Interactions Between the Genome and Epigenome in Arabidopsis Accessions

Phenotypic variation results from a combination of genetic and epigenetic differences. With the advent of deep sequencing, it is possible to examine the consequences of genetic polymorphisms genome-wide.  Arabidopsis thaliana provides an excellent model for such a study as it exists in the wild as a collection of naturally occurring inbred populations, reducing allelic complexity and yet providing a rich source of phenotypic variation. In collaboration with 454, we generated a de novo assembly of a Cape Verde Island (Cvi-0) accession. A comparison to Col-0 shows greater than 3% sequence difference between these accessions in the form of SNPs, indels, and larger structural variations. Using the Cvi-0 assembly as a reference, we have mapped the Cvi-0 transcriptome, methylome and smRNAome. A comparison of methylomes between Cvi-0, Col-0 and the Landsberg Erecta (Ler-0) accession reveals hundreds of accession–specific epialleles, some of which silence expression and are reversible in the DNA methyltransferase mutant, met1-1.Many epialleles can be explained by transposition events, and direct and inverted repeats of genes. About a third of epialleles are found to occur in closely related gene families suggesting a signifcant role for RNA directed DNA methylation occurring in trans.