Table 1.
Summary of the collections of Xanthomonas vasicola pv. musacearum.
Table 2.
Core-collection of Xanthomonas vasicola pv. musacearum and Xanthomonas vasicola strains.
Table 3.
Microsatellites, primer description and amplification conditions of the MLVA-19 scheme.
Table 4.
Nomenclature, location, function and genetic diversity of the 19 TR loci retained in the MLVA scheme of Xanthomonas vasicola pv. musacearum.
The basic statisticsd were obtained from the Xvm collection (n = 335).
Fig 1.
Genotype accumulation curve for 335 strains of Xanthomonas vasicola pv. musacearum genotyped over 19 loci.
The horizontal axis represents the number of loci randomly sampled without replacement up to n-1 loci, the vertical axis shows the number of unique multilocus genotypes observed (n = 208) in the data set. The level of 95% of unique multilocus genotype detected is indicated with a dotted red line.
Table 5.
Typeability and specificity of each XVM locus considering X.
vasicola pv. musacearum (Xvm), X. vasicola pathovars holcicola (Xvh), and vasculorum (Xvv), and other Xanthomonas species: X. oryzae pv. oryzae (Xoo); X. campestris pv. cannabis (Xcc); X. citri pv. citri (Xc), estimated by the number (percentage) of amplified strains.
Fig 2.
Minimum spanning tree (MST) of Xanthomonas vasicola pv. musacearum based on SNP haplotypes identified using goeBURST in PHYLOVIZ.
Each sequence type (ST) is displayed as a circle with a size proportional to the number of strains by which is represented. The different colors indicate the SNP haplotype. Numbers on the branches indicate the number of locus differences between the neighboring haplotypes.
Fig 3.
Correspondence between SNP haplotypes with generic clusters inferred by discriminant analysis of principal components.
The clusters are shown on the horizontal axis and the countries and SNP haplotypes are indicated on the vertical axis. The black squares represent the number of strains per SNP haplotype within the given cluster. The Figs were created using the table.value function in the R “Adegenet” package [53].
Table 6.
MLVA-19 is discriminative at the field scale.
Number of MLVA-19 haplotypes detected in three fields of Ethiopia and Uganda.