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.

sRNA profiling in Aspergillus flavus reveals differentially expressed miRNA-like RNAs response to water activity and temperature

“…Only the miRNA-like sequences were identified since they were identified in the model filamentous fungus N. crassa (Lee et al, 2010). Many milRNAs have been identified in many other fungi, such as Fusarium oxysporum (Chen et al, 2014), T. reesei (Kang et al, 2013), P. marneffei (Lau et al, 2013) and M. anisopliae (Zhou et al, 2012b), but the presence of milRNAs in aflatoxinproducing filamentous fungus A. flavus was largely unknown. In this study, we demonstrated, for the first time, experimental evidence supporting the existence of milRNAs in A. flavus.…”

Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight host candidate genes associated with quantitative disease resistance

“…The genomes of several filamentous pathogens have evolved towards compartmentalization into repeat-rich, genesparse regions that contain effector genes, and repeat-poor gene-rich regions that contain housekeeping genes (Dong et al, 2015;Fouché et al, 2018). Although there have been several sRNA profiling studies on plant pathogenic fungi (Chen et al, 2014;Mueth et al, 2015;Zhou et al, 2012), whether sRNA loci are associated with repeat-rich, gene-poor regions of fungal genomes has not yet been considered.…”

The identification of microRNAs in Ganoderma lingzhi sporocarp

“…Previously, it was generally accepted that miRNA and miRNA-like did not exist in fungus. In recent years, the small RNAs, especially miRNA-like small RNAs, were widely studied in fungal species based on the deep sequencing technology, such as Fusarium oxysporum (Schumann et al 2013;Chen et al 2014), Cryptococcus neoformans (Jiang et al 2012), Trichoderma reesei (Kang et al 2013), Penicillium marneffei (Lau et al 2013), Neurospora crassa , Sclerotinia sclerotiorum (Zhou et al 2012a), and Metarhizium anisopliae (Zhou et al 2012b).…”