Insights into the evolution of repetitive genes: Structure, organization, and expression of histone genes in Drosophila virilis

This work elucidates the repeat structure and genomic organization of histone genes and the tissue expression patterns of H1 variants in Drosophila virilis. Histone genes are a class of moderately repetitive genes which undergo a phenomenon known as concerted evolution. This phenomenon is observed by high DNA sequence identity between individual copies of the repetitive genes within a species, but less so between species. Despite the term ‘concerted evolution’ being coined almost two decades ago, the mechanisms involved and factors that influence them are still not understood. Even though individual copies of the repetitive genes are highly homogenized within a species, variation does exist. One method used to clarify the relative importance of various mechanisms to concerted evolution has been to survey this variation across an entire repetitive array. Two difficulties that have hampered such analyses have been the large size of these repetitive arrays and the lack of sufficient variation to map them. A cloning vector that can stably hold large amounts of this type of DNA is also required. In this study, we have analyzed D. virilis genomic DNA, P1 clones, subcloned histone repeats, and H1 DNA sequence variants. We find the presence of enough variation to allow for its mapping across both cytogenetic histone loci of this species. Two types of structures and arrangements exist for histone repeats in D. virilis , with tandem H1-lacking quartets and not strictly-tandem H1-containing quintets. The quintets reside at both loci, while the quartets reside at only the major locus. The quintets have an unusually high degree of repeat length variation which maps to the H4-H2A intergenic spacer and appears to be caused by the presence of the mobile genetic element pDv. Using the P1 clones, a preliminary contig assembly for both cytogenetic loci has been generated. DNA sequence from subcloned histone repeats depicts a mosaic pattern of variation. The distribution of H1 DNA sequence variants has been mapped and their expression levels analyzed. We present a model for the evolution of the structure and organization of histone repeats in D. virilis with implications for all repetitive DNAs.