Study sheds light on ancient microbial dark matter unlvnews NatureMicrobiol
, which reports a lineage workflow completion estimate of only 92% based on a general bacterial marker set, despite the genome being sealed and therefore complete. Still, most of the markers in the general bacterial marker set were present consistently across the phylum. To provide a more accurate quality estimate, the general bacterial marker set was modified to account for a few systematically missing markers. Three markers, TIGR03594, PF13603.1 and PF02978.14 were excluded. PF02978.
To encourage accurate completeness estimates in future Omnitrophota assemblies, we extended this approach to find other PVC-group single-copy marker genes that occur with a similar pattern to the marker set used to calculate genome completeness and contamination. Marker sets for Planctomycetota, Verrucomicrobiota and Chlamydiota were individually extracted from the CheckM reference data. An auxiliary marker set was generated from the union of the PVC-group marker sets.
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