Identification of plasmid content through plasmid partitioning
genes
Plasmid content was approximated by the number of plasmid partitioning
genes present in each assembly, which have been shown to be unique to
specific plasmid types and exist as single copies in Borrelia (S.
Casjens & Huang, 1993; S. R. Casjens et al., 2012; Fraser, Casjens, &
Huang, 1997). Identification of plasmid partitioning genes was performed
as outlined in Becker et al. (2020) (see Suppl. Met.). Briefly, we used
BLAST v.2.8.1 (Altschul, Gish, Miller, Myers, & Lipman, 1990; Camacho
et al., 2009) (algorithm: blastn ) to search for the presence of
plasmid partitioning genes of the PFam32, 49, 50, and 57.62 families in
the assembled SPAdes contigs. Hits were removed if they did not cover
more than half the length of the references and had lower than 80%
percent identity. After curation, we defined a plasmid being present if
at least one of the partitioning genes was present in the assembled
contigs.