The relative abundance of major clades (genera) of Symbiodiniaceae was profiled using kraken version 1.1.1 (Wood and Salzberg 2014) to classify raw reads from each sample. To ensure that this made full use of available reads and also that it was not affected by biased database composition we restricted our analysis to taxa for which a complete reference genome was available. This included the following data;
- Clade A: Symbiodinium microadriadicum from genbank
- Clade B: Breviolum sp. from OIST
- Clade C: (C1) Cladocopium sp. from reefgenomics
- Clade D: Durusdinium sp. provided courtesy of Assoc. Prof. Mauricio Rodriguez-Lanetty, Department of Biological Sciences Florida International University
- Clade F: Fugacium sp. from reefgenomics
These genomes were combined with the host A. tenuis genome as well the standard kraken bacterial sequences to build a kraken database (see 07_build_kraken.sh) using default values for kmer length (31) and minimiser length (15).
kraken was then used to classify all read pairs for all samples and the
raw outputs processed with kraken-mpa-report. This produces a report
in a format similar to MetaPhlAn’s output (see
09_run_kraken_genome.sh).
Irrespective of whether absolute read counts or proportion of reads is used the dominant symbiont clade for all locations and all but one sample was Cladocopium. A single sample from Dunk Island was dominated by Durusdinium.
Wood, Derrick E, and Steven L Salzberg. 2014. “Kraken: Ultrafast Metagenomic Sequence Classification Using Exact Alignments.” Genome Biol. 15 (3): R46.