DNAstar (Lasergene) Download 2020

The applicability of the modified software was further checked using a previously developed M. gallisepticum cgMLST schema [15] as a comparison. The sequence reads of M. gallisepticum strains from BioProject PRJNA401291 were downloaded and assembled into draft genomes. The 55 assembled draft genomes were then analysed with chewBBACA as described below. The allelic profiles of the Ridom SeqSphere+ and chewBACCA cgMLST schemas (Supplementary Table 2) were used in the creation of two Neighbor joining trees with GrapeTree software version 1.5.0 (downloaded on 2020.04.) [21] using the FastME implementation [35] as seen in Supplementary Fig. 1.

DNAstar (Lasergene) Download 2020

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The CDSs constituting our cgMLST schema were extracted from the strain MYCAV93, randomly chosen out of the available whole genomes on NCBI. These CDSs were concatenated, creating a pseudo-genome. The sequence reads of the 80 strains (all examined strains except MYCAV93) were mapped with DNASTAR LaserGene suite version 17.0.2.1 (downloaded on 2020.04.20) [39]. The SNPs were filtered and an alignment was created from the ones corresponding to the same position. The alignment was analysed with MEGA-X version 10.0.5. (downloaded on 2019.02.25) [22] and a Maximum Likelihood tree was created using the General Time Reversible model with Gamma distribution and bootstrap set to 500 iterations. The cgSNP analysis based phylogenetic tree was compared with the Neighbor joining tree based on cgMLST profiles assessed by GrapeTree software version 1.5.0 (Fig. 1). 2ff7e9595c