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We used all unique SNV positions for calculating distance between the isolates using pair wise alignment.
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Growth curves of these L. braziliensis isolates were performed and no statistically significant differences were observed between the isolates used for macrophage infection.
At this point in time VI101 had significantly (p < 0.05) lower numbers of intracellular bacteria compared to the other isolates except for Mah H1, while no significant difference were observed between the other isolates using the paired t-test.
Single nucleotide polymorphisms (SNPs) were identified between the sequenced isolates using NUCMER and dot plots were generated using MUMmerplot [ 72].
We confirmed the cluster analysis by visualizing the relationships between isolates using a transparent network analysis technique which simply connects isolates, represented as nodes within a network, based on shared SNPs.
(B ) Frequency of nonsynonymous SNP occurrence between serial isolates using different filters.
Inferring phylogenetic relationships between the known SARS-CoV isolates using existing public data has been problematic because of the potential for sequencing errors.
Briefly, an unrooted dendrogram was built based on Manhattan distances between each pair of M. avium isolates, using the neighbour-joining algorithm contained in the PHYLIP software, version 3.67.
However, a major difference between the two MHV isolates and the two IBV viruses we used was that the two MHVs were pathogenic but demonstrated different pathogenicities, neurovirulence and hepatitis, respectively, whereas the difference between the two IBV isolates used in this work was that one causes disease and the other does not.
Clinical and bacteriological characteristics were compared between katG315Thr alleles and other INH resistant isolates using the Mantel-Haenszel chi-square test.
The relationship between the F. verticillioides isolates used in each location is unknown; as such, it is possible that differences in pathogen aggressiveness could have contributed to the disparity in mean ear rot values across environments.
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