Computational protocol: Comparison of RAPD, AFLP, and EF-1α Sequences for the Phylogenetic Analysis of Fusarium oxysporum and Its formae speciales in Korea

Similar protocols

Protocol publication

[…] A pairwise alignment was calculated using the Clustal X program (). Phylogenetic relationships were estimated by MEGA 3 version 3.0 () treating all alignment gaps as missing. A maximum parsimony tree (MP) was inferred using heuristic search, branch-swapping options and tree bisection-reconnection. Confidence values for individual branches were determined by a bootstrap analysis with 100 repeated sampling of the data. [...] All monomorphic and polymorphic RAPD and AFLP bands were scored by eye and only unambiguously scored bands were used in the analyses. Because RAPDs and AFLPs are dominant markers, they were assumed that each band corresponded to a single character with two alleles, presence (1) and absence (0) of the band, respectively. The following genetic parameters were calculated using a POPGENE computer program (ver. 1.31) developed by Yeh et al. (). To determine the extent of genetic departure, we calculated the Nei genetic distance (GD) and genetic identity (GI) for each pairwise combination of accessions (). The estimation of genetic similarity (GS) between genotypes was based on the probability that an amplified fragment from one individual will also be present in another [22]. GS was converted to genetic distance (1-GS) (). Homogeneity of variance among accessions was tested by Bartlett's statistics. To elucidate the organization of variability within F. oxysporum, we examined the genetic variation by partitioning the total genetic diversity (HT) to within isolates (HS) using, the genetic diversity statistics of Nei et al. (). Wright's genetic differentiation among isolates (GT) was computed for variable loci with FSTAT (). Genetic differentiation measured by GST among isolates was also calculated. Furthermore, gene flow between the pairs of accessions was calculated from GST values by Nm = 1/4(1/GST - 1) (). […]

Pipeline specifications

Software tools Clustal W, MEGA, POPGENE
Databases RAPD
Applications Phylogenetics, Population genetic analysis
Organisms Fusarium oxysporum
Chemicals Fusaric Acid