title: Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication.
abstract: The lack of a MIRNA set and genome sequence of wild rice (Oryza rufipogon) has prevented us from determining the role of MIRNA genes in rice domestication. In this study, a genome, three small RNA populations and a degradome of O. rufipogon were sequenced by Illumina platform and the expression levels of microRNAs (miRNAs) were investigated by miRNA chips. A de novo O. rufipogon genome was assembled using c. 55× coverage of raw sequencing data and a total of 387 MIRNAs were identified in the O. rufipogon genome based on c. 5.2 million unique small RNA reads from three different tissues of O. rufipogon. Of these, O. rufipogon MIRNAs, 259 were not found in the cultivated rice, suggesting a loss of these MIRNAs in the cultivated rice. We also found that 48 MIRNAs were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some miRNAs showed significant expression differences between wild and cultivated rice, suggesting that expression of miRNA could also be a target of domestication, as demonstrated for the miR164 family. Our results illustrated that MIRNA genes, like protein-coding genes, might have been significantly shaped during rice domestication and could be one of the driving forces that contributed to rice domestication.
authors.affiliation: Department of Agronomy & Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Agronomy & Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Xuefei
authors.initials: X
authors.lastname: Bai
authors.affiliation: Department of Agronomy & Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Chenghai
authors.initials: C
authors.lastname: Yan
authors.affiliation: Department of Agronomy & Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Yiejie
authors.initials: Y
authors.lastname: Gui
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China.
authors.forename: Xinghua
authors.initials: X
authors.lastname: Wei
authors.affiliation: CSIRO Plant Industry, Canberra, ACT, 2601, Australia.
authors.forename: Qian-Hao
authors.initials: QH
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China.
authors.forename: Longbiao
authors.initials: L
authors.lastname: Guo
authors.affiliation: Department of Agronomy & Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, 310058, China.
authors.forename: Longjiang
authors.initials: L
authors.lastname: Fan
mesh_terms: D019295:Computational Biology / Q000379:methods; D018556:Crops, Agricultural / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D035683:MicroRNAs / Q000032:analysis* / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D018749:RNA, Plant / Q000032:analysis* / Q000235:genetics; D012639:Seeds / Q000235:genetics; D012641:Selection, Genetic; D017423:Sequence Analysis, RNA / Q000379:methods*; D013045:Species Specificity; D014158:Transcription, Genetic
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant