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Flowering Plant Methylomes Linked to Their Evolutionary History

NEW YORK (GenomeWeb) – A team from the US and Nigeria has characterized DNA methylation patterns in flowering plants, revealing relationships between these epigenetic marks and plants' evolutionary histories.

As they reported online today in Genome Biology, the researchers used whole-genome bisulfite sequencing to assess cytosine methylation patterns in dozens of angiosperm plant species. From these data, they detected differences in methylation context and the degree of gene body methylation depending on the flowering plant family in question.

"This study demonstrates that widespread variation in DNA methylation exists between flowering plant species," senior author Robert Schmitz, a genetics researcher at the University of Georgia, and his colleagues wrote. "The extent of the variation observed previously and now shows that there is still much to be learned about underlying causes of variation in this molecular trait."

The team explained that epigenetic features such as methylation and histone modifications "are integral to proper regulation of many aspects of the genome; including chromatin structure, transposon silencing, regulation of gene expression, and recombination."

To explore cytosine DNA methylation in more detail, the researchers performed MethylC sequencing on leaf tissue from 26 flowering plant species for which genome sequence assemblies were already available. The team then analyzed the new base resolution methylomes alongside available methylomes sequences for eight other angiosperms analyzed in the past, all within a flowering plant phylogenetic context.

In the Poaceae flowering plant family containing cereal crops and other grasses, for example, the researchers saw diminished levels of cytosine methylation in a certain sequence context in heterochromatin sequences, though sequences coding for genes appeared to have enhanced levels of that cytosine methylation.

On the other hand, the Brassicaceae family, which includes the model plant Arabidopsis thaliana as well as cabbage plants, had lower-than-usual levels of gene body methylation and declines in methylation of cytosines in specific sequence contexts such as the CHG cytosines separated by a guanine, thymine, adenine, or another cytosine base.

The general methylation features tended to correspond with the broad phylogenetic relationships between the plants. Even so, the team uncovered methylation variability within the flowering plant families and from one species to the next, with respect to sequence context, genome features, and genomic architecture.

"Extensive variation was found between species," Schmitz and his colleagues wrote, "both in levels of DNA methylation and distribution of DNA methylation, with the greatest variation being observed in non-[cytosine-guanine] contexts."