title: Comparative analyses of DNA methylation and sequence evolution using Nasonia genomes.
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.
authors.affiliation: Bioinformatics and Biostatistics Laboratory, Interdisciplinary Program in Bioinformatics, Department of Statistics, Seoul National University, Seoul, Korea.
authors.forename: Jungsun
authors.initials: J
authors.lastname: Park
authors.forename: Zuogang
authors.initials: Z
authors.lastname: Peng
authors.forename: Jia
authors.initials: J
authors.lastname: Zeng
authors.forename: Navin
authors.initials: N
authors.lastname: Elango
authors.forename: Taesung
authors.initials: T
authors.lastname: Park
authors.forename: Dave
authors.initials: D
authors.lastname: Wheeler
authors.forename: John H
authors.initials: JH
authors.lastname: Werren
authors.forename: Soojin V
authors.initials: SV
authors.lastname: Yi
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D005075:Biological Evolution; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation; D019143:Evolution, Molecular; D017344:Genes, Insect; D049750:Genome, Insect; D009154:Mutation; D059645:Mutation Rate; D014863:Wasps / Q000235:genetics*