GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure
Yu Wan, Ryan R Wick, Justin Zobel, Danielle J Ingle, Michael Inouye, Kathryn E Holt
BMC GENOMICS | BMC | Published : 2020
BACKGROUND: Horizontal gene transfer contributes to bacterial evolution through mobilising genes across various taxonomical boundaries. It is frequently mediated by mobile genetic elements (MGEs), which may capture, maintain, and rearrange mobile genes and co-mobilise them between bacteria, causing horizontal gene co-transfer (HGcoT). This physical linkage between mobile genes poses a great threat to public health as it facilitates dissemination and co-selection of clinically important genes amongst bacteria. Although rapid accumulation of bacterial whole-genome sequencing data since the 2000s enables study of HGcoT at the population level, results based on genetic co-occurrence counts and s..View full abstract
YW was supported by a Melbourne International Research Scholarship from the University of Melbourne. KEH was supported by the Bill & Melinda Gates Foundation, Seattle and a Senior Medical Research Fellowship from the Viertel Foundation of Australia.