Computational protocol: Climate change promotes parasitism in a coral symbiosis

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Protocol publication

[…] We identified the dominant Symbiodinium genotype present in our samples using direct sequencing of the ITS2 region of the nrDNA. Total genomic DNA was extracted from frozen Symbiodinium pellets using a MoBio PowerSoil DNA extraction kit. The PCR followed the ITS2 “touchdown” protocol developed by LaJeunesse []. Details of post-PCR cleanup, and Sanger sequencing are detailed in Baker et al. []. Forward and reverse sequences were aligned and trimmed using Geneious 6.0 (Biomatters Ltd). Consensus sequences were used for BLAST searches to identify the closest match in NCBI GenBank. Sequences were cross-referenced with the GeoSymbio database [].A second aliquot of the frozen cell suspension was loaded into a hemocytometer to count the total number of dividing Symbiodinium cells (doublets) relative to the total number of cells using a fluorescent microscope (80i, Nikon, Tokyo, Japan). Mitotic index (MI) was calculated as the quotient of the two measures, respectively. A total of 9426 individual cell observations were recorded across all samples from the post-incubation sampling. These data were used to simulate growth projections beyond the duration of the experiment (). […]

Pipeline specifications

Software tools Geneious, GeoSymbio
Application Phylogenetics