Abstract
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.
Highlights
The genome of an organism usually comprises various types of genes and elements; these include single-copy genes, duplicated genes, dispersed multigene families, clustered multigene families, repetitive elements and transposons, among others (Adams et al, 2000)
Structure of the histone gene repeating units from D. lutescens, D. takahashii and D. pseudoobscura To determine the structure and nucleotide sequence of the repeating units encoding the histone genes in D. lutescens, D. takahashii and D. pseudoobscura, polymerase chain reaction (PCR) products amplified from genomic DNA were cloned into a plasmid vector
The relationship between divergence and functional constraint suggested that negative selection is acting and that it has a marked influence on nucleotide divergence
Summary
The genome of an organism usually comprises various types of genes and elements; these include single-copy genes, duplicated genes, dispersed multigene families, clustered multigene families, repetitive elements and transposons, among others (Adams et al, 2000). Repeating units comprising the five replication-dependent histone genes (H1, H2A, H2B, H3 and H4) are tandemly repeated approximately 110 times in Drosophila melanogaster (Lifton et al, 1977). The members of this multigene histone family in D. melanogaster have evolved in a concerted fashion (Coen et al, 1982; Matsuo and Yamazaki, 1989b; Kakita et al, 2003). Analyzing the histone genes from various Drosophila species could provide important information about mutation bias and population size, among other issues
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