FIG 1.

Challenges associated with existing databases for MGE colocalization analysis. (A) Example accessory genes found within MGE databases, with the databases grouped by the element class that they are intended to contain. Annotation criteria and databases are provided in Supplementary Methods. ACLAME is a database of multiple element types, thus is labeled “multiple.” (B) Synthesis of Slizovskiy et al. (10). Overlap in MGE/ARG databases produces ambiguous annotations of mobile ARGs. (C) Synthesis of Smyshlyaev et al. (38). The largest phylogenetic subgroup of tyrosine recombinases includes the xerC/xerD family of simple tyrosine recombinases, meaning studies using keyword search-based databases are likely to inadvertently include false-positive sequences. IGE, integrative genomic elements; IS, insertion sequence.