Computational protocol: Limited Sexual Reproduction and Quick Turnover in the Population Genetic Structure of Phytophthora infestans in Fujian, China

Similar protocols

Protocol publication

[…] In analyzing the variation in microsatellite loci, most P. infestans isolates showed a maximum of two alleles per locus as expected for a diploid organism. However, for several cases, three alleles were detected in one locus. Loci with three alleles were modified to resemble diploid loci by assigning specific allele sizes and a binary representation of the presence or absence of specific alleles as described previously. Multilocus genotype (MLG) for each isolate was formed by joining alleles at each SSR locus in the same order. Number of MLGs, was determined using the software GENCLONE 2.0. Genotype diversity was calculated for each population using the genotypic richness R = (number of different MLGs - 1) / (total number of isolates - 1). Expected heterozygousity, observed heterozygousity and mean number of alleles (Na) were calculated by POPGEN v3.2.Pairwise population differentiation (FST) and gene flow (Nm) were estimated using GENALEX 6.5. The physical distance between pair of populations was estimated using the geographic coordinates of locations from which the populations were sampled and isolation by distance was evaluated by estimating the association between the extent of gene flow and logarithm of physical distance (km) in the populations. Genetic variation was partitioned by the analysis of molecular variance (AMOVA) using ARLEQUIN 3.5. Multilocus association in each population was tested using the software LIAN3.0. The test evaluates the null hypothesis of linkage equilibrium among loci by calculating the standardized index of association IA. All population genetic parameters were estimated with clonal uncorrected data. Principal component analysis (PCA) was performed with GENALEX 6.5 to produce map depicting the distribution of genetic diversity across geographic space. Genetic distances between isolates was calculated using GENALEX6.5 and the phylogenetic trees of the 534 isolates and 49 genotypes were reconstructed by a neighbor joining approach using MEGA5 and MST goldsoftware programme as described by Salipante and Hall, respectively. […]

Pipeline specifications

Software tools GenAlEx, Arlequin
Applications Phylogenetics, Population genetic analysis
Organisms Phytophthora infestans