Evolution of the GC content of the histone 3 gene in seven Drosophila species

The Adenine/Thymine Deleterious Selection Model for GC Content Evolution at the Third Codon Position of the Histone Genes in Drosophila

The evolution of the GC (guanine cytosine) content at the third codon position of the histone genes (H1, H2A, H2B, H3, H4, H2AvD, H3.3A, H3.3B, and H4r) in 12 or more Drosophila species is reviewed. For explaining the evolution of the GC content at the third codon position of the genes, a model assuming selection with a deleterious effect for adenine/thymine and a size effect is presented. The applicability of the model to whole-genome genes is also discussed.

The histone genes cluster in Rhynchosciara americana and its transcription profile in salivary glands during larval development

In this work we report the characterization of the Rhynchosciara americana histone genes cluster nucleotide sequence. It spans 5,131 bp and contains the four core histones and the linker histone H1. Putative control elements were detected. We also determined the copy number of the tandem repeat unit through quantitative PCR, as well as the unequivocal chromosome location of this unique locus in chromosome A band 13. The data were compared with histone clusters from the genus Drosophila, which are the closest known homologues.

Evolution of GC content in the histone gene repeating units from Drosophila lutescens, D. takahashii and D. pseudoobscura

A subset of histone genes (H1, H2A, H2B and H4), which are encoded along with H3 within repeating units, were analyzed in Drosophila lutescens, D. takahashii and D. pseudoobscura to investigate the evolutionary mechanisms influencing this multigene family and its GC content. Nucleotide divergence among species was more marked in the less functional regions. A strong inverse relationship was observed between the extent of evolutionary divergence and GC content within the repeating units; this finding indicated that the functional constraint on a region must be associated with both divergence and GC content. The GC content at 3(rd) codon positions in the histone genes from D. lutescens and D. takahashii was higher than that from D. melanogaster, while that from D. pseudoobscura was similar. These evolutionary patterns were similar to those of H3 gene regions. Based on these findings, we propose that the evolutionary mechanisms governing nucleotide content at 3(rd) codon positions tend to eliminate A and T nucleotides more frequently than G and C nucleotides. These changes might be the consequence of negative selection and would result in GC-rich 3(rd) codon positions. In addition, interspecific differences in GC content, which exhibited the same pattern for all histone genes, could be explained by different selection efficiencies that result from changes in population size.

Changes in base composition bias of nuclear and mitochondrial genes in lice (Insecta: Psocodea)

While it is well known that changes in the general processes of molecular evolution have occurred on a variety of timescales, the mechanisms underlying these changes are less well understood. Parasitic lice ("Phthiraptera") and their close relatives (infraorder Nanopsocetae of the insect order Psocodea) are a group of insects well known for their unusual features of molecular evolution. We examined changes in base composition across parasitic lice and bark lice. We identified substantial differences in percent GC content between the clade comprising parasitic lice plus closely related bark lice (=Nanopsocetae) versus all other bark lice. These changes occurred for both nuclear and mitochondrial protein coding and ribosomal RNA genes, often in the same direction. To evaluate whether correlations in base composition change also occurred within lineages, we used phylogenetically controlled comparisons, and in this case few significant correlations were identified. Examining more constrained sites (first/second codon positions and rRNA) revealed that, in comparison to the other bark lice, the GC content of parasitic lice and close relatives tended towards 50 % either up from less than 50 % GC or down from greater than 50 % GC. In contrast, less constrained sites (third codon positions) in both nuclear and mitochondrial genes showed less of a consistent change of base composition in parasitic lice and very close relatives. We conclude that relaxed selection on this group of insects is a potential explanation of the change in base composition for both mitochondrial and nuclear genes, which could lead to nucleotide frequencies closer to random expectation (i.e., 50 % GC) in the absence of any mutation bias. Evidence suggests this relaxed selection arose once in the non-parasitic common ancestor of Phthiraptera + Nanopsocetae and is not directly related to the evolution of the parasitism in lice.

Molecular characterization and evolution of the repeating units of histone genes in Drosophila americana: coexistence of quartet and quintet units in a genome

Quintet and quartet repeating units of the histone genes in Drosophila americana were cloned and characterized. Nucleotide sequence analysis of the units showed that a 3175 bp unit contained the core histone genes but lacked the H1 gene ('quartet unit') while a 5025 bp unit contained all five histone genes ('quintet unit'). Comparative analysis suggested that these repeating units diverged before the separation of D. americana and D. virilis. Multiple forms of H1 genes, differing by 5.8% of amino acids, were found in D. americana. The genomic organization of the histone gene family in D. americana was found to be very similar to that of D. virilis.

Entropy and GC Content in the beta-esterase gene cluster of the Drosophila melanogaster subgroup

We perform spectral entropy and GC content analyses in the beta-esterase gene cluster, including the Est-6 gene and the psiEst-6 putative pseudogene, in seven species of the Drosophila melanogaster species subgroup. psiEst-6 combines features of functional and nonfunctional genes. The spectral entropies show distinctly lower structural ordering for psiEst-6 than for Est-6 in all species studied. Our observations agree with previous results for D. melanogaster and provide additional support to our hypothesis that after the duplication event Est-6 retained the esterase-coding function and its role during copulation, while psiEst-6 lost that function but now operates in conjunction with Est-6 as an intergene. Entropy accumulation is not a completely random process for either gene. Structural entropy is nucleotide dependent. The relative normalized deviations for structural entropy are higher for G than for C nucleotides. The entropy values are similar for Est-6 and psiEst-6 in the case of A and T but are lower for Est-6 in the case of G and C. The GC content in synonymous positions is uniformly higher in Est-6 than in psiEst-6, which agrees with the reduced GC content generally observed in pseudogenes and nonfunctional sequences. The observed differences in entropy and GC content reflect an evolutionary shift associated with the process of pseudogenization and subsequent functional divergence of psiEst-6 and Est-6 after the duplication event.

Divergence and heterogeneity of the histone gene repeating units in the Drosophila melanogaster species subgroup

The repeating units of the histone gene cluster containing the H1, H2A, H2B and H4 genes were amplified by PCR from the Drosophila melanogaster species subgroup, i.e., D. yakuba, D. erecta, D. sechellia, D. mauritiana, D. teissieri and D. orena. The PCR products were cloned and their nucleotide sequences of about 4.6-4.8kbp were determined to elucidate the mechanism of molecular evolution of the histone gene family. The heterogeneity among the histone gene repeating units was 0.6% and 0.7% for D. yakuba and D. sechellia, respectively, indicating the same level of heterogeneity as in the H3 gene region of D. melanogaster. Divergence of the genes among species even in the most closely related ones was much greater than the heterogeneity among family members, indicating a concerted mode of evolution for the histone gene repeating units. Among the species in the D. melanogaster species subgroup, the histone gene regions as well as 3rd codon position of the coding region showed nearly the same GC contents. These results suggested that the previous conclusion on analysis of the H3 gene regions, the gene family evolution in a concerted fashion, holds true for the whole histone gene repeating unit.