Please note: This PhD seminar will take place online.

Monireh Safari, PhD candidate
David R. Cheriton School of Computer Science

Supervisor: Professor Lila Kari

Temperature is a fundamental constraint on biological systems, yet how adaptation to temperature is reflected in a genome-wide sequence of organization remains unclear. Here, we show that genome-wide distributions of short DNA sequences contain a robust signal of thermal adaptation that is largely independent of phylogeny. Using Structural Topic Modelling (STM), a machine-learning approach for identifying groups of co-occurring sequence motifs, we analyze canonical 6-mer and 9-mer frequency profiles of bacterial and archaeal genome proxies and identify motif families systematically associated with thermophiles and psychrophiles. In bacterial thermophiles, these motif families are dominated by highly specific C-stacked, G-stacked, and CG-periodic hexamers. In contrast, bacterial psychrophiles are characterized by low-complexity A-run, T-run, and AT-run motifs. Thermophilic archaea exhibit a distinct CTAG-centered motif family, suggesting that different domains may adapt to similar environmental constraints through different sequence-level solutions. Related motif families are recovered across diverse microbial lineages, indicating that thermal-adaptation signals can extend beyond shared ancestry. Notably, the identified motif families constitute only a remarkably small and highly selective subset of the hundreds of possible G+C-rich and A+T-rich sequence motifs. This indicates that thermal adaptation is associated with specific sequence architectures rather than broad shifts in nucleotide composition. These patterns are consistent with known sequence-dependent DNA physical properties, including differences in base-stacking interactions and conformational flexibility. Together, our results suggest that thermal adaptation is reflected in highly selective sequence architectures associated with DNA physical properties, revealing a physical dimension of genome organization beyond phylogenetic history and nucleotide composition. 

Attend this PhD seminar virtually on Zoom.