Ah-Fong A M, Bormann-Chung C A, Judelson H S. 2008. Optimization of transgene-mediated silencing in Phytophthora infestans and its association with small-interfering RNAs. Fungal Genetics and Biology, 45, 1197–1205.
Bachman P M, Bolognesi R, Moar W J, Mueller G M, Paradise M S, Ramaseshadri P, Tan J G, Uffman J P, Warren J, Wiggins B E, Levine S L. 2013. Characterization of the spectrum of insecticidal activity of a double-stranded RNA with targeted activity against Western Corn Rootworm (Diabrotica virgifera virgifera LeConte). Transgenic Research, 22, 1207–1222.
Bernstein E, Caudy A A, Hammond S M, Hannon G J. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409, 363–366.
Bolognesi R, Ramaseshadri P, Anderson J, Bachman P, Clinton W, Flannagan R, Ilagan O, Lawrence C, Levine S, Moar W, Mueller G, Tan J G, Uffman J, Wiggins E, Heck G, Segers G. 2012. Characterizing the mechanism of action of double-stranded RNA activity against Western Corn Rootworm (Diabrotica virgifera virgifera LeConte). PLoS ONE, 7, e47534.
Booker T R, Jackson B C, Keightley P D. 2017. Detecting positive selection in the genome. BMC Biology, 15, 98.
Cai Q, Qiao L L, Wang M, He B, Lin F M, Palmquist J, Huang S D, Jin H L. 2018. Plants send small RNAs in extracellular vesicles to fungal pathogen to silence virulence genes. Science, 360, 1126–1129.
Cappelle K, de Oliveira C F, Van Eynde B, Christiaens O, Smagghe G. 2016. The involvement of clathrin-mediated endocytosis and two Sid-1-like transmembrane proteins in double-stranded RNA uptake in the Colorado potato beetle midgut. Insect Molecular Biology, 25, 315–323.
Castel S E, Martienssen R A. 2013. RNA interference (RNAi) in the nucleus: Roles for small RNAs in transcription, epigenetics and beyond. Nature Reviews Genetics, 14, 100–112.
Chang Y W, Wang Y C, Zhang X X, Iqbal J, Du Y Z. 2021. RNA Interference of genes encoding the vacuolar-ATPase in Liriomyza trifolii. Insects, 12, 41.
Chen A H, Islam T, Ma Z Z. 2022. An integrated pest management program for managing Fusarium head blight disease in cereals. Journal of Integrative Agriculture, 21, 3434–3444.
Chen Y, Gao Q X, Huang M M, Liu Y, Liu Z Y, Liu X, Ma Z H. 2015. Characterization of RNA silencing components in the plant pathogenic fungus Fusarium graminearum. Scientific Reports, 5, 12500.
Cheng W, Song X S, Li H P, Cao L H, Sun K, Qiu X L, Xu Y B, Yang P, Huang T, Zhang J B, Qu B, Liao Y C. 2015. Host-induced gene silencing of an essential chitin synthase gene confers durable resistance to Fusarium head blight and seedling blight in wheat. Plant Biotechnology Journal, 13, 1335–1345.
Cooper B, Campbell K B. 2017. Protection against common bean rust conferred by a gene-silencing method. Phytopathology, 107, 920–927.
Court D L, Gan J, Liang Y H, Shaw G X, Tropea J E, Costantino N, Waugh D S, Ji X. 2013. RNase III: Genetics and function; structure and mechanism. Annual Review Genetics, 47, 405–431.
Duchaine T F, Wohlschlegel J A, Kennedy S, Bei Y, Conte Jr D, Pang K, Brownell D R, Harding S, Mitani S, Ruvkun G, Yates J R 3rd, Mello C C. 2006. Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell, 124, 343–354.
Fang X F, Qi Y J. 2016. RNAi in plants: An Argonaute-centered view. The Plant Cell, 28, 272–285.
Fischer S E, Butler M D, Pan Q, Ruvkun G. 2008. Trans-splicing in C. elegans generates the negative RNAi regulator ERI-6/7. Nature, 455, 491–496.
Fisher M C, Hawkins N J, Sanglard D, Gurr S J. 2018. Worldwide emergence of resistance to antifungal drugs challenges human health and food security. Science, 360, 739–742.
Ghag S B, Shekhawat U K S, Ganapathi T R. 2014. Host-induced post-transcriptional hairpin RNA-mediated gene silencing of vital fungal genes confers efficient resistance against Fusarium wilt in banana. Plant Biotechnology Journal, 12, 541–553.
Grimm D, Kay M A. 2007. Therapeutic application of RNAi: Is mRNA targeting finally ready for prime time? The Journal of Clinical Investigation, 117, 3633–3641.
Gu K X, Song X S, Xiao X M, Duan X X, Wang J X, Duan Y B, Hou Y P, Zhou M G. 2019. A β2-tubulin dsRNA derived from Fusarium asiaticum confers plant resistance to multiple phytopathogens and reduces fungicide resistance. Pesticide Biochemistry Physiology, 153, 36–46.
Hunter C P, Winston W M, Molodowitch C, Feinberg E H, Shih J, Sutherlin M, Wright A J, Fitzgerald M C. 2006. Systemic RNAi in Caenorhabditis elegans. Cold Spring Harbor Symposia on Quantitative Biology, 71, 95–100.
Ikehata H, Ono T. 2011. The mechanisms of UV mutagenesis. Journal of Radiation Research, 52, 115–125.
Joseph T T, Osman R. 2012. Convergent transmission of RNAi guide-target mismatch information across Argonaute internal allosteric network. PLoS Computation Biology, 8, e1002693.
Kanan G J, Al-Najjar H E. 2010. Isolation and growth characterization of chlorate and/or bromate resistant mutants generated by spontaneous and induced foreword mutations at several gene loci in Aspergillus niger. Brazilian Journal of Microbiology, 41, 1099–1111.
Kandasamy S K, Fukunaga R. 2016. Phosphate-binding pocket in Dicer-2 PAZ domain for high-fidelity siRNA production. Proceedings of the National Academy of Sciences of the United States of America, 113, 14031–14036.
Kennedy S, Wang D, Ruvkun G. 2004. A conserved siRNA-degrading RNase negatively regulates RNA interference in C. elegans. Nature, 427, 645–649.
Khajuria C, Ivashuta S, Wiggins E, Flagel L, Moar W, Pleau M, Miller K, Zhang Y, Ramaseshadri P, Jiang C, Hodge T, Jensen P, Chen M, Gowda A, McNulty B, Vazquez C, Bolognesi R, Haas J, Head G, Clark T. 2018. Development and characterization of the first dsRNA-resistant insect population from western corn rootworm, Diabrotica virgifera virgifera LeConte. PLoS ONE, 13, e0197059.
Koch A, Kogel K H. 2014. New wind in the sails: Improving the agronomic value of crop plants through RNAi-mediated gene silencing. Plant Biotechnology Journal, 12, 821–831.
Koch A, Kumar N, Weber L, Keller H, Imani J, Kogel K H. 2013. Host-induced gene silencing of cytochrome P450 lanosterol C14α-demethylase-encoding genes confers strong resistance to Fusarium species. Proceedings of the National Academy of Sciences of the United States of America, 110, 19324–19329.
Koch A, Biedenkopf D, Furch A, Weber L, Rossbach O, Abdellatef E, Linicus L, Johannsmeier J, Jelonek L, Goesmann A, Cardoza V, McMillan J, Mentzel T, Kogel K H. 2016. An RNAi-based control of Fusarium graminearum infections through spraying of long dsRNAs involves a plant passage and is controlled by the fungal silencing machinery. Plos Pathogens, 12, e1005901.
Koropoulis A, Alachiotis N, Pavlidis P. 2020. Detecting positive selection in populations using genetic data. In: Methods in Molecular Biology. Max Planck Institute for Evolutionary Biology, Germany. pp. 87–123.
Langmead B, Salzberg S L. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357–359.
Langmead B, Trapnell C, Pop M, Salzberg S L. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10, R25.
Lim D H, Kim J, Kim S, Carthew R W, Lee Y S. 2008. Functional analysis of dicer-2 missense mutations in the siRNA pathway of Drosophila. Biochemical and Biophysical Research Communications, 371, 525–530.
Lozano J, Gomez-Orte E, Lee H J, Belles X. 2012. Super-induction of Dicer-2 expression by alien double-stranded RNAs: An evolutionary ancient response to viral infection? Development Genes and Evolution, 222, 229–235.
Ma M Q, He W W, Xu S J, Zhang J. 2020. RNA interference in Colorado potato beetle (Leptinotarsa decemlineata): A potential strategy for pest control. Journal of Integrative Agriculture, 19, 428–437.
Maida Y, Masutomi K. 2011. RNA-dependent RNA polymerases in RNA silencing. Biological Chemistry, 392, 299–304.
Mi S J, Cai T, Hu Y G, Chen Y G, Hodges E, Ni F R, Wu L, Li S, Zhou H Y, Long C Z, Chen S, Hannon G J, Qi Y J. 2008. Sorting of small RNAs into Arabidopsis Argonaute complexes is directed by the 5´ terminal nucleotide. Cell, 133, 116–127.
Narayan R D, Blackman L M, Shan W, Hardham A R. 2010. Phytophthora nicotianae transformants lacking dynein light chain 1 produce non-flagellate zoospores. Fungal Genetics and Biology, 47, 663–671.
Nicholson P, Rezanoor H N, Simpson D R, Joyce D. 1997. Differentiation and quantification of the cereal eyespot fungi Tapesia yallundae and Tapesia acuformis using a PCR assay. Plant Pathology, 46, 842–856.
Niu D D, Hamby R, Sanchez J N, Cai Q, Yan Q, Jin H L. 2021. RNAs-a new frontier in crop protection. Current Opinion in Biotechnology, 70, 204–212.
Nowara D, Gay A, Lacomme C, Shaw J, Ridout C, Douchkov D, Hensel G, Kumlehn J, Schweizer P. 2010. HIGS: Host-induced gene silencing in the obligate biotrophic fungal pathogen Blumeria graminis. The Plant Cell, 22, 3130–3141.
Nunes C C, Dean R A. 2012. Host-induced gene silencing: A tool for understanding fungal host interaction and for developing novel disease control strategies. Molecular Plant Pathology, 13, 519–529.
O’Donnell K, Ward T J, Geiser D M, Corby Kistler H, Aoki T. 2004. Genealogical concordance between the mating type locus and seven other nuclear genes supports formal recognition of nine phylogenetically distinct species within the Fusarium graminearum clade. Fungal Genetics Biology, 41, 600–623.
de Oliveira Filho J G, Silva G D C, Cipriano L, Gomes M, Egea M B. 2021. Control of postharvest fungal diseases in fruits using external application of RNAi. Journal of Food Science, 86, 3341–3348.
Ouyang S Q, Ji H M, Feng T, Luo S J, Cheng L, Wang N. 2023. Artificial trans-kingdom RNAi of FolRDR1 is a potential strategy to control tomato wilt disease. PLoS Pathogens, 19, e1011463.
Pavelec D M, Lachowiec J, Duchaine T F, Smith H E, Kennedy S. 2009. Requirement for the ERI/DICER complex in endogenous RNA interference and sperm development in Caenorhabditis elegans. Genetics, 183, 1283–1295.
Platz A, Egyhazi S, Ringborg U, Hansson J. 2008. Human cutaneous melanoma; a review of NRAS and BRAF mutation frequencies in relation to histogenetic subclass and body site. Molecular Oncology, 1, 395–405.
Qiao L L, Lan C, Capriotti L, Ah-Fong A, Sanchez J N, Hamby R, Heller J, Zhao H W, Glass N L, Judelson H S, Mezzetti B, Niu D D, Jin H L. 2021. Spray-induced gene silencing for disease control is dependent on the efficiency of pathogen RNA uptake. Plant Biotechnology Journal, 19, 1756–1768.
Qin H N, Chen F D, Huan X L, Machida S, Song J X, Yuan Y A. 2010. Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction. RNA, 16, 474–481.
Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology Evolution, 4, 406–425.
Savary S, Willocquet L, Pethybridge S J, Esker P, McRoberts N, Nelson A. 2019. The global burden of pathogens and pests on major food crops. Nature Ecology Evolution, 3, 430–439.
Scott J G, Michel K, Bartholomay L C, Siegfried B D, Hunter W B, Smagghe G, Zhu K Y, Douglas A E. 2013. Towards the elements of successful insect RNAi. Journal of Insect Physiology, 59, 1212–1221.
Shabalina S A, Koonin E V. 2008. Origins and evolution of eukaryotic RNA interference. Trends in Ecology Evolution, 23, 578–587.
Simmer F, Tijsterman M, Parrish S, Koushika S P, Nonet M L, Fire A, Ahringer J, Plasterk R H. 2002. Loss of the putative RNA-directed RNA polymerase RRF-3 makes C. elegans hypersensitive to RNAi. Current Biology, 12, 1317–1319.
Son H Y, Park A R, Lim J Y, Shin C, Lee Y W. 2017. Genome-wide exonic small interference RNA-mediated gene silencing regulates sexual reproduction in the homothallic fungus Fusarium graminearum. Plos Genetics, 13, e1006595.
Song X S, Gu K X, Duan X X, Xiao X M, Hou Y P, Duan Y B, Wang J X, Yu N, Zhou M G. 2018. Secondary amplification of siRNA machinery limits the application of spray-induced gene silencing. Molecular Plant Pathology, 19, 2543–2560.
Song X S, Li H P, Zhang J B, Song B, Huang T, Du X M, Gong A D, Liu Y K, Feng Y N, Agboola R S, Liao Y C. 2014. Trehalose 6-phosphate phosphatase is required for development, virulence and mycotoxin biosynthesis apart from trehalose biosynthesis in Fusarium graminearum. Fungal Genetics and Biology, 63, 24–41.
Takeda A, Iwasaki S, Watanabe T, Utsumi M, Watanabe Y. 2008. The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins. Plant and Cell Physiology, 49, 493–500.
Takeshita D, Zenno S H, Lee W C, Nagata K, Saigo K, Tanokura M. 2007. Homodimeric structure and double-stranded RNA cleavage activity of the C-terminal RNase III domain of human dicer. Journal of Molecular Biology, 374, 106–120.
Taylor R J, Salas B, Secor G A, Rivera V, Gudmestad N C. 2002. Sensitivity of North American isolates of Phytophthora erythroseptica and Pythium ultimum to Mefenoxam (Metalaxyl). Plant Disease, 86, 797–802.
Teng C, Zhang H, Hammond R, Huang K, Meyers B C, Walbot V. 2020. Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize. Nature Communications, 11, 2912.
Tinoco M L P, Dias B B, Dall’Astta R C, Pamphile J A, Aragao F J. 2010. In vivo trans-specific gene silencing in fungal cells by in planta expression of a double-stranded RNA. BMC Biology, 8, 27.
Wang M, Weiberg A, Lin F M, Thomma B P, Huang H D, Jin H L. 2016. Bidirectional cross-kingdom RNAi and fungal uptake of external RNAs confer plant protection. Nature Plants, 2, 16151.
Wang Q, Xue Y, Zhang L X, Zhong Z H, Feng S H, Wang C S, Xiao L F, Yang Z L, Harris C J, Zhai J X, Yang M J, Li S S, Jacobsen S E, Du J M. 2021. Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation. Science, 374, 1152–1157.
Yin C T, Jurgenson J E, Hulbert S H. 2011. Development of a host-induced RNAi system in the wheat stripe rust fungus Puccinia striiformis f. sp tritici. Molecular Plant (Microbe Interactions), 24, 554–561.
Yoon J S, Mogilicherla K, Gurusamy D, Chen X, Chereddy S C R R, Palli S R. 2018. Double-stranded RNA binding protein, Staufen, is required for the initiation of RNAi in coleopteran insects. Proceedings of the National Academy of Sciences of the United States of America, 115, 8334–8339.
|