Data from: The HypoMethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies)
Larsson, Hanna et al. (2013), Data from: The HypoMethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies), Dryad, Dataset, https://doi.org/10.5061/dryad.88h10
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 in an uncharacterized genome remains challenging and a large number of sequences could not be classified as either repetitive DNA or as belonging to the gene space. Upon further investigation, we found that some of these uncharacterized fragments were expressed, and in most cases the expression was spatially differentiated, indicating that they might have a function. Full-length transcripts of a subset of expressed fragments also revealed that these could be long non-coding RNAs. Long non-coding RNAs have been shown to be involved in gene regulation and deserve future attention. In conclusion, our study shows that the HMPR method is effective in constructing libraries enriched for the genic fraction of the genome, while simultaneously reducing the repetitive fraction, in P. abies and may prove a valuable tool for the discovery, validation and assessment of genetic markers in population studies when combined with next generation sequencing technology.