Data from: Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers

Trujillo CA, Arias-Rojas N, Poulin L, Medina CA, Tapiero A, Restrepo S, Koebnik R, Bernal AJ

Date Published: June 24, 2014

DOI: http://dx.doi.org/10.5061/dryad.t173v

 

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Title matrix_AFLPs_llanos_Xam
Downloaded 4 times
Description Presence/ absence matrix generated using AFLPs. Xam isolates were typed using four primer combination. 57 polymorphic bands were included in this matrix.
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Title NJ_AFLP_bootstrap_llanos_Xam
Downloaded 7 times
Description Unrooted distance tree with the Neighbor-Joining algorithm was generated in SplitsTree version 4.12.3. Branch supports were determined running 1000 bootstrap replicates.
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Title Matrix_VNTR_llanos_Xam
Downloaded 4 times
Description Matrix 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.
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Title NJ_VNTR_bootstrap_llanos_Xam
Downloaded 10 times
Description VNTR 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.
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Title AFLPs Raw Data
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Description AFLPs 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.
Download AFLPs Raw data Absence-presence_Llanos_Xam (86.01 Kb)
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Title VNTR Raw data
Downloaded 4 times
Description This 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)
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Title VNTR Structure project
Downloaded 6 times
Description This 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) iterations
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Title AFLP Structure Project
Downloaded 6 times
Description This 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.
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When using this data, please cite the original publication:

Trujillo CA, Arias-Rojas N, Poulin L, Medina CA, Tapiero A, Restrepo S, Koebnik R, Bernal AJ (2014) Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers. BMC Microbiology 14: 161. http://dx.doi.org/10.1186/1471-2180-14-161

Additionally, please cite the Dryad data package:

Trujillo CA, Arias-Rojas N, Poulin L, Medina CA, Tapiero A, Restrepo S, Koebnik R, Bernal AJ (2014) Data from: Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.t173v
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