In silico identification and validation of miRNA and their DIR specific targets in Oryza sativa Indica under abiotic stress

Paniagua, 2017, Dirigent proteins in plants: modulating cell wall metabolism during abiotic and biotic stress exposure, J. Exp. Bot., 68, 3287, 10.1093/jxb/erx141 Ralph, 2006, Dirigent proteins in conifer defense: gene discovery, phylogeny, and differential wound- and insect-induced expression of a family of DIR and DIR-like genes in spruce (Picea spp.), Plant Mol. Biol., 60, 21, 10.1007/s11103-005-2226-y Cheng, 2018, Molecular characterization, evolution, and expression profiling of the dirigent (DIR) family genes in Chinese White Pear (Pyrus bretschneideri), Front. Genet., 9, 136, 10.3389/fgene.2018.00136 Song, 2019, Genome-wide identification and characterization of DIR genes in Medicago truncatula, Biochem. Genet., 57, 487, 10.1007/s10528-019-09903-7 Gang, 1999, Regiochemical control of monolignol radical coupling: a new paradigm for lignin and lignan biosynthesis, Chem. Biol., 6, 143, 10.1016/S1074-5521(99)89006-1 Burlat, 2001, Dirigent proteins and dirigent sites in lignifying tissues, Phytochemistry, 57, 883, 10.1016/S0031-9422(01)00117-0 Davin, 2000, Dirigent proteins and dirigent sites explain the mystery of specificity of radical precursor coupling in lignan and lignin biosynthesis, Plant Physiol., 123, 453, 10.1104/pp.123.2.453 Ralph, 2007, Dirigent proteins in conifer defense II: extended gene discovery, phylogeny, and constitutive and stress-induced gene expression in spruce (Picea spp.), Phytochemistry, 68, 1975, 10.1016/j.phytochem.2007.04.042 Pickel, 2013, Dirigent proteins: molecular characteristics and potential biotechnological applications, Appl. Microbiol. Biotechnol., 97, 8427, 10.1007/s00253-013-5167-4 Arasan, 2013, Characterization and expression analysis of dirigent family genes related to stresses in Brassica, Plant Physiol. Biochem., 67, 144, 10.1016/j.plaphy.2013.02.030 Wang, 2018, Proteomic response of hybrid wild rice to cold stress at the seedling stage, PloS One, 13, 10.1371/journal.pone.0198675 Morita, 2006, Changes in peroxidase activity and lignin content of cultured tea cells in response to excess manganese, Soil Sci. Plant Nutr., 52, 26, 10.1111/j.1747-0765.2006.00006.x Jin-long, 2012, A novel dirigent protein gene with highly stem-specific expression from sugarcane, response to drought, salt and oxidative stresses, Plant Cell Rep., 31, 1801, 10.1007/s00299-012-1293-1 Behr, 2015, Analysis of cell wall- related genes in organs of Medicago sativa L. Under different abiotic stresses, Int. J. Mol. Sci., 16, 16104, 10.3390/ijms160716104 Lee, 2004, MicroRNA genes are transcribed by RNA polymerase II, EMBO J., 23, 4051, 10.1038/sj.emboj.7600385 Bernstein, 2001, Role for a bidentate ribonuclease in the initiation step of RNA interference, Nature, 409, 363, 10.1038/35053110 Tang, 2003, A biochemical framework for RNA silencing in plants, Genes Dev., 17, 49, 10.1101/gad.1048103 Yi, 2003, Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs, Genes Dev., 17, 3011, 10.1101/gad.1158803 Khraiwesh, 2012, Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants, Biochim. Biophys. Acta, 1819, 137, 10.1016/j.bbagrm.2011.05.001 Shriram, 2016, MicroRNAs as potential targets for abiotic stress tolerance in plants, Front. Plant Sci., 7, 817, 10.3389/fpls.2016.00817 Dezulian, 2005, Identification of plant microRNA homologs, Bioinformatics, 22, 359, 10.1093/bioinformatics/bti802 Sunkar, 2006, Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance, Plant Cell, 18, 2051, 10.1105/tpc.106.041673 Zhou, 2007, UV-B responsive microRNA genes in Arabidopsis thaliana, Mol. Syst. Biol., 3, 10.1038/msb4100143 Bailey, 2009, MEME SUITE: tools for motif discovery and searching, Nucleic Acids Res., 37, W202, 10.1093/nar/gkp335 Finn, 2014, Pfam: the protein families database, Nucleic Acids Res., 42, D222, 10.1093/nar/gkt1223 Lu, 2019, CDD/SPARCLE: the conserved domain database in 2020, Nucleic Acids Res., 48, D265, 10.1093/nar/gkz991 Edgar, 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 32, 1792, 10.1093/nar/gkh340 Kumar, 2018, Molecular evolutionary genetics analysis across computing platforms, Mol. Biol. Evol., 35, 1547, 10.1093/molbev/msy096 Zhang, 2010, PMRD: plant microRNA database, Nucleic Acids Res., 38, D806, 10.1093/nar/gkp818 Fu, 2012, Accelerated for clustering the next-generation sequencing data, Bioinformatics, 28, 3150, 10.1093/bioinformatics/bts565 Conesa, 2005, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 21, 3674, 10.1093/bioinformatics/bti610 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 Busk, 2014, A tool for design of primers for microRNA-specific quantitative RT-qPCR, BMC Bioinf., 15, 29, 10.1186/1471-2105-15-29 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 Liao, 2016, Genome-wide analysis and environmental response profiling of dirigent family genes in rice (Oryza sativa), Genes & Genomics, 39, 47, 10.1007/s13258-016-0474-7 Gao, 2008, Toward understanding molecular mechanisms of abiotic stress responses in rice, Rice, 1, 36, 10.1007/s12284-008-9006-7 Cohen, 2019, Abiotic and biotic stresses induce a core transcriptome response in rice, Sci. Rep., 9, 1, 10.1038/s41598-019-42731-8 Kumar, 2012, Cloning, structural and expression analysis of OsSOS2 in contrasting cultivars of rice under salinity stress, Genes, Genomes Genomics, 6, 34 Purty, 2017, Structural and expression analysis of salinity stress responsive phosphoserine phosphatase from Brassica juncea L, J. Proteonomics Bioinf., 10, 119 Chatterjee, 2020, Expression analysis of serine biosynthesis pathway genes under various abiotic stress in Brassica juncea (L.) Czern, Plant Cell Biotechnol. Mol. Biol., 21, 11 Khan, 2018, Genome-wide analysis of dirigent gene family in pepper (Capsicum annuum L.) and characterization of CaDIR7 in biotic and abiotic stresses, Sci. Rep., 8 Wang, 2012, Identification of microRNAs from Amur grape (Vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics, BMC Genom., 13, 122, 10.1186/1471-2164-13-122 Xing, 2015, Shoot bending promotes flower bud formation by miRNA-mediated regulation in apple (Malus domestica Borkh.), Plant Biotechnology Journal, 14, 749, 10.1111/pbi.12425 Tang, 2017, MicroRNAs in crop improvement: fine-tuners for complex traits, Nat. Plants, 3, 17077, 10.1038/nplants.2017.77 Pereira, 2016, Plant abiotic stress challenges from the changing environment, Front. Plant Sci., 7, 1123, 10.3389/fpls.2016.01123 Zhou, 2010, Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa, J. Exp. Bot., 61, 4157, 10.1093/jxb/erq237 Nadarajah, 2019, Drought response in rice: the miRNA story, Int. J. Mol. Sci., 20, 3766, 10.3390/ijms20153766 Peng, 2020, Bioinformatic analysis reveals the functions of miRNA in rice under drought stress, Curr. Bioinf., 15, 10.2174/1574893615666200207092410 Mittal, 2015, Role of microRNAs in rice plant under salt stress, Ann. Appl. Biol., 168, 2, 10.1111/aab.12241 Mondal, 2018, Discovery of microRNA-target modules of African rice (Oryza glaberrima) under salinity stress, Sci. Rep., 8, 1, 10.1038/s41598-017-18206-z Kord, 2019, Salinity-associated microRNAs and their potential roles in mediating salt tolerance in rice colonized by the endophytic root fungus Piriformospora indica, Funct. Integr. Genom., 19, 659, 10.1007/s10142-019-00671-6 Sailaja, 2014, Prediction and expression analysis of miRNAs associated with heat stress in Oryza sativa, Rice Sci., 21, 3, 10.1016/S1672-6308(13)60164-X Mangrauthia, 2017, Genome-wide changes in microRNA expression during short and prolonged heat stress and recovery in contrasting rice cultivars, J. Exp. Bot., 68, 2399, 10.1093/jxb/erx111 Lv, 2010, Profiling of cold-stress-responsive miRNAs in rice by microarrays, Gene, 459, 39, 10.1016/j.gene.2010.03.011 Huang, 2009, Heavy metal-regulated new microRNAs from rice, J. Inorg. Biochem., 103, 282, 10.1016/j.jinorgbio.2008.10.019 Ding, 2011, Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa), J. Exp. Bot., 62, 3563, 10.1093/jxb/err046 Sun, 2019, Transcriptome analysis of rice (Oryza sativa L.) shoots responsive to cadmium stress, Sci. Rep., 9, 1 Gao, 2016, MicroRNAs modulate adaption to multiple abiotic stresses in Chlamydomonas reinhardtii, Sci. Rep., 6, 38228, 10.1038/srep38228 Yang, 2012, Genome wide analysis of intronic microRNAs in rice and Arabidopsis, J. Genet., 91, 313, 10.1007/s12041-012-0199-6 Lu, 2011, Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa, Mol. Biol. Evol., 29, 1005, 10.1093/molbev/msr282 Jeong, 2013, The role of rice microRNAs in abiotic stress responses, J. Plant Biol., 56, 187, 10.1007/s12374-013-0213-4 Kumar, 2014, Role of MicroRNAs in biotic and abiotic stress responses in crop plants, Appl. Biochem. Biotechnol., 174, 93, 10.1007/s12010-014-0914-2 Lata, 2019, Role of microRNAs in abiotic and biotic stress resistance in plants, 85, 553 Wani, 2020, miRNA applications for engineering abiotic stress tolerance in plants, Biologia, 10.2478/s11756-019-00397-7