Data from: MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild growing species

Methylation of DNA cytosines affects whether transposons are silenced and
genes are expressed, and is a major epigenetic mechanism whereby plants
respond to environmental change. Analyses of methylation-sensitive
amplification polymorphism (MS-AFLP or MSAP) have been often used to
assess methyl-cytosine changes in response to stress treatments and, more
recently, in ecological studies of wild plant populations. MSAP technique
does not require a sequenced reference genome and provides many anonymous
loci randomly distributed over the genome for which the methylation status
can be ascertained. Scoring of MSAP data, however, is not straightforward,
and efforts are still required to standardize this step to make use of the
potential to distinguish between methylation at different nucleotide
contexts. Furthermore, it is not known how accurately MSAP infers
genome-wide cytosine methylation levels in plants. Here, we analyse the
relationship between MSAP results and the percentage of global cytosine
methylation in genomic DNA obtained by HPLC analysis. A screening of
literature revealed that methylation of cytosines at cleavage sites
assayed by MSAP was greater than genome-wide estimates obtained by HPLC,
and percentages of methylation at different nucleotide contexts varied
within and across species. Concurrent HPLC and MSAP analyses of DNA from
200 individuals of the perennial herb Helleborus foetidus confirmed that
methyl-cytosine was more frequent in CCGG contexts than in the genome as a
whole. In this species, global methylation was unrelated to methylation at
the inner CG site. We suggest that global HPLC and context-specific MSAP
methylation estimates provide complementary information whose combination
can improve our current understanding of methylation-based epigenetic
processes in nonmodel plants.