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  1. Nov 2022
    1. When we expanded this analysis to chromosome-wide gene-gene correlations, we discovered a striking ‘X-shaped’ pattern of gene expression covariance (Fig. 1D). Beyond the expected diagonal reflecting coordinated gene expression at the level of operons, the anti-diagonal reflected correlations between genes at a similar distance from the origin of replication, between the “arms” of the circular chromosome, as well as a correlation between genes at the origin and terminus

      It would be really interesting to compare the patterns you observe here with the X-like genome inversion patterns that we and others have reported (e.g., see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC16139/). These patterns basically show that the distance a gene is from the origin of replication is conserved but the side of the origin it is on is not.

      Those inversion patterns have been seen in some but not all comparisons of closely related bacterial and archaeal genomes. So it seems there are some taxa where the distance a gene is from the origin is not conserved over evolutionary time. It would be interesting to know if these taxa show the X-like patternb you report for gene expression.