An important aspect of gene expression is DNA modification and chromatin structure. Maize seems to be in particular suited for this purpose because the portion of the genome representing active genes is rather small. The maize genome has an even higher percentage of repeat elements than the human genome, 85% versus 50%. Therefore, detection of such epigenetic marks in maize had to be highly enriched for a fraction of the genome. Indeed, this specific histone acetylation correlated well with transcribed genes and could be verified with many known examples of genetic loci. 

Transcriptional analysis of seed development has shown that many of them are not expressed despite a normal gene structure. That has prompted us to investigate how epigenetic silencing could play a role in repressing gene expression. We applied bisulfite DNA sequencing, which can detect the methylation of DNA sequences. The methylation pattern of specific gene clusters can then be related to the transcriptional activity of them during seed development. There were several findings:

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Duckweeds are ideal material for physiological, biochemical, and genomic studies because of their direct contact with medium, rapid growth and relatively small genome sizes. They are valuable for bio-manufacturing through genetic engineering technology. Progress in duckweed-based commercial products can be easily maintained by vegetative reproduction in aseptic cultivation for decades. The small size of the plant is ideal for maintaining diverse accessions and therefore ideal for DNA-level evolutionary studies. Some species, such as Lemna minor, are used by the Environmental Protection Agency (EPA) for measuring water quality; their growth rates are sensitive to a wide range of environmental contaminants such as metals, nitrates, and phosphates. Rapid growth also offers practical applications of duckweeds as a biofuel crop.

The Spirodela Polyrhiza (Greater Duckweed) Genome v3.1 has been sequenced by using 454 with 20X coverage and the assembly was of very high quality improved by FPC. 20 chromosome-aligned sequences and a pseudomolecule 0 containing all unsorted and short sequences. The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution by Cao, Hieu; Vu, Giang; Wang, Wenqin; Appenroth, Klaus; Messing, Joachim; Schubert, Ingo. New Phytologist, 2015.

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