The HypoMethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies)

To evaluate the usefulness of Reduced Representation Libraries (RRL) in species with large and highly repetitive genomes such as conifers, we employed Hypomethylated Partial Restriction (HMPR) on the genome of Norway spruce (Picea abies). The HMPR method preferentially removes the repetitive fraction of the genome, which is commonly hypermethylated. Hence, RRLs should be enriched for the hypomethylated gene space. For comparison a standard shotgun library was constructed and samples of the respective libraries were obtained through Sanger sequencing. We obtained a nine-fold gene enrichment, a value which is slightly higher than for other plant species. The higher relative efficiency of HMPR is probably a consequence of the large Norway spruce genome size since the probability of finding genes in a standard shotgun library is very small. The amount of repetitive DNA was reduced by 45% in the RRLs, demonstrating the ability to efficiently remove hypermethylated DNA. Annotating sequences ...