Computational protocol: Specificity of Lipoxygenase Pathways Supports Species Delineation in the Marine Diatom Genus Pseudo-nitzschia

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Protocol publication

[…] A 25 ml subsample was collected from each culture in exponential growth phase and genomic DNA was extracted following []. DNA was amplified by PCR using the primers D1R and D3Ca [], [] for the hypervariable domains D1 and D3 of the LSU rDNA and two degenerated primers, rbcL1 and rbcL7 [] for the rbcL. PCR conditions and sequence analyses were carried out as reported in []. The accession number of the sequences produced within this investigation is reported in . Additional LSU rDNA and rbcL sequences of other Pseudo-nitzschia species were downloaded from GenBank, aligned by eyeball and used to build Maximum Likelihood phylogenies. Strain codes and GenBank accession numbers are reported in . Maximum-likelihood trees were inferred based on the substitution models selected through the Akaike information criterion option implemented in jModeltest [] using MEGA5 [], with 100 bootstrap replicates. Best fit models were GTR + I + G (I= 0.59; γ = 0.2266) for rbcL and GTR + I + G (I= 0.69; γ = 0.2180) for LSU. […]

Pipeline specifications

Software tools jModelTest, MEGA
Application Phylogenetics
Chemicals Carbon, Fatty Acids, Unsaturated, Oxygen, Eicosapentaenoic Acid