Comparative Analyses of DNA Methylation and Sequence Evolution Using Nasonia Genomes
Open Access
- 20 June 2011
- journal article
- research article
- Published by Oxford University Press (OUP) in Molecular Biology and Evolution
- Vol. 28 (12), 3345-3354
- https://doi.org/10.1093/molbev/msr168
Abstract
The functional and evolutionary significance of DNA methylation in insect genomes remains to be resolved. Nasonia is well situated for comparative analyses of DNA methylation and genome evolution, since the genomes of a moderately distant outgroup species as well as closely related sibling species are available. Using direct sequencing of bisulfite-converted DNA, we uncovered a substantial level of DNA methylation in 17 of 18 Nasonia vitripennis genes and a strong correlation between methylation level and CpG depletion. Notably, in the sex-determining locus transformer, the exon that is alternatively spliced between the sexes is heavily methylated in both males and females, whereas other exons are only sparsely methylated. Orthologous genes of the honeybee and Nasonia show highly similar relative levels of CpG depletion, despite ∼190 My divergence. Densely and sparsely methylated genes in these species also exhibit similar functional enrichments. We found that the degree of CpG depletion is negatively correlated with substitution rates between closely related Nasonia species for synonymous, nonsynonymous, and intron sites. This suggests that mutation rates increase with decreasing levels of germ line methylation. Thus, DNA methylation is prevalent in the Nasonia genome, may participate in regulatory processes such as sex determination and alternative splicing, and is correlated with several aspects of genome and sequence evolution.Keywords
This publication has 40 references indexed in Scilit:
- The genome of the fire ant Solenopsis invictaProceedings of the National Academy of Sciences, 2011
- Draft genome of the red harvester ant Pogonomyrmex barbatusProceedings of the National Academy of Sciences of the United States of America, 2011
- Conserved role of intragenic DNA methylation in regulating alternative promotersNature, 2010
- Single base–resolution methylome of the silkworm reveals a sparse epigenomic mapNature Biotechnology, 2010
- Conservation and divergence of methylation patterning in plants and animalsProceedings of the National Academy of Sciences, 2010
- DNA Methylation and Genome Evolution in Honeybee: Gene Length, Expression, Functional Enrichment Covary with the Evolutionary Signature of DNA MethylationGenome Biology and Evolution, 2010
- Functional Conservation of DNA Methylation in the Pea Aphid and the HoneybeeGenome Biology and Evolution, 2010
- DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis melliferaProceedings of the National Academy of Sciences, 2009
- PAML 4: Phylogenetic Analysis by Maximum LikelihoodMolecular Biology and Evolution, 2007
- Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genomeNature Genetics, 2007