DATA AVAILABILITY STATEMENT : In-house software tool SeqWord MotifMapper 3.1 developed for this study for visualization and analysis of methylation profiles supplemented with all input files: GBK genomes and GFF files generated by the program ipdSummary for H. lucertense and its symbiont, containing genome methylation data at different growth conditions: https://zenodo.org/doi/10.5281/zenodo.10700787. Accession numbers in the NCBI repository: Whole genome sequences: Halorhabdus sp. SVX81 – CP104322; H. lucertense SVX82 – CP104741-44; and Ca. Na. occultus SVXNc – CP104395; PacBio raw read data: Archaeal consortium I, PacBio Exp 1.1 – SRX22141242; Archaeal consortium I, PacBio Exp 1.2 – SRX22141245; Archaeal consortium II, PacBio Exp 2.1 – SRX22141234; Archaeal consortium II, PacBio Exp 2.2 – SRX22141235; Archaeal consortium III, PacBio Exp 3.1 – SRX22141243; Archaeal consortium III, PacBio Exp 3.2 – SRX22141244; Archaeal consortium IV, PacBio Exp 4 – SRX22141246; RNA-seq data: Archaeal consortium I, Illumina-RNA Exp 1.1 – SRX22141247; Archaeal consortium I, Illumina-RNA Exp 1.2 – SRX22141248; Archaeal consortium II, Illumina-RNA Exp 2.1 – SRX22141249; Archaeal consortium I, Illumina-RNA Exp 2.2 – SRX22141236; Archaeal consortium III, Illumina-RNA Exp 3.1 – SRX22141237; Archaeal consortium III, Illumina-RNA Exp 3.2 – SRX22141238; Archaeal consortium IV; Archaeal consortium IV, Illumina-RNA Exp 4.1 – SRX22141239; Archaeal consortium IV, Illumina-RNA Exp 4.2 – SRX22141240; Illumina-RNA Exp 4.3 – SRX22141241; PacBio methylation data: H. lucentense Exp.I – SUPPF_0000005533; H. lucentense Exp.II – SUPPF_0000005534; H. lucentense Exp.III – SUPPF_0000005535; H. lucentense Exp.IV – SUPPF_0000005536; Ca. Nanohaloarchaeota archaeon SVXNc Exp.II – SUPPF_0000005537; Ca. Nanohaloarchaeota archaeon SVXNc Exp.IV – SUPPF_0000005538.
SUPPLEMENTARY FIGURE S1. Atlas view of the genome of H. lucertense SVX82g composed of the chromosome and the three plasmids shown as brown and dark-green arcs. Genomic islands identified by the SeqWord Genome Island Sniffer and the respective metrics: GC content; the ratio of generalized relative variance (GRV) versus relative variance (RV) of distribution of nucleotide tetramers normalized by GC content (n1_4mer); and distance D between local and global tetramer frequency patterns calculated in a 5 kbp sliding window stepping 2 kbp used for detection of genomic islands (see http://seqword.bi.up.ac.za/sniffer/index.html for more detail) are shown respectively by pink blocks and coloured histograms as explained in the legend. Locations of methyltransferase (MT) and restriction endonuclease (RE) genes are depicted by triangle red marks.
SUPPLEMENTARY FIGURE S2. Venn diagrams, contingency tables, and estimated Chi2 metrics visualize the distribution of unmethylated CTAG motifs on the chromosome (A) and the plasmids (B); and unmethylated CCTTG motifs on the chromosome (C) and the plasmids (D) of H. lucertense SVX82 in different experiments: (I) pure (axenic) culture on d-xylose; (II) binary culture with the ectosymbiont Ca. N. occultus SVXNc on d-xylose; (III) binary culture with Halorabdus sp. SVX81 on xylan; (IV) trinary culture with Halorabdus sp. SVX81 and the ectosymbiont Ca. N. occultus SVXNc on xylan.
SUPPLEMENTARY FIGURE S3. Venn diagrams, contingency tables, and estimated Chi2 metrics visualize the distribution of unmethylated GTCGAGG motifs on the chromosome (A) and the plasmids (B); and unmethylated GRAGAAG motifs on the chromosome (C) and the plasmids (D) of H. lucertense SVX82 in different experiments: (I) pure (axenic) culture on d-xylose; (II) binary culture with the ectosymbiont Ca. N. occultus SVXNc on d-xylose; (III) binary culture with Halorabdus sp. SVX81 on xylan; (IV) trinary culture with Halorabdus sp. SVX81 and the ectosymbiont Ca. N. occultus SVXNc on xylan.
SUPPLEMENTARY FIGURE S4. Venn diagrams, contingency tables, and estimated Chi2 metrics visualize the distribution of methylated GDGcHC motifs on the chromosome (A) and the plasmids (B) of H. lucertense SVX82 in different experiments: (I) pure (axenic) culture on d-xylose; (II) binary culture with the ectosymbiont Ca. N. occultus SVXNc on d-xylose; (III) binary culture with Halorabdus sp. SVX81 on xylan; (IV) trinary culture with Halorabdus sp. SVX81 and the ectosymbiont Ca. N. occultus SVXNc on xylan.
SUPPLEMENTARY TABLE S1. Composition of consortia used in this study (120 h of cultivation).
SUPPLEMENTARY TABLE S2. SRA NCBI database accession numbers of the raw SMRT PacBio genomic reads and Illumina RNA reads generated for this study.
SUPPLEMENTARY TABLE S3. Protein coding genes H. lucertense SVX82 with cTAG methylation within 20 bp upstream of the start codon.
SUPPLEMENTARY TABLE S4. Methylation and expression of genes with multiple GRAGa G methylation motifs within their sequences.
SUPPLEMENTARY VIDEO S1. Three-dimensional (segmented) view of host (SVX82, maroon outer layer) and DPANN (SVXNc, cyan outer layer) interaction showing extensive membrane blebbing from the DPANN SVXNc at the DPANN-host interface.
