Taxonomic evaluation of putative Streptomyces scabiei strains held in the ARS Culture Collection (NRRL) using multi-locus sequence analysis

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 109, Issue 3, 2016, Pages 349-356

  Labeda, David P ^a  

^a NATIONAL CENTER FOR AGRICULTURAL UTILIZATION RESEARCH   (United States)

Author keywords

Actinobacteria; Streptomycetaceae; Systematics

Indexed keywords

ARTICLE; ATPD GENE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; GYRB GENE; HOUSEKEEPING GENE; MULTILOCUS SEQUENCE TYPING; NEW SPECIES; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RECA GENE; RPOB GENE; STREPTOMYCES; STREPTOMYCES EUROPAEISCABIEI; STREPTOMYCES SCABIEI; TAXONOMIC IDENTIFICATION; TRPB GENE; CLASSIFICATION; DNA BARCODING; GENETICS; MICROBIOLOGICAL EXAMINATION;

BACTERIOLOGICAL TECHNIQUES; DNA BARCODING, TAXONOMIC; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; STREPTOMYCES;

EID: 84959146776     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-015-0637-6     Document Type: Article

References (22)

1. Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Klenk H-P, Clément C, Ouhdouch Y, van Wezel GP (2016) Taxonomy, physiology, and natural products of Actinobacteria. Microbiol Mol Biol Rev 80:1–43
2. Bouchek-Mechiche K, Gardan L, Normand P, Jouan B (2000) DNA relatedness among strains of Streptomyces pathogenic to potato in France: description of three new species, S. europaeiscabiei sp. nov. and S. stelliscabiei sp. nov. associated with common scab, and S. reticuliscabiei sp. nov. associated with netted scab. Int J Syst Evol Microbiol 50:91–99
3. Burkhalid RA, Chung SY, Loria R (1998) nec1, a gene conferring a necrogenic pheonotipe, is conserved in plant-pathogenic Streptomyces species and lined to a transposase pseudogene. Mol Plant-Microbe Interact 11:960–967
4. Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772
5. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
6. Guindon S, Gascuel O (2003) A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Syst Biol 52:696–704
7. Jolley K, Maiden M (2010) BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinform 11:595
8. Kämpfer P, Glaeser SP, Parkes L, van Keulen G, Dyson P (2015) The Family Streptomycetaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes, actinobacteria, 4th edn. Springer, Berlin, pp 889–1010
9. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780
10. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
11. Labeda DP (2011) Multi-locus sequence analysis of phytopathogenic species of the genus Streptomyces. Int J Syst Evol Microbiol 61:2525–2531
12. Labeda DP, Doroghazi JP, Ju K-S, Metcalf WW (2014) Taxonomic evaluation of Streptomyces albus and related species using multi-locus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov. Int J Syst Evol Microbiol 64:894–900
13. Lambert DH, Loria R (1989a) Streptomyces scabies sp. nov., nom. rev. Int J Syst Bacteriol 39:387–392
14. Lambert DH, Loria R (1989b) Streptomyces acidiscabies sp. nov. Int J Syst Bacteriol 39:393–396
15. Miyajima K, Tanaka F, Takeuchi T, Kuninaga S (2008) Streptomyces turgidiscabies sp. nov. Int J Syst Bacteriol 48:495–502
16. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New York
17. Park DH, Kim JS, Kwon SW, Wilson C, YuYM HurJH, Lim CK (2003) Streptomyces luridiscabiei sp. nov., Streptomyces puniciscabiei sp. nov. and Streptomyces niveiscabiei sp. nov., which cause potato common scab disease in Korea. Int J Syst Evol Microbiol 53:2049–2054
18. Rong X, Huang Y (2012) Taxonomic evaluation of the Streptomyces hygroscopicus clade using multi-locus sequence analysis and DNA–DNA hybridization, validating the MLSA scheme for the systematics of the whole genus. Syst Appl Microbiol 35:7–18
19. Saitou N, Nei M (1987) Theneighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
20. Shirling E, Gottlieb DA (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340
21. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526
22. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30:2725–2729