Computational protocol: “Candidatus Similichlamydia laticola”, a Novel Chlamydia-like Agent of epitheliocystis in Seven Consecutive Cohorts of Farmed Australian Barramundi, Lates calcarifer (Bloch)

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Protocol publication

[…] The 298 bp signature sequences of known Chlamydia-like epitheliocystis agents and the near full-length 16S rRNA regions sequenced here and data from representative Chlamydiales species and outgroup taxa obtained from GenBank were aligned and trimmed as previously described [].The software jModelTest version 0.1.1 [] estimated TIM3+G and GTR+I+G as the best nucleotide substitution models for the signature sequence and near full-length datasets, respectively. Maximum likelihood (with 1,000 bootstraps) and Bayesian Inference (with 10,000,000 generations) analyses were performed using the software package MEGA5 [] and Mr Bayes version 3.1.2 [] run on the CIPRES portal [] to explore relationships among these epitheliocystis taxa as previously described []. [...] Following visual inspection of the H&E stained gill sections, the prevalence (expressed as a percentage) and intensity (intensity = cysts per section/filament per section) of cysts were calculated. The presence of CLOs detected by PCR was calculated as a prevalence (expressed as a percentage). Statistical analyses were conducted with the IBM SPSS Statistics package, version 20.0.0.1 (2011). Since the distribution of the data was non-normal (even after transformations), the non-parametric Kruskal-Wallis test with post-hoc comparisons and Mann-Whitney U test were used. A Spearman’s rank correlation test was used to identify if a significant relationship existed between fish length and the prevalence of epitheliocystis. […]

Pipeline specifications

Software tools jModelTest, MEGA, CIPRES Science Gateway, SPSS
Applications Miscellaneous, Phylogenetics
Organisms Lates calcarifer
Diseases Chlamydia Infections