DOI: 10.5061/dryad.8mc79
title: Data from: A new method for studying population genetics of cyst nematodes based on Pool-Seq and genome-wide allele frequency analysis

description: Cyst nematodes are important agricultural pests responsible for billions
 of dollars of losses each year. Plant resistance is the most effective
 management tool, but it requires a close monitoring of population
 genetics. Current technologies for pathotyping and genotyping cyst
 nematodes are time-consuming, expensive and imprecise. In this study, we
 capitalized on the reproduction mode of cyst nematodes to develop a simple
 population genetic analysis pipeline based on genotyping-by-sequencing and
 Pool-Seq. This method yielded thousands of SNPs and allowed us to study
 the relationships between populations of different origins or pathotypes.
 Validation of the method on well-characterized populations also
 demonstrated that it was a powerful and accurate tool for population
 genetics. The genomewide allele frequencies of 23 populations of golden
 nematode, from nine countries and representing the five known pathotypes,
 were compared. A clear separation of the pathotypes and fine genetic
 relationships between and among global populations were obtained using
 this method. In addition to being powerful, this tool has proven to be
 very time- and cost-efficient and could be applied to other cyst nematode
 species.
description: Sample
 descriptionDetails 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).Detail on
 samples.xlsxSupplemental Table
 1Population
 differentiation (Fst) of 23 worldwide populations of Globodera
 rostochiensis estimated from genome-wide allele frequencies at 604
 loci.Suppl
 Table1.docxCustom scripts and
 softwaresA link where all the
 custom scripts and softwares used in this paper can be
 found.scripts.txtPstI-MspI SNP table - UNEAK - 23 worldwide populationsGenerated 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).UNEAK_PstI-MspI_23pop_0,8_0,01_SNP.txtPstI-MspI SNP table - PoPoolation2 - 23 worldwide populationsGenerated 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).Popoolation2_PstI-MspI_23pop_0,01_5_rc_cntApeKI SNP table - UNEAK - 23 worldwide populationsGenerated 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).UNEAK_ApekI_23pop_0,8_0,01_SNP.txtApeKI SNP table - PoPoolation2 - 23 worldwide populationsGenerated 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).Popoolation2_ApekI_23pop_0,01_5_rc_cntInput file for PHYLIP - 23 worldwide populationsAllele 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.Phylip_23pop_1_0,01_20.txtUNEAK PstI-MspI allele frequencies - Validation assay - 28 Quebec populations from 2 fields + 1 outgroupAllele 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.UNEAK_PstI-MspI_29pop_1_0,01_20_SNP.txtInput file for PHYLIP - Validation assay - 28 Quebec populations from 2 fields + 1 outgroupAllele 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.Phylip_29pop_1_0,01_20.txtSupplemental Figure 1Relationship 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).Suppl Fig1.pngSupplemental Figure 2Number 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).Suppl Fig2.pngSupplemental Figure 3Principal 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).Suppl Fig3.pngSupplemental Figure 4Principal 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.Suppl Fig4.png