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

• Published in: BMC genomics Vol. 9; no. 1; p. 282
• Main Authors: Chan, Agnes P, Melake-Berhan, Admasu, O'Brien, Kimberly, Buckley, Stephanie, Quan, Hui, Chen, Dan, Lewis, Matthew, Banks, Jo Ann, Rabinowicz, Pablo D
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 12.06.2008; BioMed Central; BMC
• Subjects: Base Composition; Base Sequence; DNA damage; DNA Methylation; DNA Primers - genetics; DNA, Chloroplast - chemistry; DNA, Chloroplast - genetics; DNA, Plant - chemistry; DNA, Plant - genetics; Epigenesis, Genetic; Expressed Sequence Tags; Genome, Plant; Genomic libraries; Influence; Molecular Sequence Data; Physiological aspects; Plant genetics; Repetitive Sequences, Nucleic Acid; Selaginella; Selaginellaceae - genetics; United States
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-9-282

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. 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. 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.