| Summary: | <p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are endogenous small RNAs having large-scale regulatory effects on plant development and stress responses. Extensive studies of miRNAs have only been performed in a few model plants. Although miRNAs are proved to be involved in plant cold stress responses, little is known for winter-habit monocots. <it>Brachypodium distachyon</it>, with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of <it>Brachypodium </it>miRNAs.</p> <p>Results</p> <p>High-throughput sequencing and whole-genome-wide data mining led to the identification of 27 conserved miRNAs, as well as 129 predicted miRNAs in <it>Brachypodium</it>. For multiple-member conserved miRNA families, their sizes in <it>Brachypodium </it>were much smaller than those in rice and <it>Populus</it>. The genome organization of miR395 family in <it>Brachypodium </it>was quite different from that in rice. The expression of 3 conserved miRNAs and 25 predicted miRNAs showed significant changes in response to cold stress. Among these miRNAs, some were cold-induced and some were cold-suppressed, but all the conserved miRNAs were up-regulated under cold stress condition.</p> <p>Conclusion</p> <p>Our results suggest that <it>Brachypodium </it>miRNAs are composed of a set of conserved miRNAs and a large proportion of non-conserved miRNAs with low expression levels. Both kinds of miRNAs were involved in cold stress response, but all the conserved miRNAs were up-regulated, implying an important role for cold-induced miRNAs. The different size and genome organization of miRNA families in <it>Brachypodium </it>and rice suggest that the frequency of duplication events or the selection pressure on duplicated miRNAs are different between these two closely related plant species.</p>
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