Support for multiple classes of local expression clusters in XXXX , but no evidence for gene order conservation.

@entity375 @entity238
BACKGROUND: Gene order in eukaryotic genomes is not random, with genes with similar expression profiles tending to cluster. In @entity375 , the model taxon for gene order analysis, such syntenic clusters of non-homologous genes tend to be conserved over evolutionary time. Whether similar clusters show gene order conservation in other lineages is, however, undecided. Here, we examine this issue in @entity238 using high-resolution chromosome rearrangement data. RESULTS: We show that @entity238 has at least three classes of expression clusters: first, as observed in mammals, large clusters of functionally unrelated housekeeping genes; second, small clusters of functionally related highly co-expressed genes; and finally, as previously defined by Spellman and Rubin, larger domains of co-expressed but functionally unrelated genes. The latter are, however, not independent of the small co-expression clusters and likely reflect a methodological artifact. While the small co-expression and housekeeping/essential gene clusters resemble those observed in @entity375 , in contrast to @entity375 , we see no evidence that any of the three cluster types are preserved as synteny blocks. If anything, adjacent co-expressed genes are more likely to become rearranged than expected. Again in contrast to @entity375 , in @entity238 , gene pairs with short intergene distance or in divergent orientations tend to have higher rearrangement rates. These findings are consistent with co-expression being partly due to shared chromatin environment. CONCLUSIONS: We conclude that, while similar in terms of cluster types, gene order evolution has strikingly different patterns in @entity375 and in @entity238 , although recombination is associated with gene order rearrangement in both.
