5.1. Identification of Borg genomes and manual genome curation

Metagenomic datasets on ggKbase (ggkbase.berkeley.edu) were searched for contigs with a dominant taxonomic profile matching Methanoperedens (Archaea; Euryarchaeaota; Methanomicrobia; Methanosarcinales; Candidatus Methanoperedens; Candidatus Methanoperedens nitroreducens). Manual genome binning was performed based on contig taxonomy, coverage, GC content (25% to 35% GC), and presence of nucleotide TRs.

Manual curation of Borg genomes was performed in Geneious Prime 2021.2.2 (https://www.geneious.com). It involved piecing together and verifying by paired reads placement, fragments of approximately the same GC content, sequencing reads coverage, phylogenetic profile, and relatedness to known Borgs into a single chromosome. Subsequently, careful visualization of the patterns of read discrepancies was used to locate local assembly errors, most of which were fixed by either relocating paired reads or introducing previously unplaced paired reads.