Coexpression of linked gene pairs persists long after their separation. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes. The evolutionary dynamics of eukaryotic gene order. Altogether, our results provide insights on the evolution of gene clustering as well as a broad catalogue of evolutionarily conserved gene clusters whose function remains to be elucidated. Finally, horizontal gene transfer of entire clusters was somewhat restricted, with the exception of those associated with secondary metabolism. However, convergent evolution-that is, independent appearance of the same cluster-was more prevalent than anticipated. We found that most clusters originated once and were transmitted vertically, coupled to differential loss. We used phylogenomics to characterize the evolutionary history of these clusters. Additionally, most clusters did not encode transcription factors, suggesting that they are regulated distally. We inferred 12,120 cluster families, which comprised roughly one third of the gene space and were enriched in genes associated with diverse cellular functions. We surveyed 341 fungal genomes to discover gene clusters shared by different species, independently of their functions. Furthermore, mechanisms of the formation, maintenance and evolution of gene clusters remain unknown. However, little is known about how gene clustering patterns vary among taxa or with respect to functional roles. In eukaryotes, multiple examples of metabolic gene clusters are known, particularly among fungi and plants. Gene clusters comprise genomically co-localized and potentially co-regulated genes that tend to be conserved across species.
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