Figure 2.

BLAST top hit analysis of P. tricornutum genes. (A) Comparison of the number of genes of unambiguous taxonomic origin, identified by BLAST top hit analysis of the complete Phatr3 protein annotations against six different reference libraries, constructed using UniRef, jgi genomes and other transcriptome libraries, and six different patterns of taxon inclusion: a library containing all sequences from the tree of life; all sequences except those from pennate diatoms; all except those from diatoms; all except those from stramenopiles; all except those from SAR clade members; and all except those from SAR and CCTH clade members. The right-hand graph (II) shows similar values calculated for reference libraries from which all algae with a suspected history of secondary endosymbiosis other than ochrophytes were removed. Note that in this case a separate value for a reference library excluding SAR and CCTH clade taxa is not provided, as all it is not known when secondary endosymbioses arose within CCTH clade lineages²¹, hence all CCTH clade taxa were excluded from the analysis. (B) Comparison of the proportion of genes that yield top hits against five different categories (all prokaryotes, the Deinococcus-Thermus clade only, all red algae, and green groups, and all amorphea) following the removal of different groups from the complex algae-free dataset. Total number of genes within each category is indicated beneath it in round brackets. Data labels for each value are provided in the corresponding segment; where the segment is too small to accommodate the corresponding value, the value is placed outside the chart, and shaded to match the color of the segment. The largest value recorded for each gene category corresponds to the most probable evolutionary time point at which genes were acquired; for example, the largest number of genes of red algal affinity were recovered following the removal of all algae with plastids of secondary or higher endosymbiotic derivation from the reference dataset, indicating a large-scale donation of red algal genes into algae with plastids of secondary or higher endosymbiotic derivation.