Contig sequences were annotated as plasmidic using manual read tracking and four different software tools: PlasmidFinder with a minimum coverage of 75 % and the KMA mapping method (Carattoli et al., 2014); PlasForest v1.2 with a batch size of 500 (Pradier et al., 2021); Platon v1.7 in “accuracy” and “meta” modes (Schwengers et al., 2020); and PlasX using MMseqs v10.6 (Yu et al., 2024).
How to detect plasmidic contigs
For each sample, mapping rates were calculated concerning the total number of reads in that sample, both for all contig-mapping reads and specifically for those reads classified by Kraken2 to at least one species of the GTDB plasmids database, hereafter referred to as “GTDBp reads.”
To figure out the role of plasmid in microbial population
Computational studies that analyzed HGT events among bacterial genomes revealed that HGT frequency positively and strongly correlates with the similarity of tRNA pools between donors and acceptors
We tested a broad range of Enterobacteriaceae conjugative plasmids for their sensitivity to the growth stage of the donors and identified three distinct regulation types.