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Background  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.  Brachypodium distachyon , with close evolutionary relationship to cool-season cereals, has recently emerged as a novel model plant. There are few reports of  Brachypodium  miRNAs.    Results  High-throughput sequencing and whole-genome-wide data mining led to the identification of 27 conserved miRNAs, as well as 129 predicted miRNAs in  Brachypodium . For multiple-member conserved miRNA families, their sizes in  Brachypodium  were much smaller than those in rice and  Populus . The genome organization of miR395 family in  Brachypodium  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.    Conclusion  Our results suggest that  Brachypodium  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  Brachypodium  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.

Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response