Widespread homologous recombination within and between Streptomyces species

ISME Journal

Volumn 4, Issue 9, 2010, Pages 1136-1143

  Doroghazi, James R ^a   Buckley, Daniel H ^a  

^a Cornell University ^*  (United States)

Author keywords

gene exchange; HGT; homologous recombination; population; species; Streptomyces

Indexed keywords

BACTERIAL DNA;

BACTERIUM; GENE TRANSFER; GENETIC ANALYSIS; MICROBIAL COMMUNITY; MUTATION; PHYLOGENY; POLYMORPHISM; POPULATION STRUCTURE; SOIL MICROORGANISM;

ARTICLE; BACTERIUM IDENTIFICATION; DNA FINGERPRINTING; DNA SEQUENCE; GENETIC LINKAGE; GENETIC RECOMBINATION; GENETICS; GENOTYPE; GEOGRAPHY; HORIZONTAL GENE TRANSFER; ISOLATION AND PURIFICATION; MICROBIOLOGY; SEQUENCE HOMOLOGY; STREPTOMYCES;

BACTERIAL TYPING TECHNIQUES; DNA FINGERPRINTING; DNA, BACTERIAL; GENE TRANSFER, HORIZONTAL; GENETIC LINKAGE; GENOTYPE; GEOGRAPHY; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOIL MICROBIOLOGY; STREPTOMYCES;

BACTERIA (MICROORGANISMS); POSIBACTERIA; STREPTOMYCES; STREPTOMYCES FLAVOGRISEUS; STREPTOMYCETACEAE; STREPTOMYCINEAE;

EID: 77956094202     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2010.45     Document Type: Article

References (36)

1. Alacevic M. (1963). Interspecific recombination in Streptomyces. Nature 197: 1323.
2. Anderson AS, Wellington EMH. (2001). The taxonomy of Streptomyces and related genera. Int J Syst Evol Microbiol 51: 797-814.
3. Bryant D, Moulton V. (2004). Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21: 255-265.
4. Chater KF, Hopwood DA, Kieser T, Thompson CJ. (1982). Gene cloning in Streptomyces. Curr Top Microbiol Immunol 96: 69-95.
5. Didelot X, Falush D. (2007). Inference of bacterial microevolution using multilocus sequence data. Genetics 175: 1251-1266.
6. Doolittle WF, Bapteste E. (2007). Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci USA 104: 2043-2049.
7. Elnakeeb MA, Lecheval HA. (1963). Selective isolation of aerobic actinomycetes. Appl Microbiol 11: 75-85.
8. Eppley JM, Tyson GW, Getz WM, Banfield JF. (2007). Genetic exchange across a species boundary in the archaeal genus Ferroplasma. Genetics 177: 407-416.
9. Falush D, Stephens M, Pritchard JK. (2003). Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
10. Feil EJ, Maiden MCJ, Achtman M, Spratt BG. (1999). The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis. Mol Biol Evol 16: 1496-1502.
11. Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP. (2009). The bacterial species challenge: making sense of genetic and ecological diversity. Science 323: 741-746.
12. Fraser C, Hanage WP, Spratt BG. (2007). Recombination and the nature of bacterial speciation. Science 315: 476-480.
13. Guo YP, ZhengW, Rong XY, Huang Y. (2008). A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. Int J Syst Evol Microbiol 58: 149-159.
14. Hanage WP, Fraser C, Spratt BG. (2005). Fuzzy species among recombinogenic bacteria. BMC Biol 3: 6.
15. Haubold B, Hudson RR. (2000). LIAN 3.0: detecting linkage disequilibrium in multilocus data. Bioinformatics 16: 847-848.
16. Hopwood DA. (2006). Soil to genomics: the Streptomyces chromosome. Annu Rev Genet 40: 1-23.
17. Hopwood DA, Lydiate DJ, Malpartida F, Wright HM. (1985). Conjugative sex plasmids of Streptomyces. Basic Life Sci 30: 615-634.
18. Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, PolzMF. (2008). Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science 320: 1081-1085.
19. Huson DH, Bryant D. (2006). Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254-267.
20. Ishaque M, Kluepfel D. (1980). Cellulase complex of a mesophilic streptomyces strain. Can J Microbiol 26: 183-189.
21. Kampfer P, Kroppenstedt RM, Dott W. (1991). A numerical classification of the genera Streptomyces and Streptoverticillium using miniaturized physiological tests. J Gen Microbiol 137: 1831-1891.
22. Kataoka M, Seki T, Yoshida T. (1991). Regulation and function of the Streptomyces plasmid psn22 genes involved in pock formation and inviability. J Bacteriol 173: 7975-7981.
23. Koeppel A, Perry EB, Sikorski J, Krizanc D, Warner A, Ward DM et al. (2008). Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc Natl Acad Sci USA 105: 2504-2509.
24. Konstantinidis KT, Tiedje JM. (2005). Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102: 2567-2572.
25. Lomovskaya ND, Voeykova TA, Mkrtumian NM. (1977). Construction and properties of hybrids obtained in interspecific crosses between Streptomyces coelicolor A3(2) and Streptomyces griseus Kr15. J Gen Microbiol 98: 187-198.
26. Mallet J. (2008). Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation. Philos Trans R Soc Lond B Biol Sci 363: 2971-2986.
27. Martin DP, Williamson C, Posada D. (2005). RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21: 260-262.
28. McVean G, Awadalla P, Fearnhead P. (2002). A coalescentbased method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
29. Papke RT, Zhaxybayeva O, Feil EJ, Sommerfeld K, Muise D, Doolittle WF. (2007). Searching for species in haloarchaea. Proc Natl Acad Sci USA 104: 14092-14097.
30. Perez-Losada M, Browne EB, Madsen A, Wirth T, Viscidi RP, Crandall KA. (2006). Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data. Infect Genet Evol 6: 97-112.
31. Sheppard SK,McCarthy ND, Falush D,Maiden MCJ. (2008). Convergence of Campylobacter species: implications for bacterial evolution. Science 320: 237-239.
32. Shimodaira H, Hasegawa M. (1999). Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16: 1114-1116.
33. Shirling EB, Gottlieb D. (1970). Report of the International Streptomyces Project 5 Years of Collaborative Research. Prauser H (Ed). The Actinomycetales. The Jena International Symposium on Taxonomy, 439pIllus Veb Gustav Fischer Verlag: Jena E, Germany, 79-89.
34. Stoycheva Z, Todorov T, Peltekova V. (1994). Intergeneric crosses between Streptomyces ambofaciens and Saccharopolyspora erythraea. Folia Microbiologica 39: 13-18.
35. Vos M, Didelot X. (2009). A comparison of homologous recombination rates in bacteria and archaea. ISME J 3: 199-208.
36. Wang SJ, Chang HM, Lin YS, Huang CH, Chen CW. (1999). Streptomyces genomes: circular genetic maps from the linear chromosomes. Microbiology 145: 2209-2220.