Evolution of Gene Direction on Chromosomes

Gene direction on a chromosome is a basic aspect of genome biology. In some sequenced genomes, genes with coordinated expression were sometimes reported to be clustered. To investigate the evolution of gene direction, we analyzed 2,061 genomes/chromosomes. Archaeans, bacteria, and protozoa have genes characterized mainly by same-direction neighbors, with up to 391 genes in tandem in protozoan Leishmania infantum. Whereas, fungi and photosynthetic protists have genes mainly characterized by opposite-direction neighbors.  Plant and animal species usually have more same-direction gene pairs than opposite-direction ones, but the difference is quite slim, and opposite patterns can be identified in some species. There is clearly a shift in gene direction during evolution of biological complexity.