Kantar, M., Akpınar, B.A., Valárik, M., Lucas, S.J., Doležel, J., Hernández, P., Budak, H.
FUNCTIONAL & INTEGRATIVE GENOMICS
12:
465-479,
2012
Keywords:
Triticum aestivum, microRNA, miRNA prediction, Sub-genomic analysis, Next-generation sequencing
Abstract:
In this study, a survey of miRNAs using the nextgeneration
sequencing data was performed at subgenomic
level. After analyzing shotgun sequences from chromosome
4A of bread wheat (Triticum aestivum L.), a total of 68
different miRNAs were predicted in silico, of which 37 were
identified in wheat for the first time. The long arm of the
chromosome was found to harbor a higher variety (51) and
representation (3,928) of miRNAs compared with the short
arm (49; 2,226). Out of the 68 miRNAs, 32 were detected to
be common to both arms, revealing the presence of separate
miRNA clusters in the two chromosome arms. The differences
in degree of representation of the different miRNAs
were found to be highly variable, ranging 592-fold, which
may have an effect on target regulation. Targets were retrieved
for 62 (out of 68) of wheat-specific, newly identified
miRNAs indicated that fundamental aspects of plant morphology
such as height and flowering were predicted to be
affected. In silico expression blast analysis indicated 24 (out
of 68) were found to give hits to expressed sequences. This is
the first report of species- and chromosome-specific miRNAs.
Fulltext: contact IEB authors
IEB authors: Jaroslav Doležel,
Miroslav Valárik
Čeština
English