leguminosarum is an alpha-proteobacterial N-2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841.Results: The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes ( Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were overrepresented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens.Conclusion: Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.

AB - Background: Rhizobium leguminosarum is an alpha-proteobacterial N-2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841.Results: The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes ( Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were overrepresented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens.Conclusion: Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.

KW - AGROBACTERIUM-TUMEFACIENS C58

KW - SYMBIOTIC NITROGEN-FIXATION

KW - 3 GROEL HOMOLOGS

KW - BACTERIAL GENOMES

KW - ESCHERICHIA-COLI

KW - BV-VICIAE

KW - BIOVAR VICIAE

KW - FIELD POPULATIONS

KW - EVOLUTIONARY IMPLICATIONS

KW - TRANSFERRED GENES

U2 - 10.1186/gb-2006-7-4-r34

DO - 10.1186/gb-2006-7-4-r34

M3 - Article

SN - 1474-760X

VL - 7

SP - -

JO - Genome biology

JF - Genome biology

IS - 4

M1 - R34

ER -