El was implemented under a constant population size scenario and fiveEl was implemented under a

May 17, 2018

El was implemented under a constant population size scenario and five
El was implemented under a constant population size scenario and five independent runs were generated. PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28461585 Convergence was then evaluated with ESS values and trace plots were explored with the software TRACER 1.5. Runs were combined using LOGCOMBINER and trees were plotted using FIGTREE v1.3.2 and DENSITREE 2.0.1. Split decomposition analyses were performed with SPLITSTREE, version 4 [66], by using LogDet distances, equal edge lengths, and 1000 bootstrap replicates.Population genetic analysesWe used the linkage model in STRUCTURE [67] to identify groups with distinct allele frequencies [54, 68, 69]. This procedure assigns a probability of ancestry for each polymorphic nucleotide for a given number of groups, K, and also estimates q, the combined probability of ancestry from each of the K groups for each individual isolate. As given by the Evanno’s test [70], we chose three groups for this report because repeated analyses (200,000 iterations following a burn-in period of 80,000 iterations) with K between 1 and 10 showed that the model probability increased dramatically between K = 2 and K = 3 and only slowly thereafter. A cut-off value of q 0.80 was then used to assign individual isolates to one of the three groups that largely matched the classical nomenclature. Unassigned isolates were designated as “hybrid” strains.AM152 msds Sapriel et al. BMC Genomics (2016) 17:Page 13 ofRecombination and mutationWe tested for recombination within the 3 subspecies for all loci independently, as well as for the concatenated MLST loci using the software LDHAT v2.2 [49]. LDHAT employs a coalescent-based method to estimate the population-scaled mutation ( = 2Ne) and recombination ( = 2Ner) rates, where Ne is the effective population size, r the rate at which recombination events separate adjacent nucleotides and is the mutation rate per nucleotide. The ratio r/ were calculated as (/L)/, where L is the gene length (sequence length). This PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28045099 r/ ratio ranges from 0, which indicates full clonal reproduction, to > > 1, which is expected under free recombination. Significance of the evidence for recombination was tested using nonparametric, permutation-based tests implemented in LDHAT (Lkmax and G4 tests). To avoid strains overrepresentation, the analysis was conducted on the sole STs. Concatenated sequences recombination rates confidence intervals were calculated using likelihood curve method.Mycobacterium abscessus subsp. bolletii CIP 108541 genomic sequence was deposited on NCBI whole genome shotgun project with accession number JRMF00000000. Mycobacterium abscessus subsp. bolletii CIP 108297 was deposited on NCBI whole genome shotgun project with accession number JRMG00000000.Mosaic strains DNA sequencing and genome assemblyM. bolletii and M. massiliense reference strains DNA sequencing and genome assemblyThe genomic DNAs of Mycobacterium abscessus subsp bolletii reference strain CIP 108541 and Mycobacterium abscessus subsp bolletii CIP 108297 (former M. massiliense reference strain) were sequenced at the Genopole of the Institut Pasteur by using the Genome Analyzer IIx (Illumina Inc., San Diego, USA) with a coverage rate of 175X and 170X, respectively. 36 bp single-end reads were generated and aligned against the reference genome of M. abscessus (EMBL accession number: CU458896) [41] by using MAQ [71]. In order to prevent the presence of potential amplification contaminants, duplicated reads were removed from the alignment maps. Two reads were considered as a duplicate.