title: Exploring microRNA-like small RNAs in the filamentous fungus Fusarium oxysporum.
abstract: RNA silencing such as quelling and meiotic silencing by unpaired DNA (MSUD) and several other classes of special small RNAs have been discovered in filamentous fungi recently. More than four different mechanisms of microRNA-like RNAs (milRNAs) production have been illustrated in the model fungus Neurospora crassa including a dicer-independent pathway. To date, very little work focusing on small RNAs in fungi has been reported and no universal or particular characteristic of milRNAs were defined clearly. In this study, small RNA and degradome libraries were constructed and subsequently deep sequenced for investigating milRNAs and their potential cleavage targets on the genome level in the filamentous fungus F. oxysporum f. sp. lycopersici. As a result, there is no intersection of conserved miRNAs found by BLASTing against the miRBase. Further analysis showed that the small RNA population of F. oxysporum shared many common features with the small RNAs from N. crassa and other fungi. According to the known standards of miRNA prediction in plants and animals, milRNA candidates from 8 families (comprising 19 members) were screened out and identified. However, none of them could trigger target cleavage based on the degradome data. Moreover, most major signals of cleavage in transcripts could not match appropriate complementary small RNAs, suggesting that other predominant modes for milRNA-mediated gene regulation could exist in F. oxysporum. In addition, the PAREsnip program was utilized for comprehensive analysis and 3 families of small RNAs leading to transcript cleavage were experimentally validated. Altogether, our findings provided valuable information and important hints for better understanding the functions of the small RNAs and milRNAs in the fungal kingdom.
authors.affiliation: Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
authors.affiliation: Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Jiang
authors.affiliation: The National Key Facilities for Crop Genetic Resources and Improvement, Institute of crop sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Qiyan
authors.initials: Q
authors.lastname: Jiang
authors.affiliation: The National Key Facilities for Crop Genetic Resources and Improvement, Institute of crop sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Xianjun
authors.initials: X
authors.lastname: Sun
authors.affiliation: Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.affiliation: The National Key Facilities for Crop Genetic Resources and Improvement, Institute of crop sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: The National Key Facilities for Crop Genetic Resources and Improvement, Institute of crop sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Hu
mesh_terms: D000818:Animals; D005670:Fusarium / Q000235:genetics* / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D034622:RNA Interference; D012331:RNA, Fungal / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D012331:RNA, Fungal