The Peri-Centromeric Heterochromatin of Barley is a Permissive Environment for Gene Diversity, Expression and Evolution

The low-recombining peri-centromeric heterochromatin (LR-PCH) of barley contains roughly a quarter of the genes for the species, in a genomic environment that has been reported to be antagonistic to both the expression and evolution of genes. In this study the diversity, expression and evolution of genes in the LR-PCH of barley were compared to their counterparts in the euchromatin. Ka and Ks analysis of gene evolution within wild barley shows low nucleotide diversity in the LR-PCH but no major difference in protein evolution between these genomic environments, despite the severely restricted recombination of the LR-PCH, showing that this environment is permissive for gene evolution. Similarly, no significant differences in average transcript level were detectable between the LR-PCH and the euchromatin, suggesting that accessibility of a barley gene to the transcription machinery is unaffected by its global chromatin compartment. Lastly, the effects of long-term LR-PCH residency on gene evolution was explored by examining duplicated gene pairs derived from the cereal grass whole genome duplication event ca. 60 MYa. 290 high confidence pairs were identified, or roughly 2% of barley’s gene complement. These are distributed between the LR-PCH and the euchromatin, with a significant bias towards the latter. Again, we see no obvious impact of the LR-PCH on the sequence evolution of gene pairs. However, the LR-PCH contains slightly fewer gene duplicates than the euchromatin, consistent with a lower creation rate by unequal homologous recombination.