DOI: 10.5061/dryad.t173v
title: Data from: Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers

description: Background: Molecular typing of pathogen populations is an important tool
 for the development of effective strategies for disease control. Diverse
 molecular markers have been used to characterize populations of
 Xanthomonas axonopodis pv. manihotis (Xam), the main bacterial pathogen of
 cassava. Recently, diversity and population dynamics of Xam in the
 Colombian Caribbean coast were estimated using AFLPs, where populations
 were found to be dynamic, diverse and with haplotypes unstable across
 time. Aiming to examine the current state of pathogen populations located
 in the Colombian Eastern Plains, we also used AFLP markers and we
 evaluated the usefulness of Variable Number Tandem Repeats (VNTRs) as new
 molecular markers for the study of Xam populations. Results: The
 population analyses showed that AFLP and VNTR provide a detailed and
 congruent description of Xam populations from the Colombian Eastern
 Plains. These two typing  strategies clearly separated strains from the
 Colombian Eastern Plains into distinct  populations probably because of
 geographical distance. Although the majority of analyses were congruent
 between typing markers, fewer VNTRs were needed to detect a higher number
 of genetic populations of the pathogen as well as a higher genetic flow
 among sampled locations than those detected by AFLPs. Conclusions: This
 study shows the advantages of VNTRs over AFLPs in the surveillance of
 pathogen populations and suggests the implementation of VNTRs in studies
 that involve large numbers of Xam isolates in order to obtain a more
 detailed overview of the pathogen to improve the strategies for disease
 control.
description: matrix_AFLPs_llanos_XamPresence/ absence matrix generated using AFLPs. Xam isolates were typed using four primer combination. 57 polymorphic bands were included in this matrix.NJ_AFLP_bootstrap_llanos_XamUnrooted distance tree with the Neighbor-Joining algorithm was generated in SplitsTree version 4.12.3. Branch supports were determined running 1000 bootstrap replicates.Matrix_VNTR_llanos_XamMatrix generated by presence or absence of an allele in a specific VNTR locus. In total 5 VNTR loci were used. The allele number for each locus is variable and those are described in the table 1 of the manuscript.NJ_VNTR_bootstrap_llanos_XamVNTR data were used to created an unrooted distance tree with the Neighbor-Joining algorithm in SplitsTree version 4.12.3. One thousand bootstrap replicates were run.NJ_VNTR_llanos_Xam.nexAFLPs Raw DataAFLPs Raw data matrix. This data were obtained from the presence or absence of band in the polyacrylamide gels. 111 isolates were includes and 57 band were scored. These data were implemented to generate the distance tree and the Minimum Spanning Network using SplitsTree version 4.12.3 and BioNumerics software (version 7.1) respectively.AFLPs Raw data Absence-presence_Llanos_XamVNTR Raw dataThis file contains the numbers of the repeats obtained from the sequenced VNTR loci. These data were implemented to generated the Minimum Spanning Network using BioNumerics software (version 7.1)VNTR Structure projectThis file contains the STRUCTURE project generated using the repeats of the sequenced VNTRs. Xam isolates were assigned into genetic populations using a clustering algorithm based on Bayesian model in STRUCTURE 2.3.3 without prior population information. Genetic clusters of the isolates were generated with independent allele frequencies and five thousand replicates during burning period and 100.000 Monte Carlo Markov chain (MCMC) iterationsVNTR_llanos_Structure_Xam.spjAFLP Structure ProjectThis file contains the STRUCTURE project generated using the AFLP data. Xam isolates were assigned into genetic populations using a clustering algorithm based on Bayesian model in STRUCTURE 2.3.3 without prior population information. Genetic clusters of the isolates were generated with independent allele frequencies and five thousand replicates during burning period and 100.000 Monte Carlo Markov chain (MCMC) iterations.AFLP_Structure_llanos_Xam.spj