|Bai, Wei -|
|Cai, Ao -|
|Rz, Zhang -|
|Li, Aili -|
|Huo, Naxin -|
|Li, Shan -|
|Jia, Jizeng -|
|Qi, Yijun -|
Submitted to: Functional and Integrative Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 17, 2009
Publication Date: June 5, 2009
Citation: Bai, W., Cai, A., Rz, Z., Li, A., Huo, N., Li, S., Gu, Y.Q., Yabut, L., Jia, J., Qi, Y. 2009. Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Functional and Integrative Genomics. 9:532-541. Interpretive Summary: Brachypodium distachyon is an emerging model system for temperate grasses including most important food crops such as wheat. Small RNAs (smRNA) and microRNAs (miRNAs) are important regulators in plant development and physiology. This study characterized smRNAs and miRNAs in Brachypodium as compared to these in wheat. The research provides important base-line data to researchers involved in a variety of area of plant biology, and will promote Brachypodium as model for wheat for the improvement of crop production.
Technical Abstract: Brachypodium distachyon is a promising model for studying temperate grasses, most importantly wheat. Small RNA (smRNAs), especially 21 nt and 24 nt smRNAs, play essential roles in plant development and physiology. We performed seep sequencing of smRNA repertoires in Brachypodium and wheat and found that these two species shared only ~3% of their smRNAs. Twenty-four nucleotide (nt) smRNAs were the most dominant, but the least redundant for both Brachypodium and wheat. In addition to numerous conserved microRNA (miRNAs), 13 and 39 novel miRNAs were predicted in Brachypodium and wheat respectively and a subset of miRNAs were experimentally confirmed. Unexpectedly, only ~9% of smRNAs were shared by Brachypodium smRNA derived from reproductive and vegetative tissues and significant differential expression of smRNAs were observed. Wheat smRNAs were found to have perfect match to more than 13% OF estS INVESTIGATED. Many of these ESTs represented genes involved in endogenous and exogenous stresses and stimuli as indicated by Gene Ontology analysis, indicating that the regulation of stress responsive genes may heavily involve smRNAs. smRNAs of 21 nt were the most abundant among smRNAs matching wheat ESTs, whereas 23 nt dominated the smRNA mapped to their own genomic sequences. When Brachypodium and wheat smRNAs were mapped to rice chromosomes similar distribution pattern were found. There conserved smRNAs were located at both genic and intergenic regions with more 21 nt smRNA than 24 nt ones, indicating 21 nt smRNAs were evolutionarily more conserved. The conservation and divergence of smRNA repertoires in grass species were discussed.