sorting the wheat from the chaff identifying mirnas in genomic survey sequences of triticum aestivum chromosome 1al排序的小麦从谷壳中识别microrna基因调查小麦染色体序列1.pdfVIP

Sorting the Wheat from the Chaff: Identifying miRNAs in Genomic Survey Sequences of Triticum aestivum Chromosome 1AL Stuart J. Lucas, Hikmet Budak* Faculty of Engineering and Natural Sciences, Sabanci University, Orhanlı, Istanbul, Turkey Abstract Individual chromosome-based studies of bread wheat are beginning to provide valuable structural and functional information about one of the world’s most important crops. As new genome sequences become available, identifying miRNA coding sequences is arguably as important a task as annotating protein coding sequences, but one that is not as well developed. We compared conservation-based identification of conserved miRNAs in 1.5 6coverage survey sequences of wheat chromosome 1AL with a predictive method based on pre-miRNA hairpin structure alone. In total, 42 sequences expected to encode conserved miRNAs were identified on chromosome 1AL, including members of several miRNA families that have not previously been reported to be expressed in T. aestivum. In addition, we demonstrate that a number of sequences previously annotated as novel wheat miRNAs are closely related to transposable elements, particularly Miniature Inverted Terminal repeat Elements (MITEs). Some of these TE-miRNAs may well have a functional role, but separating true miRNA coding sequences from TEs in genomic sequences is far from straightforward. We propose a strategy for annotation to minimize the risk of mis-identifying TE sequences as miRNAs. Citation: Lucas SJ, Budak H (2012) Sorting the Wheat from the Chaff: Identifying miRNAs in Genomic Survey Sequences of Triticum aestivum Chromosome 1AL. PLoS ONE 7(7): e40859. doi:10.1371/journal.pone.0040859 Editor: A. Aziz Aboobaker, Nottingham University, United Kingdom Received March 13, 2012; Accepted June 14, 2012; Published July