Data from: A new method for studying population genetics of cyst nematodes based on Pool-Seq and genome-wide allele frequency analysis

Mimee B, Duceppe M, Véronneau P, Lafond-Lapalme J, Jean M, Belzile F, Bélair G

Date Published: April 2, 2015

DOI: http://dx.doi.org/10.5061/dryad.8mc79

 

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Title Sample description
Downloaded 16 times
Description Details about the origin (Country, province and field) of the samples, which experiment and figures they were used in and accession numbers (bioproject and biosample numbers).
Download Detail on samples.xlsx (14.31 Kb)
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Title Supplemental Table 1
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Description Population differentiation (Fst) of 23 worldwide populations of Globodera rostochiensis estimated from genome-wide allele frequencies at 604 loci.
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Title Custom scripts and softwares
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Description A link where all the custom scripts and softwares used in this paper can be found.
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Title PstI-MspI SNP table - UNEAK - 23 worldwide populations
Downloaded 18 times
Description Generated with mnC=0.8, minCov=1 and a MAF=0.01. Use this file as input to generate the “UNEAK-PstI/MspI” SNP tables with different parameters (mnC, minCov and MAF) using the countCleaner script found at https://bitbucket.org/mimeeb/gbs (Windows-based software).
Download UNEAK_PstI-MspI_23pop_0,8_0,01_SNP.txt (552.2 Kb)
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Title PstI-MspI SNP table - PoPoolation2 - 23 worldwide populations
Downloaded 7 times
Description Generated with mnC=1, minCov=5 and a MAF=0.01. Use this file as input to generate the “PoPoolation2-PstI/MspI” SNP tables with different parameters (minCov and MAF) using the countCleaner script found at https://bitbucket.org/mimeeb/gbs (Windows-based software).
Download Popoolation2_PstI-MspI_23pop_0,01_5_rc_cnt (494.2 Kb)
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Title ApeKI SNP table - UNEAK - 23 worldwide populations
Downloaded 5 times
Description Generated with mnC=0.8, minCov=1 and a MAF=0.01. Use this file as input to generate the “UNEAK-ApeKI” SNP tables with different parameters (mnC, minCov and MAF) using the countCleaner script found at https://bitbucket.org/mimeeb/gbs (Windows-based software).
Download UNEAK_ApekI_23pop_0,8_0,01_SNP.txt (860.9 Kb)
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Title ApeKI SNP table - PoPoolation2 - 23 worldwide populations
Downloaded 8 times
Description Generated with mnC=1, minCov=5 and a MAF=0.01. Use this file as input to generate the “PoPoolation2- ApeKI” SNP tables with different parameters (minCov and MAF) using the countCleaner script found at https://bitbucket.org/mimeeb/gbs (Windows-based software).
Download Popoolation2_ApekI_23pop_0,01_5_rc_cnt (28.33 Kb)
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Title Input file for PHYLIP - 23 worldwide populations
Downloaded 14 times
Description Allele frequencies calculated from UNEAK exact counts (mnC=1, minCov=20 and MAF=0.01) and used for phylogenetic tree analysis of the 23 Globodera rostochiensis worldwide populations.
Download Phylip_23pop_1_0,01_20.txt (103.2 Kb)
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Title UNEAK PstI-MspI allele frequencies - Validation assay - 28 Quebec populations from 2 fields + 1 outgroup
Downloaded 11 times
Description Allele frequencies calculated from UNEAK exact counts (mnC=1, minCov=20 and MAF=0.01) and used for principal component analysis (PCA) of Globodera rostochiensis populations from two fields of the province of Quebec, Canada and an unrelated population from France.
Download UNEAK_PstI-MspI_29pop_1_0,01_20_SNP.txt (43.92 Kb)
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Title Input file for PHYLIP - Validation assay - 28 Quebec populations from 2 fields + 1 outgroup
Downloaded 16 times
Description Allele frequencies calculated from UNEAK exact counts (mnC=1, minCov=20 and MAF=0.01) and used for phylogenetic tree analysis of Globodera rostochiensis populations from two fields of the province of Quebec, Canada and an unrelated population from France.
Download Phylip_29pop_1_0,01_20.txt (41.95 Kb)
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Title Supplemental Figure 1
Downloaded 6 times
Description Relationship between the median coverage (median number of reads/locus/population supporting each SNP) and the number of SNPs retained by the two pipelines at a minimum allele frequency of 1% (MAF = 0.01) and 5% (MAF = 0.05).
Download Suppl Fig1.png (31.07 Kb)
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Title Supplemental Figure 2
Downloaded 31 times
Description Number of SNPs retained by UNEAK and PoPoolation2 pipelines at different parameter values on an ApeKI library from 23 worldwide populations of Globodera rostochiensis. ‘MAF’ is the minimum allele frequency; ‘minCov’ is the minimum number of reads/locus/population required to accept a SNP; ‘mnC’ is the minimum proportion of populations in which a locus must have been scored to be accepted. PoPoolation2 does not allow missing data (mnC = 1.0). *The number of SNPs identified by UNEAK was not influenced by the ‘mnC’ value when the minimum allele frequency was set to 5% (MAF = 0.05).
Download Suppl Fig2.png (69.71 Kb)
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Title Supplemental Figure 3
Downloaded 16 times
Description Principal component analyses of 23 worldwide populations of Globodera rostochiensis from different pathotypes (Ro1, Ro2, Ro3, Ro4, Ro5 and a mixed population of Ro2/Ro3). Calculated with the prcomp() function in R. Based on genome-wide allele frequencies of different number of loci obtained from the PstI/MspI library supported by six different minimum coverage values (minCov = 5, 10, 20, 30, 40 or 50 reads/locus/population). Computed by the PoPoolation2 pipeline with a minimum allele frequency of 1% (MAF = 0.01) and no missing data allowed (mnC = 1.0).
Download Suppl Fig3.png (92.45 Kb)
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Title Supplemental Figure 4
Downloaded 7 times
Description Principal component analysis of 23 worldwide populations of Globodera rostochiensis. Calculated with the prcomp() function in R. Based on genome-wide allele frequencies of 1,277 loci obtained from the PstI/MspI library, and computed by the PoPoolation2 pipeline with a minimum allele frequency of 1% (MAF = 0.01), no missing data allowed (mnC = 1.0) and a minimum coverage of 20 reads/SNP/population (minCov = 20). Colors represent the different pathotypes: Black = Ro1; Yellow = Ro2; Green = Ro3; Red = Ro4; Blue = Ro5 and Grey is the mixed Ro2/3 sample.
Download Suppl Fig4.png (76.14 Kb)
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When using this data, please cite the original publication:

Mimee B, Duceppe M, Véronneau P, Lafond-Lapalme J, Jean M, Belzile F, Bélair G (2015) A new method for studying population genetics of cyst nematodes based on Pool-Seq and genome-wide allele frequency analysis. Molecular Ecology Resources 15(6): 1356–1365. http://dx.doi.org/10.1111/1755-0998.12412

Additionally, please cite the Dryad data package:

Mimee B, Duceppe M, Véronneau P, Lafond-Lapalme J, Jean M, Belzile F, Bélair G (2015) Data from: A new method for studying population genetics of cyst nematodes based on Pool-Seq and genome-wide allele frequency analysis. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.8mc79
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