Sorting the wheat from the chaff: identifying miRNAs in genomic survey sequences of Triticum aestivum chromosome 1AL.

Stuart J Lucas,Hikmet Budak,A Aziz Aboobaker

doi:10.1371/journal.pone.0040859

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× coverage 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.

Highlights

Bread wheat (Triticum aestivum L.) is arguably the world’s most important crop plant, occupying 17% of all cultivated land and supplying about 55% of all carbohydrates [1], but its large (,16 GB) genome has not yet been sequenced owing to its complex and repetitive nature
When searching computationally for putative miRNA sequences in a large plant genome such as wheat, there is a significant risk of generating false positives from non-miRNA inverted repeat sequences, and getting the right balance between selectivity and sensitivity is difficult [25]
As genomic sequences of crop species become available, characterizing their miRNA populations is an important element in developing a full picture of their gene expression and regulation

Summary

Introduction

Bread wheat (Triticum aestivum L.) is arguably the world’s most important crop plant, occupying 17% of all cultivated land and supplying about 55% of all carbohydrates [1], but its large (,16 GB) genome has not yet been sequenced owing to its complex and repetitive nature. T. aestivum is a hexaploid believed to derive from serial hybridization events between three different diploid wheat ancestors [2]. For this reason each of its 7 chromosomes is present in 3 phylogenetically related but divergent sub-genomes (formula AABBDD, 6 n = 42). Plant miRNA genes are generally independent of protein-coding genes, and produce a long primary transcript (pri-miRNA) that undergoes 2 cleavage events, the first giving a precursor (pre-miRNA) that folds into a hairpin structure, the second extracting the mature 19– 24 nt miRNA from the stem of the hairpin (recently reviewed in [7]). The complementary sequence (referred to as miRNA*) was generally thought to be degraded, but recent evidence suggests that in many cases it may be functional [10]

Methods

Results

Conclusion