PMID- 25141304 OWN - NLM STAT- MEDLINE DCOM- 20150511 LR - 20211021 IS - 1932-6203 (Electronic) IS - 1932-6203 (Linking) VI - 9 IP - 8 DP - 2014 TI - Exploring microRNA-like small RNAs in the filamentous fungus Fusarium oxysporum. PG - e104956 LID - 10.1371/journal.pone.0104956 [doi] LID - e104956 AB - 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. FAU - Chen, Rui AU - Chen R AD - Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, China. FAU - Jiang, Nan AU - Jiang N AD - Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China. FAU - Jiang, Qiyan AU - Jiang Q AD - The National Key Facilities for Crop Genetic Resources and Improvement, Institute of crop sciences, Chinese Academy of Agricultural Sciences, Beijing, China. FAU - Sun, Xianjun AU - Sun X AD - The National Key Facilities for Crop Genetic Resources and Improvement, Institute of crop sciences, Chinese Academy of Agricultural Sciences, Beijing, China. FAU - Wang, Yong AU - Wang Y AD - Tianjin Institute of Agricultural Quality Standard and Testing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, China. FAU - Zhang, Hui AU - Zhang H AD - The National Key Facilities for Crop Genetic Resources and Improvement, Institute of crop sciences, Chinese Academy of Agricultural Sciences, Beijing, China. FAU - Hu, Zheng AU - Hu Z AD - The National Key Facilities for Crop Genetic Resources and Improvement, Institute of crop sciences, Chinese Academy of Agricultural Sciences, Beijing, China. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20140820 PL - United States TA - PLoS One JT - PloS one JID - 101285081 RN - 0 (MicroRNAs) RN - 0 (RNA, Fungal) SB - IM MH - Animals MH - Fusarium/*genetics/metabolism MH - Gene Expression Regulation, Fungal MH - MicroRNAs/*genetics/metabolism MH - RNA Interference MH - RNA, Fungal/*genetics/metabolism PMC - PMC4139310 COIS- Competing Interests: The authors have declared that no competing interests exist. EDAT- 2014/08/21 06:00 MHDA- 2015/05/12 06:00 PMCR- 2014/08/20 CRDT- 2014/08/21 06:00 PHST- 2014/05/21 00:00 [received] PHST- 2014/07/12 00:00 [accepted] PHST- 2014/08/21 06:00 [entrez] PHST- 2014/08/21 06:00 [pubmed] PHST- 2015/05/12 06:00 [medline] PHST- 2014/08/20 00:00 [pmc-release] AID - PONE-D-14-22753 [pii] AID - 10.1371/journal.pone.0104956 [doi] PST - epublish SO - PLoS One. 2014 Aug 20;9(8):e104956. doi: 10.1371/journal.pone.0104956. eCollection 2014.