Exploring MicroRNA-Like Small RNAs in the Filamentous Fungus Fusarium oxysporum

Exploring MicroRNA-Like Small RNAs in the Filamentous Fungus Fusarium oxysporum

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 Neu...

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Main Authors: Chen, Rui, Jiang, Nan, Jiang, Qiyan, Sun, Xianjun, Wang, Yong, Zhang, Hui, Hu, Zheng
Format: Online
Language:English
Published: Public Library of Science 2014
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139310/
id pubmed-4139310
recordtype oai_dc
spelling pubmed-41393102014-08-25 Exploring MicroRNA-Like Small RNAs in the Filamentous Fungus Fusarium oxysporum Chen, Rui Jiang, Nan Jiang, Qiyan Sun, Xianjun Wang, Yong Zhang, Hui Hu, Zheng Research Article 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. Public Library of Science 2014-08-20 /pmc/articles/PMC4139310/ /pubmed/25141304 http://dx.doi.org/10.1371/journal.pone.0104956 Text en © 2014 Chen et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Chen, Rui
Jiang, Nan
Jiang, Qiyan
Sun, Xianjun
Wang, Yong
Zhang, Hui
Hu, Zheng
spellingShingle Chen, Rui
Jiang, Nan
Jiang, Qiyan
Sun, Xianjun
Wang, Yong
Zhang, Hui
Hu, Zheng
Exploring MicroRNA-Like Small RNAs in the Filamentous Fungus Fusarium oxysporum
author_facet Chen, Rui
Jiang, Nan
Jiang, Qiyan
Sun, Xianjun
Wang, Yong
Zhang, Hui
Hu, Zheng
author_sort Chen, Rui
title Exploring MicroRNA-Like Small RNAs in the Filamentous Fungus Fusarium oxysporum
title_short Exploring MicroRNA-Like Small RNAs in the Filamentous Fungus Fusarium oxysporum
title_full Exploring MicroRNA-Like Small RNAs in the Filamentous Fungus Fusarium oxysporum
title_fullStr Exploring MicroRNA-Like Small RNAs in the Filamentous Fungus Fusarium oxysporum
title_full_unstemmed Exploring MicroRNA-Like Small RNAs in the Filamentous Fungus Fusarium oxysporum
title_sort exploring microrna-like small rnas in the filamentous fungus fusarium oxysporum
description 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.
publisher Public Library of Science
publishDate 2014
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139310/
_version_ 1613125954985525248

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