Morphology and phylogenetic relationships of MALVs. Tree topology is based on maximum likelihood analysis of concatenated SSU and LSU rRNA gene sequences (>3900 nucleotide positions; 7.1% gaps). Node support is shown by RAxML bootstraps (non-parametric) and MrBayes posterior probabilities. Black circles indicate a maximum support in both analyses. Sequences obtained in this study are printed in bold. Numbers in polygons refer to the number of grouped taxa, roman numerals signify the different MALV groups (compare with Guillou et al., 2008), and the arrows indicate parasitic clades. Removal/addition of the long-branching sequence (dotted line) did not change the tree topology. Micrographs show the organisms (including hosts) whose genomic DNA has been sequenced (not available for FACS-derived samples LP-1 and L67-2). L67-3 represents a disrupted copepod (identified by the extremities) with an attached cyst containing spores of the parasitic dinoflagellate Chytriodinium (Ch). The copepod was isolated after the cyst burst and released the spores, but it is not clear if the MALV is associated with the animal or the dinoflagellate. The micrograph of L67-6 shows a tintinnid ciliate. Since two non-related MALV II 18 S rRNA gene sequences (with 93.8% similarity; Supplementary Figure 2) and one 28 S rRNA gene sequence were obtained from three different contigs of this sample, its phylogenetic position is not shown in the SSU/LSU rRNA gene tree. L67-1 and L67-4 are assumed to represent host-free MALV cells. L67-4 is represented by two phylotypes with a SSU and a LSU sequence similarity of 97.9% and 98.6%, respectively. Length of the cleaned assembly, number of redundant/non-redundant KO homologs, number of hits to Tara Oceans V9 data (not available for L67-6, for which the V9 region was not sampled), and collection depth are presented beside each photo.