title: Genome-wide and single-base resolution DNA methylomes of the Pacific oyster Crassostrea gigas provide insight into the evolution of invertebrate CpG methylation.
abstract: BACKGROUND
  Studies of DNA methylomes in a wide range of eukaryotes have revealed both conserved and divergent characteristics of DNA methylation among phylogenetic groups. However, data on invertebrates particularly molluscs are limited, which hinders our understanding of the evolution of DNA methylation in metazoa. The sequencing of the Pacific oyster Crassostrea gigas genome provides an opportunity for genome-wide profiling of DNA methylation in this model mollusc.
  
  
  RESULTS
  Homologous searches against the C. gigas genome identified functional orthologs for key genes involved in DNA methylation: DNMT1, DNMT2, DNMT3, MBD2/3 and UHRF1. Whole-genome bisulfite sequencing (BS-seq) of the oyster's mantle tissues revealed that more than 99% methylation modification was restricted to cytosines in CpG context and methylated CpGs accumulated in the bodies of genes that were moderately expressed. Young repeat elements were another major targets of CpG methylation in oysters. Comparison with other invertebrate methylomes suggested that the 5'-end bias of gene body methylation and the negative correlation between gene body methylation and gene length were the derived features probably limited to the insect lineage. Interestingly, phylostratigraphic analysis showed that CpG methylation preferentially targeted genes originating in the common ancestor of eukaryotes rather than the oldest genes originating in the common ancestor of cellular organisms.
  
  
  CONCLUSIONS
  Comparative analysis of the oyster DNA methylomes and that of other animal species revealed that the characteristics of DNA methylation were generally conserved during invertebrate evolution, while some unique features were derived in the insect lineage. The preference of methylation modification on genes originating in the eukaryotic ancestor rather than the oldest genes is unexpected, probably implying that the emergence of methylation regulation in these 'relatively young' genes was critical for the origin and radiation of eukaryotes.
authors.forename: Xiaotong
authors.initials: X
authors.lastname: Wang
authors.forename: Qiye
authors.initials: Q
authors.lastname: Li
authors.forename: Jinmin
authors.initials: J
authors.lastname: Lian
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.forename: Lijun
authors.initials: L
authors.lastname: Jin
authors.forename: Huimin
authors.initials: H
authors.lastname: Cai
authors.forename: Fei
authors.initials: F
authors.lastname: Xu
authors.forename: Haigang
authors.initials: H
authors.lastname: Qi
authors.forename: Linlin
authors.initials: L
authors.lastname: Zhang
authors.forename: Fucun
authors.initials: F
authors.lastname: Wu
authors.forename: Jie
authors.initials: J
authors.lastname: Meng
authors.forename: Huayong
authors.initials: H
authors.lastname: Que
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Fang
authors.affiliation: Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China. xguo@hsrl.rutgers.edu.
authors.forename: Ximing
authors.initials: X
authors.lastname: Guo
authors.forename: Guofan
authors.initials: G
authors.lastname: Zhang
mesh_terms: D000818:Animals; D005075:Biological Evolution; D022762:CCAAT-Enhancer-Binding Proteins / Q000235:genetics; D018899:CpG Islands; D049896:Crassostrea / Q000145:classification / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D007448:Invertebrates / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D022762:CCAAT-Enhancer-Binding Proteins; D004268:DNA-Binding Proteins; D004247:DNA; D004248:DNA (Cytosine-5-)-Methyltransferases