Bérdy J: Bioactive microbial metabolites. J Antibiot (Tokyo). 2005, 58 (1): 1-26. 10.1038/ja.2005.1.
Article
Google Scholar
Rong X, Liu N, Ruan J, Huang Y: Multilocus sequence analysis of Streptomyces griseus isolates delineating intraspecific diversity in terms of both taxonomy and biosynthetic potential. Antonie Van Leeuwenhoek. 2010, 98 (2): 237-248. 10.1007/s10482-010-9447-z.
Article
CAS
PubMed
Google Scholar
Rong XY, Huang Y: Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA-DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species. Int J Syst Evol Microbiol. 2010, 60: 696-703. 10.1099/ijs.0.012419-0.
Article
CAS
PubMed
Google Scholar
Guo Y, Zheng W, Rong X, Huang Y: A multilocus phylogeny of the Streptomyces griseus 16S rRNA gene clade: use of multilocus sequence analysis for streptomycete systematics. Int J Syst Evol Microbiol. 2008, 58 (1): 149-159. 10.1099/ijs.0.65224-0.
Article
CAS
PubMed
Google Scholar
Rong XY, Huang Y: Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst Appl Microbiol. 2012, 35 (1): 7-18. 10.1016/j.syapm.2011.10.004.
Article
CAS
PubMed
Google Scholar
Rong XY, Guo YP, Huang Y: Proposal to reclassify the Streptomyces albidoflavus clade on the basis of multilocus sequence analysis and DNA-DNA hybridization, and taxonomic elucidation of Streptomyces griseus subsp solvifaciens. Syst Appl Microbiol. 2009, 32 (5): 314-322. 10.1016/j.syapm.2009.05.003.
Article
CAS
PubMed
Google Scholar
Hopwood DA: Soil to genomics: the streptomyces chromosome. Annu Rev Genet. 2006, 40: 1-23. 10.1146/annurev.genet.40.110405.090639.
Article
CAS
PubMed
Google Scholar
Doroghazi JR, Buckley DH: Widespread homologous recombination within and between Streptomyces species. ISME J. 2010, 4 (9): 1136-1143. 10.1038/ismej.2010.45.
Article
CAS
PubMed
Google Scholar
Flardh K: Essential role of DivIVA in polar growth and morphogenesis in Streptomyces coelicolor A3(2). Mol Microbiol. 2003, 49 (6): 1523-1536. 10.1046/j.1365-2958.2003.03660.x.
Article
PubMed
Google Scholar
Schwedock J, McCormick JR, Angert ER, Nodwell JR, Losick R: Assembly of the cell division protein FtsZ into ladder-like structures in the aerial hyphae of Streptomyces coelicolor. Mol Microbiol. 1997, 25 (5): 847-858. 10.1111/j.1365-2958.1997.mmi507.x.
Article
CAS
PubMed
Google Scholar
Hopwood DA, Glauert AM: Observations on the chromatinic bodies of Streptomyces coelicolor. J Biophys Biochem Cytol. 1960, 8 (1): 257-265. 10.1083/jcb.8.1.257.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lin YS, Kieser HM, Hopwood DA, Chen CW: The chromosomal DNA of Streptomyces lividans 66 is linear. Mol Microbiol. 1993, 10 (5): 923-933. 10.1111/j.1365-2958.1993.tb00964.x.
Article
CAS
PubMed
Google Scholar
Lin YS, Chen CW: Instability of artificially circularized chromosomes of Streptomyces lividans. Mol Microbiol. 1997, 26 (4): 709-719. 10.1046/j.1365-2958.1997.5991975.x.
Article
CAS
PubMed
Google Scholar
Volff JN, Viell P, Altenbuchner J: Artificial circularization of the chromosome with concomitant deletion of its terminal inverted repeats enhances genetic instability and genome rearrangement in Streptomyces lividans. Mol Gen Genet. 1997, 253 (6): 753-760. 10.1007/s004380050380.
Article
CAS
PubMed
Google Scholar
Weaver D, Karoonuthaisiri N, Tsai HH, Huang CH, Ho ML, Gai SN, Patel KG, Huang JQ, Cohen SN, Hopwood DA, Chen CW, Kao CM: Genome plasticity in Streptomyces: identification of 1 Mb TIRs in the S. coelicolor A3(2) chromosome. Mol Microbiol. 2004, 51 (6): 1535-1550. 10.1111/j.1365-2958.2003.03920.x.
Article
CAS
PubMed
Google Scholar
Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Ōmura S: Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol. 2003, 21 (5): 526-531. 10.1038/nbt820.
Article
PubMed
Google Scholar
Hopwood DA, Wright HM: A plasmid of Streptomyces coelicolor carrying a chromosomal locus and its inter-specific transfer. The J Gen Microbiol. 1973, 79 (2): 331-342. 10.1099/00221287-79-2-331.
Article
CAS
Google Scholar
Ohnishi Y, Ishikawa J, Hara H, Suzuki H, Ikenoya M, Ikeda H, Yamashita A, Hattori M, Horinouchi S: Genome sequence of the streptomycin-producing microorganism streptomyces griseus IFO 13350. J Bacteriol. 2008, 190 (11): 4050-4060. 10.1128/JB.00204-08.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, et al: Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature. 2002, 417 (6885): 141-147. 10.1038/417141a.
Article
PubMed
Google Scholar
Omura S, Ikeda H, Ishikawa J, Hanamoto A, Takahashi C, Shinose M, Takahashi Y, Horikawa H, Nakazawa H, Osonoe T, Kikuchi H, Shiba T, Sakaki Y, Hattori M: Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc Natl Acad Sci U S A. 2001, 98 (21): 12215-12235. 10.1073/pnas.211433198.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kharel MK, Nybo SE, Shepherd MD, Rohr J: Cloning and characterization of the ravidomycin and chrysomycin biosynthetic gene clusters. Chembiochem. 2010, 11 (4): 523-532. 10.1002/cbic.200900673.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ziemert N, Lechner A, Wietz M, Millán-Aguiñaga N, Chavarria KL, Jensen PR: Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora. Proc Natl Acad Sci U S A. 2014, 111 (12): E1130-E1139. 10.1073/pnas.1324161111.
Article
CAS
PubMed Central
PubMed
Google Scholar
Rong X, Doroghazi JR, Cheng K, Zhang L, Buckley DH, Huang Y: Classification of Streptomyces phylogroup pratensis (Doroghazi and Buckley, 2010) based on genetic and phenotypic evidence, and proposal of Streptomyces pratensis sp. nov. Syst Appl Microbiol. 2013, 36 (6): 401-407. 10.1016/j.syapm.2013.03.010.
Article
CAS
PubMed
Google Scholar
Doroghazi JR, Buckley DH: A model for the effect of homologous recombination on microbial diversification. Genome Biol Evol. 2011, 3: 1349-10.1093/gbe/evr110.
Article
CAS
PubMed Central
PubMed
Google Scholar
Fraser C, Hanage WP, Spratt BG: Recombination and the nature of bacterial speciation. Science. 2007, 315 (5811): 476-480. 10.1126/science.1127573.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ishaque M, Kluepfel D: Cellulase complex of a mesophilic Streptomyces strain. Can J Microbiol. 1980, 26 (2): 183-189. 10.1139/m80-028.
Article
CAS
PubMed
Google Scholar
El-Nakeeb MA, Lechevalier HA: Selective isolation of aerobic actinomycetes. Appl Microbiol. 1963, 11 (2): 75-77.
CAS
PubMed Central
PubMed
Google Scholar
Ottow JCG: Rose Bengal as a selective aid in the isolation of fungi and actinomycetes from natural sources. Mycologia. 1972, 64 (2): 304-315. 10.2307/3757834.
Article
CAS
PubMed
Google Scholar
Darling ACE, Mau B, Blattner FR, Perna NT: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004, 14 (7): 1394-1403. 10.1101/gr.2289704.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ: Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 2010, 11: 119-10.1186/1471-2105-11-119.
Article
Google Scholar
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and clustal X version 2.0. Bioinformatics. 2007, 23 (21): 2947-2948. 10.1093/bioinformatics/btm404.
Article
CAS
PubMed
Google Scholar
Felsenstein J: Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985, 39 (4): 783-791. 10.2307/2408678.
Article
Google Scholar
Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25 (17): 3389-3402. 10.1093/nar/25.17.3389.
Article
CAS
PubMed Central
PubMed
Google Scholar
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH: CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res. 2011, 39: D225-D229. 10.1093/nar/gkq1189.
Article
CAS
PubMed Central
PubMed
Google Scholar
Alexa A, Rahnenfuhrer J: topGO: topGO: Enrichment analysis for Gene Ontology. R Package Version 2.18.0. 2010, 28:
Google Scholar
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5 (10): R80-10.1186/gb-2004-5-10-r80.
Article
PubMed Central
PubMed
Google Scholar
Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R: AntiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 2011, 39 (suppl 2): W339-W346.
Article
CAS
PubMed Central
PubMed
Google Scholar
Price MN, Dehal PS, Arkin AP: FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS One. 2010, 5 (3): e9490-10.1371/journal.pone.0009490.
Article
PubMed Central
PubMed
Google Scholar
Huerta-Cepas J, Dopazo J, Gabaldón T: ETE: a python Environment for Tree Exploration. BMC Bioinform. 2010, 11 (1): 24-10.1186/1471-2105-11-24.
Article
Google Scholar
Li R, Lloyd EP, Moshos KA, Townsend CA: Identification and characterization of the carbapenem MM 4550 and its gene cluster in streptomyces argenteolus ATCC 11009. Chem Bio Chem. 2014, 15 (2): 320-331. 10.1002/cbic.201300319.
Article
CAS
PubMed Central
PubMed
Google Scholar
Nunez LE, Mendez C, Brana AF, Blanco G, Salas JA: The biosynthetic gene cluster for the beta-lactam carbapenem thienamycin in Streptomyces cattleya. Chem Biol. 2003, 10 (4): 301-311. 10.1016/S1074-5521(03)00069-3.
Article
CAS
PubMed
Google Scholar
Doroghazi JR, Albright JC, Goering AW, Ju K-S, Haines RR, Tchalukov KA, Labeda DP, Kelleher NL, Metcalf WW: A roadmap for natural product discovery based on large-scale genomics and metabolomics. Nat Chem Biol. 2014, 10 (11): 963-968. 10.1038/nchembio.1659.
Article
CAS
PubMed Central
PubMed
Google Scholar
Boratyn GM, Schaffer A, Agarwala R, Altschul SF, Lipman DJ, Madden TL: Domain enhanced lookup time accelerated BLAST. Biol Direct. 2012, 7 (1): 12-10.1186/1745-6150-7-12.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hudson R, Kaplan N: Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics. 1985, 111 (1): 147-211.
CAS
PubMed Central
PubMed
Google Scholar
Suerbaum S, Smith JM, Bapumia K, Morelli G, Smith NH, Kunstmann E, Dyrek I, Achtman M: Free recombination within Helicobacter pylori. Proc Natl Acad Sci U S A. 1998, 95 (21): 12619-12624. 10.1073/pnas.95.21.12619.
Article
CAS
PubMed Central
PubMed
Google Scholar
Supply P, Warren RM, Bañuls AL, Lesjean S, Van Der Spuy GD, Lewis LA, Tibayrenc M, Van Helden PD, Locht C: Linkage disequilibrium between minisatellite loci supports clonal evolution of Mycobacterium tuberculosis in a high tuberculosis incidence area. Mol Microbiol. 2003, 47 (2): 529-538. 10.1046/j.1365-2958.2003.03315.x.
Article
CAS
PubMed
Google Scholar
He J, Hertweck C: Biosynthetic origin of the rare nitroaryl moiety of the polyketide antibiotic aureothin: involvement of an unprecedented N-oxygenase. J Am Chem Soc. 2004, 126 (12): 3694-3695. 10.1021/ja039328t.
Article
CAS
PubMed
Google Scholar
Lukjancenko O, Wassenaar TM, Ussery DW: Comparison of 61 sequenced escherichia coli genomes. Microb Ecol. 2010, 60 (4): 708-720. 10.1007/s00248-010-9717-3.
Article
CAS
PubMed Central
PubMed
Google Scholar
Donati C, Hiller NL, Tettelin H, Muzzi A, Croucher NJ, Angiuoli SV, Oggioni M, Hotopp JCD, Hu FZ, Riley DR, Covacci A, Mitchell TJ, Bentley SD, Kilian M, Ehrlich GD, Rappuoli R, Moxon ER, Masignani V: Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol. 2010, 11 (10): R107-10.1186/gb-2010-11-10-r107.
Article
CAS
PubMed Central
PubMed
Google Scholar
Jacobsen A, Hendriksen RS, Aaresturp FM, Ussery DW, Friis C: The Salmonella enterica Pan-genome. Microb Ecol. 2011, 62 (3): 487-504. 10.1007/s00248-011-9880-1.
Article
PubMed Central
PubMed
Google Scholar
Xu Z, Chen X, Li L, Li T, Wang S, Chen H, Zhou R: Comparative genomic characterization of actinobacillus pleuropneumoniae. J Bacteriol. 2010, 192 (21): 5625-5636. 10.1128/JB.00535-10.
Article
CAS
PubMed Central
PubMed
Google Scholar
Deng X, Phillippy AM, Li Z, Salzberg SL, Zhang W: Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification. BMC Genomics. 2010, 11 (1): 500-10.1186/1471-2164-11-500.
Article
PubMed Central
PubMed
Google Scholar
Lefebure T, Bitar PDP, Suzuki H, Stanhope MJ: Evolutionary dynamics of complete campylobacter Pan-genomes and the bacterial species concept. Genome Biol Evol. 2010, 2: 646-655. 10.1093/gbe/evq048.
Article
PubMed Central
PubMed
Google Scholar
Joseph SJ, Didelot X, Gandhi K, Dean D, Read TD: Interplay of recombination and selection in the genomes of Chlamydia trachomatis. Biol Direct. 2011, 6: 28-10.1186/1745-6150-6-28.
Article
PubMed Central
PubMed
Google Scholar
Choulet F, Aigle B, Gallois A, Mangenot S, Gerbaud C, Truong C, Francou F-X, Fourrier C, Guérineau M, Decaris B: Evolution of the terminal regions of the Streptomyces linear chromosome. Mol Biol Evol. 2006, 23 (12): 2361-2369. 10.1093/molbev/msl108.
Article
CAS
PubMed
Google Scholar
Yim G, Wang HH, FRS JD: Antibiotics as signalling molecules. Philos Transact Royal Society B: Biol Sci. 2007, 362 (1483): 1195-1200. 10.1098/rstb.2007.2044.
Article
CAS
Google Scholar
Champness WC: New loci required for Streptomyces coelicolor morphological and physiological differentiation. J Bacteriol. 1988, 170 (3): 1168-1174.
CAS
PubMed Central
PubMed
Google Scholar
Eccleston M, Ali RA, Seyler R, Westpheling J, Nodwell J: Structural and genetic analysis of the BldB protein of streptomyces coelicolor. J Bacteriol. 2002, 184 (15): 4270-4276. 10.1128/JB.184.15.4270-4276.2002.
Article
CAS
PubMed Central
PubMed
Google Scholar
Pope MK, Green B, Westpheling J: The bldB gene encodes a small protein required for morphogenesis, antibiotic production, and catabolite control in Streptomyces coelicolor. J Bacteriol. 1998, 180 (6): 1556-1562.
CAS
PubMed Central
PubMed
Google Scholar
Eccleston M, Willems A, Beveridge A, Nodwell JR: Critical residues and novel effects of overexpression of the streptomyces coelicolor developmental protein BldB: evidence for a critical interacting partner. J Bacteriol. 2006, 188 (23): 8189-8195. 10.1128/JB.01119-06.
Article
CAS
PubMed Central
PubMed
Google Scholar
Makarova KS, Wolf YI, Koonin EV: Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct. 2009, 4 (1): 19-10.1186/1745-6150-4-19.
Article
PubMed Central
PubMed
Google Scholar