10.5061/DRYAD.88H10
Larsson, Hanna
Uppsala University
de Paoli, Emanuele
University of Udine
Morgante, Michele
University of Udine
Lascoux, Martin
Uppsala University
Gyllenstrand, Niclas
Swedish University of Agricultural Sciences
Data from: The HypoMethylated Partial Restriction (HMPR) method reduces
the repetitive content of genomic libraries in Norway spruce (Picea abies)
Dryad
dataset
2013
reduced representation
Picea abies
HMPR libraries
2013-02-26T18:29:52Z
2013-02-26T18:29:52Z
en
https://doi.org/10.1007/s11295-012-0582-8
7491761 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
Hpa1N_libGenomic DNA sequences in
fasta-formatHpa01N_libHpa1S_libHpa01S_libHpy1N_libHpy01N_libHpy1S_libHpy01S_libUF_lib