Computational protocol: High prevalence of Trichomonas gallinae in wild columbids across western and southern Europe

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Protocol publication

[…] Forward and reverse sequences were assembled and trimmed with CLC Main Workbench 7.6.1 (CLC bio, Qiagen). With NCBI Blast [] we checked every sequence for its closest GenBank match and downloaded these as reference sequences (see Additional file : Table S1 for an overview about the percentage of identity to the closest GenBank match). Additionally, we downloaded the closest GenBank matches, obtained for columbids by Lennon et al. []. This enables the direct comparison of Trichomonas lineages occurring in stock doves, wood pigeons and turtle doves from the UK to Germany, Italy and Spain. Tritrichomonas foetus (GenBank accession number DQ243911.1 []) was used as outgroup for phylogenetic analysis following previous studies []. We aligned all sequences using BioEdit []. The nucleotide substitution model that best fitted our alignment was determined with MEGA 6.0 [] using Bayesian Information Criterion scores. The phylogenetic tree was also inferred with MEGA 6.0 [] using the Maximum Likelihood algorithm and employing the Tamura 3 substitution model with invariant sites. Node support was assessed after 1000 bootstrap pseudo-replicates. The GenBank accession numbers of analysed sequences are given in Additional file : Table S3. […]

Pipeline specifications

Software tools CLC Main Workbench, BLASTN, BioEdit, MEGA
Application Phylogenetics
Diseases Trichomonas Infections