Table 4.

Enriched gained and lost Gene Ontology terms for select clades

	Enriched gained GO terms	P-value	Enriched lost GO terms	P-value
Corticata	Cobalamin biosynthetic process	3.2E-7	Small GTPase mediated signal transduction	7.9E-3
	Photosynthesis	2.3E-6	Lipid transport	1.1E-2
Archaeplastida	Photosynthesis	3.1E-25	Carbohydrate metabolic process	9.1E-4
	Glycyl-tRNA aminoacylation	1.8E-2	Xylan catabolic process	4.8E-3
Viridiplantae	Photosynthesis	2.7E-3	Tryptophan catabolic process to kynurenine	7.1E-3
	Protein import into mitochondrial outer membrane	7.1E-3	Sulfur compound biosynthetic process	1.3E-2
Protostomia	Sensory perception of smell	4.3E-3	Protein secretion by the type II secretion system	3.4E-3
			Cell adhesion	4.2E-3

The two terms with the lowest P-values are shown (calculated by the Ontologizer 2.0 software [63] with the Topology-Elim algorithm [64]). Prototypical regulatory terms are in bold text, prototypical metabolic terms are in italics (for detailed results see Additional files 5 and 6).