6-0 of the supplementary R package phangorn [38]. To simplify
interpretation of results, haplotypes were named A-Q on the basis of their respective position https://www.selleckchem.com/products/azd9291.html in the phylogenetic tree. Support for clusters was evaluated using the bootstrap test of phylogeny (1000 repeats) and clusters with values of less than 50% collapsed [39]. The clustering of very closely related haplotypes, defined as those differing at only one locus, was examined using eBURST v 3.0 [40]. Homoplasy and extent of recombination events were investigated using Splits Decomposition, as implemented in Splitstree v 4 [41], by depicting conflicting signals in the data caused by recombination events. The resulting network was consistent with the phylogenetic analysis, and no reticulation was evident, indicating that the evolutionary relationships have not been affected by recombination or homoplasy (data not shown). The discriminatory power of a typing system was estimated using the Hunter-Gaston discriminatory index HGDI [42]. The index provides a
probability that two randomly sampled unrelated isolates will be placed into different typing groups/haplotypes. The minimum number of loci required to distinguish all the strains was determined. Acknowledgements The authors would like to thank Drs. Sandy G. Murray and David Bruno (Marine Scotland Science, Aberdeen, United Kingdom) for valuable comments which greatly improved the manuscript draft. Electronic supplementary material
Addition al file 1: Table S1: Exoribonuclease List of amplified and analysed tandem repeat loci within the R. S63845 concentration salmoninarum genome. (DOC 56 KB) Additional file 2: Table S2: List of R. salmoninarum isolates used for tandem repeat polymorphism analysis. (DOC 62 KB) References 1. Sanders JE, Fryer JL: Renibacterium salmoninarum gen. nov., sp. nov., the causative agent of bacterial kidney disease in salmonid fishes. Int Syst Bacteriol 1980, 30:496–502.CrossRef 2. Gutenberger SK, Giovannoni SJ, Field KG, Fryer JL, Rohovec JS: A phylogenetic comparison of the 16S rRNA sequence of the fish pathogen, Renibacterium salmoninarum , to gram-positive bacteria. FEMS Microbiol Lett 1991, 77:151–156.CrossRef 3. Koch CF, Rainey FA, Stackebrandt E: 16S rDNA studies on members of Arthrobacter and Micrococus: and aid for their future taxonomic restructuring. FEMS Microbiol Lett 1994, 123:167–172.CrossRef 4. Wiens GD, Rockey DD, Wu Z, Chang J, Levy R, Crane S, Chen DS, Capri GR, Burnett JR, PCI-34051 Sudheesh PS, Shipma MJ, Burd H, Bhattacharyya A, Rhodes LD, Kaul R, Strom MS: Genome sequence of the fish pathogen Renibacterium salmoninarum suggests reductive evolution away from an environmental Arthrobacter ancestor. J Bacteriol 2008, 190:6970–6982.PubMedCentralPubMedCrossRef 5. Evelyn TPT: Bacterial kidney disease – BKD. In Bacterial Diseases of Fish. Edited by: Inglis V, Roberts RJ, Bromage NR. Oxford, United Kingdom: Blackwell Scientific Publications; 1993:177–195. 6.