Fig. 3: Unique Heimdallarchaeal mobile elements with viral and transposable features.

a, CRISPR-targeted mobile elements in the two Heimdallarchaeum genomes with viral features (HeimV1 and HeimV2) and without viral features (HeimM1 and HeimM2). The orange/black solid/dashed lines highlight connections between the CRISPR spacers recovered from two geographically distant vent sites in the Gulf of California (Pescadero and Guaymas Basins) to their matching target (protospacers) within the two genomes derived from Pescadero. b–e, Gene synteny of HeimM1 and HeimM2, with legend as shown in c. All tRNA genes were annotated with amino acid abbreviations followed by their anticodon, for example, GlyCCC. b, HeimM1 was integrated next to C2 Cas gene operon and is targeted by a pair of C1 CRISPR spacers. c, HeimM2 contains a repeat peptide-encoding gene that was targeted by a Pescadero Basin spacer. d, HeimV2 was compared with its related transposons discovered in this study—aloposons. e, HeimV1 was compared with two other MAGs belonging to different clades within the Heimdall group. f, Left, normalized sequencing coverage around HeimV1, highlighted in the blue background. Light pink and dark pink show single- and paired-end sequencing on the same DNA sample; grey shows the paired-end sequencing data of a second DNA sample from a different culture. The dashed line highlights the V shape, a signature of the bidirectionally self-replicating circular virus genome. Each dot is an average value binned at a 1 kb interval. Right, illustration depicting the integrated (bottom) and replicating (top) circular states indicated by the plot on the left. The arrows indicate the genomic integration next to the tRNA gene GlyCCC by a viral integrase.