Legumes select symbiosis island sequence variants in Bradyrhizobium

Molecular Ecology

Volumn 21, Issue 7, 2012, Pages 1769-1778

  Parker, Matthew A ^a  

^a BINGHAMTON UNIVERSITY   (United States)

Author keywords

multiple niche polymorphism; phylogenetic clustering; phylogeography; symbiosis

Indexed keywords

BACTERIAL DNA;

ARTICLE; BRADYRHIZOBIUM; DNA SEQUENCE; FABACEAE; GENE LINKAGE DISEQUILIBRIUM; GENETIC SELECTION; GENETICS; GENOMIC ISLAND; HORIZONTAL GENE TRANSFER; MICROBIOLOGY; PHYLOGENY; SYMBIOSIS;

BRADYRHIZOBIUM; DNA, BACTERIAL; FABACEAE; GENE TRANSFER, HORIZONTAL; GENOMIC ISLANDS; LINKAGE DISEQUILIBRIUM; PHYLOGENY; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA; SYMBIOSIS;

BACTERIA (MICROORGANISMS); BRADYRHIZOBIUM;

EID: 84859102885     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05497.x     Document Type: Article

References (48)

1. Bailly X, Olivieri I, de Mita S, et al. (2006) Recombination and selection shape the molecular diversity pattern of nitrogen-fixing Sinorhizobium sp. associated to Medicago. Molecular Ecology, 15, 2719-2734. (Pubitemid 44215449)
2. Cohan F, Perry EB, (2007) A systematics for discovering the fundamental units of bacterial diversity. Current Biology, 17, R373-R386. (Pubitemid 46702658)
3. Doignon-Bourcier F, Sy A, Willems A, et al. (1999) Diversity of bradyrhizobia from 27 tropical Leguminosae species native of Senegal. Systematic and Applied Microbiology, 22, 647-661. (Pubitemid 30093269)
4. Ehlers J, Gibbard PL, (2004) Quaternary Glaciations: Extent and Chronology 2: Part II North America. Elsevier, Amsterdam.
5. Fraser CE, Alm J, Polz MF, et al. (2009) The bacterial species challenge: making sense of genetic and ecological diversity. Science, 323, 741-746.
6. Gueye F, Moulin L, Sylla S, Ndoye I, Béna G, (2009) Genetic diversity and distribution of Bradyrhizobium and Azorhizobium strains associated with the herb legume Zornia glochidiata sampled from across Senegal. Systematic and Applied Microbiology, 32, 387-399.
7. Haubold B, Hudson RR, (2000) LIAN 3.0: detecting linkage disequilibrium in multilocus data. Bioinformatics, 16, 847-848.
8. Haukka K, Lindstrom K, Young JPW, (1998) Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America. Applied and Environmental Microbiology, 64, 419-426. (Pubitemid 28079799)
9. Huson DH, Bryant D, (2006) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution, 23, 254-267. (Pubitemid 43100040)
10. Jarabo-Lorenzo A, Perez-Galdona R, Donate-Correa J, et al. (2003) Genetic diversity of bradyrhizobial populations from diverse geographic origins that nodulate Lupinus spp. and Ornithopus spp. Systematic and Applied Microbiology, 26, 611-623. (Pubitemid 37486520)
11. Kaneko T, Nakamura Y, Sato S, et al. (2000) Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Research, 7, 331-338.
12. Kaneko T, Nakamura Y, Sato S, et al. (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Research, 9, 189-197. (Pubitemid 36307023)
13. Kündig C, Hennecke H, Göttfert M, (1993) Correlated physical and genetic map of the Bradyrhizobium japonicum 110 genome. Journal of Bacteriology, 175, 613-622. (Pubitemid 23046920)
14. Lafay B, Burdon JJ, (1998) Molecular diversity of rhizobia occurring on native shrubby legumes in southeastern Australia. Applied and Environmental Microbiology, 64, 3989-3997. (Pubitemid 28463004)
15. Laguerre G, Nour SM, Macheret V, et al. (2001) Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. Microbiology, 147, 981-993. (Pubitemid 32401338)
16. Lewis G, Schrire B, Mackinder B, Lock M, (2005) Legumes of the World. Royal Botanical Gardens, Kew, Richmond, U.K.
17. Librado P, Rozas J, (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
18. Magee DW, Ahles HE, (1999) Flora of the Northeast. A Manual of the Vascular Flora of New England and Adjacent New York. University of Massachusetts Press, Amherst, Massachusetts.
19. Martin DP, Williamson C, Posada D, (2005) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics, 2, 260-262. (Pubitemid 40202028)
20. Martinez-Romero E, (2009) Coevolution in Rhizobium-legume symbiosis? DNA and Cell Biology, 28, 361-370.
21. Moulin LG, Bena G, Boivin-Masson C, Stepkowski T, (2004) Phylogenetic analyses of symbiotic nodulation genes support vertical and lateral gene co-transfer within the Bradyrhizobium genus. Molecular Phylogenetics and Evolution, 30, 720-732. (Pubitemid 38260970)
22. Mueller JC, (2004) Linkage disequilibrium for different scales and applications. Briefings in Bioinformatics, 5, 355-364.
23. Mutch LA, Young JPW, (2004) Diversity and specificity of Rhizobium leguminosarum biovar viciae on wild and cultivated legumes. Molecular Ecology, 13, 2435-2444. (Pubitemid 38946431)
24. Nandasena KG, O'Hara GW, Tiwari RP, Howieson JG, (2006) Rapid in situ evolution of nodulating strains for Biserrula pelecinus L. through lateral transfer of a symbiosis island from the original mesorhizobial inoculant. Applied and Environmental Microbiology, 72, 7365-7367. (Pubitemid 44748456)
25. Nzoue A, Miche L, Klonowska A, et al. (2009) Multilocus sequence analysis of bradyrhizobia isolated from Aeschynomene species in Senegal. Systematic and Applied Microbiology, 32, 400-412.
26. Oh HS, Chun JY, Lee MS, Min KH, Lee SH, Cheon CI, (2000) Role of hsfA gene on host-specificity by Bradyrhizobium japonicum in a broad range of tropical legumes. Canadian Journal of Microbiology, 46, 81-84.
27. Parker MA, (2004) rRNA and dnaK relationships of Bradyrhizobium sp. nodule bacteria from four papilionoid legume trees in Costa Rica. Systematic and Applied Microbiology, 27, 334-342. (Pubitemid 38724494)
28. Parker MA, (2008) Symbiotic relationships of legumes and nodule bacteria on Barro Colorado Island, Panama: a review. Microbial Ecology, 55, 662-672. (Pubitemid 351601280)
29. Parker MA, Kennedy DA, (2006) Diversity and relationships of bradyrhizobia from legumes native to eastern North America. Canadian Journal of Microbiology, 52, 1148-1157. (Pubitemid 46639427)
30. Parker MA, Lafay B, Burdon JJ, van Berkum P, (2002) Conflicting phylogeographic patterns in rRNA and nifD indicate regionally-restricted gene transfer in Bradyrhizobium. Microbiology, 148, 2557-2565.
31. Perret X, Staehelin C, Broughton WJ, (2000) Molecular basis of symbiotic promiscuity. Microbiology and Molecular Biology Reviews, 64, 180-201. (Pubitemid 30143845)
32. Provan J, Bennett KD, (2008) Phylogeographic insights into cryptic glacial refugia. Trends in Ecology and Evolution, 23, 564-571.
33. Radford A, Ahles HE, Bell CR, (1968) Manual of the Vascular Flora of the Carolinas. University of North Carolina Press, Chapel Hill, North Carolina.
34. Ronquist F, Huelsenbeck JP, (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574. (Pubitemid 37038874)
35. Sadowsky MJ, Cregan PB, Gottfert M, et al. (1991) The Bradyrhizobium japonicum nolA gene and its involvement in the genotype-specific nodulation of soybeans. Proceedings of the National Academy of Sciences of the USA, 88, 637-641. (Pubitemid 21915521)
36. Schierup MH, Vekemans X, Charlesworth D, (2000) The effect of subdivision on variation at multi-allelic loci under balancing selection. Genetical Research, 76, 51-62. (Pubitemid 30649602)
37. Shin J-H, Blay S, McNeney B, Graham J, (2006) LDheatmap: an R function for graphical display of pairwise linkage disequilibria between single nucleotide polymorphisms. Journal of Statistical Software, 16, 1-9, Code Snippet 3.
38. Slatkin M, (2008) Linkage disequilibrium-understanding the evolutionary past and mapping the medical future. Nature Reviews Genetics, 9, 477-485. (Pubitemid 351693977)
39. Souza V, Nguyen TT, Hudson RR, et al. (1992) Hierarchical analysis of linkage disequilibrium in Rhizobium populations: evidence for sex? Proceedings of the National Academy of Sciences of the USA, 89, 8389-8393.
40. Spoerke JM, Wilkinson HH, Parker MA, (1996) Nonrandom genotypic associations in a legume-Bradyrhizobium mutualism. Evolution, 50, 146-154.
41. Stepkowski T, Hughes CE, Law IJ, et al. (2007) Diversification of lupine Bradyrhizobium strains: evidence from nodulation gene trees. Applied and Environmental Microbiology, 73, 3254-3264. (Pubitemid 46834977)
42. Sullivan JT, Patrick HN, Lowther WL, Scott DB, Ronson CW, (1995) Nodulating strains of Rhizobium loti arise through chromosomal symbiotic gene transfer in the environment. Proceedings of the National Academy of Sciences USA, 92, 8985-8989.
43. Sullivan JT, Trzebiatowski JR, Cruickshank RW, et al. (2002) Comparative sequence analysis of the symbiosis island of Mesorhizobium loti Strain R7A. Journal of Bacteriology, 184, 3086-3095. (Pubitemid 34517833)
44. Vinuesa P, Rademaker JLW, de Bruijn FJ, Werner D, (1998) Genotypic characterization of Bradyrhizobium strains nodulating endemic woody legumes of the Canary Islands by PCR-restriction fragment length polymorphism analysis of genes encoding 16S rRNA (16S rDNA) and 16S-23S rDNA intergenic spacers, repetitive extragenic palindromic PCR genomic fingerprinting, and partial 16S rDNA sequencing. Applied and Environmental Microbiology, 64, 2096-2104. (Pubitemid 28252770)
45. Vinuesa P, Silva C, Werner D, Martinez-Romero E, (2005) Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Molecular Phylogenetics and Evolution, 34, 29-54. (Pubitemid 39587982)
46. Webb CO, Ackerly DD, Kembel SW, (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24, 2098-2100.
47. Wernegreen JJ, Harding EE, Riley MA, (1997) Rhizobium gone native: unexpected plasmid stability of indigenous Rhizobium leguminosarum. Proceedings of the National Academy of Sciences of the USA, 94, 5483-5488. (Pubitemid 27214810)
48. Zaykin DV, Pudovkin A, Weir BS, (2008) Correlation-based inference for linkage disequilibrium with multiple alleles. Genetics, 180, 533-535.