Extremeophiles and Extreme Environments

Environment And Taxonomy Shape The Genomic Signature Of Prokaryotic Extremophiles

By Keith Cowing
Status Report
December 28, 2023
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Environment And Taxonomy Shape The Genomic Signature Of Prokaryotic Extremophiles
Number of true genera (blue) vs. the number of genera identified by seven clustering algorithms, for each environment category in the Temperature Dataset (left), respectively the pH Dataset (right). Only true genera that are represented by more than two sequences in the respective dataset (Temperature or pH) are considered, and only clusters meeting the quality criteria are counted. — biorxiv.org

This study provides comprehensive quantitative evidence suggesting that adaptations to extreme temperatures and pH imprint a discernible environmental component in the genomic signature of microbial extremophiles.

Both supervised and unsupervised machine learning algorithms were used to analyze genomic signatures, each computed as the k-mer frequency vector of a 500 kbp DNA fragment arbitrarily selected to represent a genome. Computational experiments classified/clustered genomic signatures extracted from a curated dataset of ∼700 extremophile (temperature, pH) bacteria and archaea genomes, at multiple scales of analysis, 1 ≤k ≤6.

The supervised learning resulted in high accuracies for taxonomic classifications at 2 ≤k ≤6, and medium to medium-high accuracies for environment category classifications of the same datasets at 3 ≤k ≤6. For k = 3, our findings were largely consistent with amino acid compositional biases and codon usage patterns in coding regions, previously attributed to extreme environment adaptations.

The unsupervised learning of unlabelled sequences identified several exemplars of hyperthermophilic organisms with large similarities in their genomic signatures, in spite of belonging to different domains in the Tree of Life.

Environment and taxonomy shape the genomic signature of prokaryotic extremophiles, biorxiv.org

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