Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.

ABSTRACT: Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue remains are absent. Detecting ancient plant and animal DNA in environmental samples relies on using extensive eukaryotic reference genome databases for profiling metagenomics data. However, many eukaryotic genomes contain regions with high sequence similarity to microbial DNA, which can lead to the misclassification of bacterial and archaeal reads as eukaryotic. This issue is especially problematic in ancient eDNA datasets, where plant and animal DNA is typically present at very low abundance. In this study, we present a method for identifying bacterial- and archaeal-like sequences in eukaryotic genomes and apply it to nearly 3,000 reference genome

SUBMITTER: Oskolkov N 

PROVIDER: S-EPMC12491943 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature