Nanomotif: Leveraging DNA Methylation Motifs for Genome Recovery and Host Association of Plasmids in Metagenomes from Complex Microbial Communities

2024/05/02 by Søren Heidelbach, Sebastian Mølvang Dall, Jeppe Støtt Bøjer +10 · 1 voice · 2 citations
Biochemistry, Genetics and Molecular Biology · #Genomics and Phylogenetic Studies #RNA modifications and cancer #Protist diversity and phylogeny

paper · pdf · doi:10.1101/2024.04.29.591623

openalex publication_date 2024/05/02 · openalex created_date 2024/05/03 · openalex updated_date 2026/07/15

Abstract

Abstract DNA methylation is found across all domains of life but is a rarely used feature in recovery of metagenome-assembled genomes (MAGs). Recently, Oxford Nanopore introduced all context methylation detection models. We leveraged this to develop Nanomotif, which identifies and exploits methylation motifs for enhanced MAG recovery. We demonstrate how Nanomotif enables database-independent contamination removal from high-quality MAGs and host association of plasmids directly from Nanopore sequencing data in complex metagenomes.

Citations

• Pfam: The protein families database in 2021
• tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes
• CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
• Identification of mobile genetic elements with geNomad

Cited by

• Long-read metagenomics and methylation-based binning allow the description of the emerging high-risk antibiotic resistance genes and their hidden hosts in complex communities
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Discussions

• If you are looking for a somewhat similar ONT tool, Nanomotif might be a place to start: doi.org/10.1101/2024... [bsky, 0 points, 0 comments]

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