Reply to: Genome contamination may lead to an overestimation of horizontal gene transfer inferences
Abstract
We thank Godron et al. for their interest in our previous article 1 and their detailed Matters Arising analysis of potential genome contamination 2 . Godron et al. 2 argue that many of the putative horizontal gene transfer (HGT) events we identified using Sequence Read Archive (SRA) data were actually artifacts of contamination. They report that 30 of the 34 transfer events identified in our confirmatory analysis likely arose from contaminant sequences rather than true host acquisitions. For example, in one Staphylococcaceae isolate (SRA: ERR212931) where we reported a catI resistance gene alongside the IS1 mobile element, their re-assembly indicated that the contig was derived from Acinetobacter contaminant DNA.
Fields of Study & Subjects
Genetic Associations and Epidemiology
Evolution and Genetic Dynamics
Genetic Mapping and Diversity in Plants and Animals
Publication details
- Journal / source
- Nature Communications
- Publisher
- Springer Science and Business Media LLC
- Volume
- 17
- Issue
- 1
- Publication date
- 19 May 2026
- Language
- EN