Mazaheri, M., Kianian, P.M.A., Mergoum, M., Valentini, G.L., Seetan, R., Pirseyedi, S.M., Kumar, A., Gu, Y.Q., Stein, N., Kubaláková, M., Doležel, J., Denton, A.M., Kianian, S.F.
THE PLANT GENOME
7:
1-8,
2014
Keywords:
Abstract:
Barley is a model plant in genomic studies of Triticeae species.
However, barley’s large genome size and high repetitive
sequence content complicate the whole-genome sequencing.
The majority of the barley genome is composed of transposable
elements (TEs). In this study, TE repeat junctions (RJs) were
used to develop a large-scale molecular marker platform, as
a prerequisite to genome assembly. A total of 10.22 Gb of
barley nonassembled 454 sequencing data were screened
with RJPrimers pipeline. In total, 9,881,561 TE junctions were
identified. From detected RJs, 400,538 polymerase chain
reaction (PCR)-based RJ markers (RJMs) were designed across
the genome, with an average of 39 markers/Mb. The utility of
designed markers was tested using a random subset of RJMs.
Over 94% of the markers successfully amplified amplicons,
among which ~90% were genome specific. In addition to
marker design, identified RJs were utilized to detect 1190,885
TEs across the genome. In gene-poor regions of the genome
Gypsy elements comprised the majority of TEs (~65%), while in
gene-rich regions Gypsy, Copia, and Mariner were the main
transposons, each representing an average ~23% of total TEs.
The numerous RJ primer pairs developed in this study will be a
valuable resource for barley genomic studies including genomic
selection, fine mapping, and genome assembly. In addition, the
results of this study show that characterizing RJs provides insight
into TE composition of species without a sequenced genome but
for which short-read sequence data is available.
Fulltext: contact IEB authors
IEB authors: Jaroslav Doležel,
Marie Kubaláková
