Abstract
BackgroundThere has been remarkably little study of nucleotide substitution rate variation among plant nuclear genes, in part because orthology is difficult to establish. Orthology is even more problematic for intergenic regions of plant nuclear genomes, because plant genomes generally harbor a wealth of repetitive DNA. In theory orthologous intergenic data is valuable for studying rate variation because nucleotide substitutions in these regions should be under little selective constraint compared to coding regions. As a result, evolutionary rates in intergenic regions may more accurately reflect genomic features, like recombination and GC content, that contribute to nucleotide substitution.ResultsWe generated a set of 66 intergenic sequences in Arabidopsis lyrata, a close relative of Arabidopsis thaliana. The intergenic regions included transposable element (TE) remnants and regions flanking the TEs. We verified orthology of these amplified regions both by comparison of existing A. lyrata – A. thaliana genetic maps and by using molecular features. We compared substitution rates among the 66 intergenic loci, which exhibit ~5-fold rate variation, and compared intergenic rates to a set of 64 orthologous coding sequences. Our chief observations were that the average rate of nucleotide substitution is slower in intergenic regions than in synonymous sites, that rate variation in both intergenic and coding regions correlate with GC content, that GC content alone is not sufficient to explain differences in rates between intergenic and coding regions, and that rates of evolution in intergenic regions correlate negatively with gene density.ConclusionOur observations indicated that mutation rates vary among genomics regions as a function of base composition, suggesting that previous observations of "selective constraint" on non-coding regions could more accurately be attributed to a GC effect instead of selection. The negative correlation between nucleotide substitution rate and gene density provides a potential neutral explanation for a previously documented correlation between gene density and polymorphism levels within A. thaliana. Finally, we discuss potential forces that could contribute to rapid synonymous rates, and provide evidence to suggest that transcription-related mutation contributes to rate differences between intergenic and synonymous sites.
Highlights
There has been remarkably little study of nucleotide substitution rate variation among plant nuclear genes, in part because orthology is difficult to establish
The intergenic data are contrasted to a second data set consisting of large (> 400 bp) exonic sequences from A. lyrata and A. thaliana. With these two data sets, we address several questions about Arabidopsis nucleotide substitution rates, such as: i) do intergenic sequences evolve at rates similar to synonymous sites in coding data? ii) do any genomic features, like GC content or recombination, correlate with nucleotide substitution rate variation among loci? iii) what can be inferred about the relative contribution of mutation and selection to nucleotide substitution? and iv) do intergenic regions provide any hints to the mechanisms that contribute to genome size differences between A. lyrata and A. thaliana?
It is clear that GC content is a major determinant of evolutionary rate variation, between sequence types and among loci
Summary
There has been remarkably little study of nucleotide substitution rate variation among plant nuclear genes, in part because orthology is difficult to establish. In theory orthologous intergenic data is valuable for studying rate variation because nucleotide substitutions in these regions should be under little selective constraint compared to coding regions. Evolutionary rates in intergenic regions may more accurately reflect genomic features, like recombination and GC content, that contribute to nucleotide substitution. The primary processes that contribute to nucleotide substitution rates are mutation, selection, and population history, but their relative contributions can vary substantially among genes and genomic regions. Our understanding about the evolutionary forces that contribute to nucleotide substitution rates has been based primarily on the study of coding regions. The important point is that it can be difficult to disentangle the contribution of selection and mutation to rate variation among coding regions
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