The influence of chromosome organization on genome evolution in Sulfolobus archaea

The DNA sequence and structural organization of chromosomes influence the expression of genetic information. Recent work has revealed that in the crenarchaeon Sulfolobus, chromosomes spatially organize into A and B compartments, having high and low gene expression respectively. Additionally, the A compartment contains the replication origins. Here, we characterize the influence of replication and compartmentalization on primary sequence evolution in multiple Sulfolobus species. Distance from an origin of replication shapes mutation rates within the B but not the A compartment, highlighting a possible effect of replication termination. Additionally, the A compartment is less mutagenic with stronger purifying selection than the B compartment. Interestingly, implementation of the Assay for Transposase-Accessible Chromatin (ATAC-Seq) reveals the B compartment is less accessible than the A compartment. Taken together, our data suggest that compartmentalization can influence chromosome evolution, with the A compartment serving as a haven for stable maintenance of gene sequence while the B compartment is specialized in diversification.