Novel microRNAs associated with the immune response to cucumber mosaic virus in hot pepper (Capsicum annuum L.)

Brodersen, 2008, Widespread translational inhibition by plant miRNAs and siRNAs, Science, 320, 1185, 10.1126/science.1159151 Lee, 1993, The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14, Cell, 75, 843, 10.1016/0092-8674(93)90529-Y Dexheimer, 2020, MicroRNAs: from mechanism to organism, Front. Cell Dev. Biol., 8, 409, 10.3389/fcell.2020.00409 Zhang, 2019, Roles of small RNAs in virus-plant interactions, Viruses, 11, 827, 10.3390/v11090827 Martins, 2020, Identification, characterization, and expression analysis of cowpea (Vigna unguiculata [L.] Walp.) miRNAs in response to cowpea severe mosaic virus (CPSMV) challenge, Plant Cell Rep., 39, 1061, 10.1007/s00299-020-02548-6 Liu, 2020, Genome-wide microRNA profiling using oligonucleotide microarray reveals regulatory networks of microRNAs in Nicotiana benthamiana during Beet necrotic yellow vein virus infection, Viruses, 12, 310, 10.3390/v12030310 Prigigallo, 2019, Potato virus Y infection alters small RNA metabolism and immune response in tomato, Viruses, 11, 1100, 10.3390/v11121100 Davenport, 2001, Genera Solanacearum: the genera of Solanaceae Illustrated, arranged according to a new system by Armando T, Hunziker. Syst Bot, 29, 221, 10.1600/036364404772974130 Khan, 2014, Pharmacological importance of an ethnobotanical plant: Capsicum annuum L, Nat. Prod. Res., 28, 1267, 10.1080/14786419.2014.895723 Reilly, 2001, Determination of capsaicin, dihydrocapsaicin, and nonivamide in self-defense weapons by liquid chromatography–mass spectrometry and liquid chromatography–tandem mass spectrometry, J. Chromatogr. A, 912, 259, 10.1016/S0021-9673(01)00574-X Fan, 2019, Rapid and sensitive detection of cucumber mosaic virus by reverse transcription loop-mediated isothermal amplification, Acta Biochim. Biophys. Sin., 51, 223, 10.1093/abbs/gmy159 Liu, 2019, Identification, distribution and occurrence of viruses in the main vegetables of China, Sci. Agric. Sin., 52, 239 Wei, 2017, Change of catalase activity in interaction of tobacco and cucumber mosaic virus, Tobacco science and Technology, 50, 19 Martin, 2011, Cutadapt removes adapter sequences from high-throughput sequencing reads, Embnet Journal, 17, 10, 10.14806/ej.17.1.200 Qin, 2014, Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization, Proc. Natl. Acad. Sci. USA, 111, 5135, 10.1073/pnas.1400975111 Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 Griffiths-Jones, 2003, Rfam: an RNA family database, Nucleic Acids Res., 31, 439, 10.1093/nar/gkg006 Griffiths-Jones, 2007, miRBase: tools for microRNA genomics, Nucleic Acids Res., 36, D154, 10.1093/nar/gkm952 Friedländer, 2012, miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades, Nucleic Acids Res., 40, 37, 10.1093/nar/gkr688 Zuker, 2003, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res., 31, 3406, 10.1093/nar/gkg595 Meyers, 2008, Criteria for annotation of plant MicroRNAs, Plant Cell, 20, 3186, 10.1105/tpc.108.064311 Anders, 2010, Analysing RNA-Seq data with the DESeq package, Mol. Biol., 43, 1 Dai, 2018, psRNATarget: a plant small RNA target analysis server (2017 release), Nucleic Acids Res., 46, W49, 10.1093/nar/gky316 Zhang, 2005, miRU: an automated plant miRNA target prediction server, Nucleic Acids Res., 33, W701, 10.1093/nar/gki383 Kertesz, 2007, The role of site accessibility in microRNA target recognition, Nat. Genet., 39, 1278, 10.1038/ng2135 Tian, 2020, PlantRegMap: charting functional regulatory maps in plants, Nucleic Acids Res., 48, D1104 Bu, 2021, KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis, Nucleic Acids Res., 49, W317, 10.1093/nar/gkab447 Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res., 13, 2498, 10.1101/gr.1239303 Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCt method, Methods, 25, 402, 10.1006/meth.2001.1262 Li, 2016, MicroRNAs in control of plant development, J. Cell. Physiol., 231, 303, 10.1002/jcp.25125 Luo, 2011, The role of miR319 in plant development regulation, Yi Chuan, 33, 1203, 10.3724/SP.J.1005.2011.01203 Kosugi, 1997, PCF1 and PCF2 specifically bind to cis elements in the rice proliferating cell nuclear antigen gene, Plant Cell, 9, 1607 Li, 2005, Arabidopsis TCP20 links regulation of growth and cell division control pathways, Proc. Natl. Acad. Sci. USA, 102, 12978, 10.1073/pnas.0504039102 Danisman, 2016, TCP transcription factors at the interface between environmental challenges and the plant's growth responses, Front. Plant Sci., 7, 1930, 10.3389/fpls.2016.01930 Mukhtar, 2011, Independently evolved virulence effectors converge onto hubs in a plant immune system network, Science, 333, 596, 10.1126/science.1203659 Fei, 2013, Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks, Plant Cell, 25, 2400, 10.1105/tpc.113.114652 Liu, 2020, PhasiRNAs in plants: their biogenesis, genic sources, and roles in stress responses, development, and reproduction, Plant Cell, 32, 3059, 10.1105/tpc.20.00335 Fei, 2016, Small RNAs add zing to the zig-zag-zig model of plant defenses, Mol. Plant Microbe Interact., 29, 165, 10.1094/MPMI-09-15-0212-FI Han, 2019, Origin and evolution of the plant immune system, New Phytol., 222, 70, 10.1111/nph.15596 Li, 2010, Misexpression of miR482, miR1512, and miR1515 increases soybean nodulation, Plant Physiol., 153, 1759, 10.1104/pp.110.156950 Canto-Pastor, 2019, Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato, Proc. Natl. Acad. Sci. USA, 116, 2755, 10.1073/pnas.1814380116 Ouyang, 2014, MicroRNAs suppress NB domain genes in tomato that confer resistance to Fusarium oxysporum, PLoS Pathog., 10, 10.1371/journal.ppat.1004464 Yu, 2013, The Chinese wild grapevine (Vitis pseudoreticulata) E3 ubiquitin ligase Erysiphe necator-induced RING finger protein 1 (EIRP1) activates plant defense responses by inducing proteolysis of the VpWRKY11 transcription factor, New Phytol., 200, 834, 10.1111/nph.12418 Qiao, 2017, Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L, Mol. Genet. Genom., 292, 37, 10.1007/s00438-016-1253-5