title: Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv.
abstract: The small RNA transcriptomes of bread wheat and its emerging model Brachypodium distachyon were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNAs) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of expressed sequence tags, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5' rapid amplification of complementary DNA ends experiments demonstrated their capability to cleave predicted target genes including three disease-resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in B. distachyon.
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, Pr China.
authors.forename: Bo
authors.initials: B
authors.lastname: Wei
authors.forename: Tao
authors.initials: T
authors.lastname: Cai
authors.forename: Rongzhi
authors.initials: R
authors.lastname: Zhang
authors.forename: Aili
authors.initials: A
authors.lastname: Li
authors.forename: Naxin
authors.initials: N
authors.lastname: Huo
authors.forename: Shan
authors.initials: S
authors.lastname: Li
authors.forename: Yong Q
authors.initials: YQ
authors.lastname: Gu
authors.forename: John
authors.initials: J
authors.lastname: Vogel
authors.forename: Jizeng
authors.initials: J
authors.lastname: Jia
authors.forename: Yijun
authors.initials: Y
authors.lastname: Qi
authors.forename: Long
authors.initials: L
authors.lastname: Mao
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D006109:Poaceae / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014908:Triticum / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D022661:RNA, Untranslated