Computational protocol: Exploring Diversity among Norwegian Borrelia Strains Originating from Ixodes ricinus Ticks

Similar protocols

Protocol publication

[…] The sequences for each housekeeping gene were aligned by the MUSCLE algorithm and concatenated in MEGA 5.1 []. The sequences were analysed with BLAST to confirm the correct Borrelia genospecies []. Each locus and the concatenated sequence of all eight loci were analysed. The MEGA 5.1 software was used to draw a distance matrix neighbour-joining tree (bootstrapped 500 iterations) with the concatenated DNA sequences. Sequences from B. duttonii were added from the BLAST database [] to root the neighbour-joining tree. B. duttonii is a Borrelia species that causes relapsing fever []. Sequences from four reference species from the MLST database were included in the analysis, B. burgdorferi s.s. (B31), B. afzelii (VS461), B. valaisiana (70865B), and B. garinii (20047). To compare allele sequences and sequences types (STs) and to identify identical sequences, the nonredundant database (NRDB) written by Warren Gish at Washington University was used (http://pubmlst.org/analysis/). All known alleles and STs were retrieved from the Borrelia MLST database for comparison (http://borrelia.mlst.net/). STs that were not found in the MLST database were submitted to the MLST database for proper numbering. Statistical analysis was performed with MEGA 5.1. The mean pairwise genetic difference (within and between groups) was calculated using the Kimura 2-parameter model. Average nonsynonymous substitutions and synonymous substitutions (dN/dS) were calculated using the modified Nei-Gojobori method (Jukes-Cantor). The number of polymorphic sites (PS) and the nucleotide diversity (π) were calculated using Tajima's test of neutrality. The index of association, both standard and classic, was calculated using START2 [].To compare the relationship between Norwegian Borrelia strains and European Borrelia strains a goeBURST minimum spanning tree was generated using PHYLOViZ 1.0 software []. […]

Pipeline specifications

Software tools MEGA, BURST, PHYLOViZ
Databases nrDB MLST.net PubMLST
Applications Phylogenetics, WGS analysis
Organisms Ixodes ricinus, Borreliella afzelii, Borreliella garinii
Diseases Borrelia Infections, Sprains and Strains