Open Access Research article

The highest-copy repeats are methylated in the small genome of the early divergent vascular plant Selaginella moellendorffii

Agnes P Chan1, Admasu Melake-Berhan1, Kimberly O'Brien13, Stephanie Buckley14, Hui Quan15, Dan Chen1, Matthew Lewis1, Jo Ann Banks2 and Pablo D Rabinowicz136*

Author Affiliations

1 J. Craig Venter Institute (JCVI), Rockville, MD 20850, USA

2 Department of Botany and Plant Pathology, Lilly Hall, Purdue University, West Lafayette, IN 47907, USA

3 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA

4 Program in Oncology, University of Maryland School of Medicine, Baltimore, MD 21201, USA

5 Applied Biosystems, 2130 Woodward St., Austin, TX 78744, USA

6 Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA

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BMC Genomics 2008, 9:282  doi:10.1186/1471-2164-9-282

Published: 12 June 2008

Abstract

Background

The lycophyte Selaginella moellendorffii is a vascular plant that diverged from the fern/seed plant lineage at least 400 million years ago. Although genomic information for S. moellendorffii is starting to be produced, little is known about basic aspects of its molecular biology. In order to provide the first glimpse to the epigenetic landscape of this early divergent vascular plant, we used the methylation filtration technique. Methylation filtration genomic libraries select unmethylated DNA clones due to the presence of the methylation-dependent restriction endonuclease McrBC in the bacterial host.

Results

We conducted a characterization of the DNA methylation patterns of the S. moellendorffii genome by sequencing a set of S. moellendorffii shotgun genomic clones, along with a set of methylation filtered clones. Chloroplast DNA, which is typically unmethylated, was enriched in the filtered library relative to the shotgun library, showing that there is DNA methylation in the extremely small S. moellendorffii genome. The filtered library also showed enrichment in expressed and gene-like sequences, while the highest-copy repeats were largely under-represented in this library. These results show that genes and repeats are differentially methylated in the S. moellendorffii genome, as occurs in other plants studied.

Conclusion

Our results shed light on the genome methylation pattern in a member of a relatively unexplored plant lineage. The DNA methylation data reported here will help understanding the involvement of this epigenetic mark in fundamental biological processes, as well as the evolutionary aspects of epigenetics in land plants.