Computational protocol: Prevalence and Molecular Identification of Nematode and Dipteran Parasites in an Australian Alpine Grasshopper (Kosciuscola tristis)

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Protocol publication

[…] Sequences of 18S rDNA were manually checked for read error and then assembled into optimized contigs using Geneious (version 5.5.6, Bioinformatics software Biomatters Ltd, New Zealand). Contigs covered 1409 and 655 nucleotides for the Nematoda and Diptera isolates, respectively. A BlastN search (www.ncbi.gov) including only sequences with >95% query coverage was performed to assign contigs to the lowest resolution taxonomic group. Sequences generated from this study were supplemented with publicly available sequences representing major lineages of Nematoda and Diptera (accession numbers given in ) and aligned using ClustalW with default parameters []. The nucleotide sequences identified in this study were submitted to GenBank under the accession numbers (JQ894729—JQ894732).Phylogenetic analysis was performed using Bayesian Markov Chain Monte Carlo method implemented in BEAST v1.8.0 []. For all analyses the random local molecular clock and the General Time Reversible substitution model accounting for estimates of invariable sites (I) and the gamma distribution parameter (G) were used. The analysis was conducted using a Bayesian skyride coalescent tree prior. We performed two independent analyses of 20 million generations that were combined after appropriate burnin (~10%) to produce 10,000 trees. Branch placement within the phylogenetic tree was used to assign isolates from this study to family level. […]

Pipeline specifications

Software tools Geneious, BLASTN, Clustal W, BEAST
Application Phylogenetics
Organisms Caenorhabditis elegans
Diseases Nematode Infections