Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. While most studies focus on protein-coding gene transfers, the Bhattacharya lab investigated exhaustive DNA transfers uncovering key insights into the connectivity of genomes in communities. Using the ‘term frequency-inverse document frequency’ (TF-IDF) approach, they found the majority of horizontal gene transfers detected were non-coding DNA, suggesting HGT is not solely a process of transferring adaptive, protein-coding genes. Several protein-coding HGTs were identified that encode functions like transposition, restriction-modification, and biofilm formation, indicating these mechanisms may facilitate HGT in this extremophilic microbial community. The TF-IDF approach can be used to identify recent horizontal gene transfers, including both coding and non-coding DNA transfers, within an extremophilic microbial community, providing insights into the mechanisms and ecological implications of genome connectivity.
Network of the final putative HGTs identified in this study, created in Cytoscape v.3.10.1 (Shannon et al. 2003). Nodes represent MAGs grouped by taxonomic class (for prokaryotes and viruses). Bacterial classes are shown as blue nodes, archaeal classes as orange nodes, the viral MAG that passed validation as a yellow node, and each Cyanidiophyceae species as its own green node. Edges represent the filtered putative HGT events detected between each group, with the directionality of the transfer indicated by the direction of the arrow. Edges coloured red indicate sequences putatively encoding transposases. Edges in green are the restriction endonuclease and site-specific DNA methyltransferase. Tan edges indicate other protein-coding sequences. Edge thickness represents the length of the putative HGT, i.e., thinner edges means shorter HGT regions (minimum = 100-bp) and thicker means longer HGT regions (maximum = 946-bp). Photo of Yellowstone National Park from D. Bhattacharya, representing the biological context that exists for facilitating these genomic interactions. Made with Biorender.com.
Van Etten J, Stephens TG, Bhattacharya D. Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community. Environ Microbiol. 2025 Feb;27(2):e70048. doi: 10.1111/1462-2920.70048. PMID: 39900484; PMCID: PMC11790422. https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.70048
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