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Genomic dissection of small RNA s in wild rice ( Oryza rufipogon ): lessons for rice domestication
Author(s) -
Wang Yu,
Bai Xuefei,
Yan Chenghai,
Gui Yiejie,
Wei Xinghua,
Zhu QianHao,
Guo Longbiao,
Fan Longjiang
Publication year - 2012
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/j.1469-8137.2012.04304.x
Subject(s) - oryza rufipogon , domestication , biology , genome , gene , genetics , rna , oryza , oryza sativa , small rna
Summary 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 (mi RNA s) were investigated by mi RNA chips. A de novo O. rufipogon genome was assembled using c . 55× coverage of raw sequencing data and a total of 387 MIRNA s 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 MIRNA s, 259 were not found in the cultivated rice, suggesting a loss of these MIRNA s in the cultivated rice. We also found that 48 MIRNA s were novel in the cultivated rice, suggesting that they were potential targets of domestication selection. Some mi RNA s showed significant expression differences between wild and cultivated rice, suggesting that expression of mi RNA 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.