Fig. 4

Large paralog gene families are present in the Euglena gracilis genome. Several orthogroups contain many E. gracilis paralogs. The phylogenetic distribution of one large orthogroup, the nucleotidylcyclase III domain-containing proteins, is shown. Lineage groupings are colour coded: gray, all eukaryotes (and collapsed for clarity); red, N. gruberi; amber, B. saltans; and green, E. gracilis. Clades containing only Euglena sequences are boxed in green. Each sequence has been assigned a domain composition (colour gradient black to teal to blue), number of predicted trans-membrane domains (colour coded red to orange to black gradient). To obtain this phylogenetic tree, sequences with likely low coverage (less than 30% of the length of the overall alignment) were removed during alignment to avoid conflicting homology or artefact generation. Domain compositions identified are nucleotidylcyclase III, BLUF, NIT, P-loopNTPase, HAMP and Cache1