The genome of Rhizobium leguminosarum has recognizable core and accessory components

Genome Biology e2YVt0oau0lulns6.mgeea7r,cIshsue 4, Article R34 Re The genome of Rhizobium leguminosarum has recognizable core and accessory components J Peter W Young 2 Lisa C Crossman 0 Andrew WB Johnston 1 Nicholas R Thomson 0 Zara F Ghazoui 2 Katherine H Hull 2 Margaret Wexler 1 Andrew RJ Curson 1 Jonathan D Todd 1 Philip S Poole 3 Tim H Mauchline 3 Alison K East 3 Michael A Quail 0 Carol Churcher 0 Claire Arrowsmith 0 Inna Cherevach 0 Tracey Chillingworth 0 Kay Clarke 0 Ann Cronin 0 Paul Davis 0 Audrey Fraser 0 Zahra Hance 0 Heidi Hauser 0 Kay Jagels 0 Sharon Moule 0 Karen Mungall 0 Halina Norbertczak 0 Ester Rabbinowitsch 0 Mandy Sanders 0 Mark Simmonds 0 Sally Whitehead 0 Julian Parkhill 0 0 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus , Cambridge , UK 1 School of Biological Sciences, University of East Anglia , Norwich , UK 2 Department of Biology, University of York , York , UK 3 School of Biological Sciences, University of Reading , Reading , UK Background: Rhizobium leguminosarum is an -proteobacterial N2-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. - Background The symbiosis between legumes and N2-fixing bacteria (rhizobia) is of huge agronomic benefit, allowing many crops to be grown without N fertilizer. It is a sophisticated example of coupled development between bacteria and higher plants, culminating in the organogenesis of root nodules [1]. There have been many genetic analyses of rhizobia, notably of Sinorhizobium meliloti (the symbiont of alfalfa), Bradyrhizobium japonicum (soybean), and Rhizobium leguminosarum, which has biovars that nodulate peas and broad beans (biovar viciae), clovers (biovar trifolii), or kidney beans (biovar phaseoli). The Rhizobiales, an -proteobacterial order that also includes mammalian pathogens Bartonella and Brucella and phytopathogenic Agrobacterium, have diverse genomic architectures. The single chromosome of Bartonella is small (1.6-1.9 Mb [2]), but the larger (approximately 3.3 Mb) Brucella genomes comprise two circles [3-5]. Genomes of the plantassociated bacteria are larger still; that of A. tumefaciens is about 5.6 Mb, with one circular and one linear chromosome, plus two native plasmids [6,7]. To date, three rhizobial genomes have been sequenced. S. meliloti 1021 has a 3.5 Mb chromosome plus two megaplasmids, namely pSymA (1.35 Mb) and pSymB (1.68 Mb), with the former having genes for nodulation (nod) and symbiotic N2 fixation (nif and fix) [8]. In contrast, the symbiosis genes of Mesorhizobium loti MAFF303099 (which nodulates Lotus) and of B. japonicum USDA110 are on chromosomal 'symbiosis islands', with the chromosome of the latter (9.1 Mb) being among the largest yet known in bacteria [9,10]. Rhizobium leguminosarum has yet another genomic architecture: one circular chromosome and several large plasmids, the plasmid portfolio varying markedly among isolates in terms of sizes, numbers, and incompatibility groups [11-14]. The subject of the present study, R. leguminosarum biovar viciae (Rlv) strain 3841 (a spontaneous streptomycin-resistant mutant of field isolate 300 [15,16]), has six large plasmids; pRL10 is the pSym (symbiosis plasmid) and pRL7 and pRL8 are transferable by conjugation [17]. The distinction between 'chromosome' and 'plasmid' has become blurred in recent years with the discovery that many bacteria have more than one replicon with over a million base pairs. For example, the second replicon of Brucella melitensis 16M is called a chromosome (1.18 Mb) [3], whereas the equivalent in S. meliloti 1021 is referred to as a megaplasmid (pSymB; 1.68 Mb) [8]. They both replicate using the repABC system as is typical of plasmids, and both carry the only copies of certain essential genes, although the B. melitensis chromosome II has many more of these as well as a complete ribosomal RNA operon. What combination of size, replication system, rRNA genes, and essentiality should qualify a replicon to be called a chromosome is probably more a matter of semantics than of biology. A more important distinction, in our view, is between 'core' and 'accessory' genomes. This distinction predates the genomics era; indeed, it has been discussed for more than a quarter of a century. Davey and Reanney [18] contrasted 'universal' and 'peripheral' genes, or 'conserved' and 'experimental' DNA. Campbell [19] wrote of 'euchromosomal' and 'accessory' DNA and explained how gene transfer was important in shaping the latter. He pointed out that genes carried by plasmids or transposons were 'available to all cells of the species, though not actually present in them' and 'should typically be genes that are needed occasionally rather than continually under natural conditions'. Furthermore, the need to function in different genetic backgrounds meant that 'evolution must limit the development of specific interactions between their products and those of universal genes'. This would tend to sharpen the separation between the euchromosomal and accessory gene pools, although transfer between them would remain possible. The expectation is that particular accessory genes will often be absent from closely related strains or species, and as comparative data became available such genes were indeed found in large numbers [20]. They often had a nucleotide composition different from the bulk of the genome, and this property ha (...truncated)