Transcriptional search to identify and assess reference genes for expression analysis in Solanumlycopersicum under stress and hormone treatment conditions

Alwine, 1977, Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes, Proceedings of the National Academy of Sciences of the United States of America, 74, 5350, 10.1073/pnas.74.12.5350 Andersen, 2004, Normalization of real-time quantitative reverse transcription-PCR data: a model based variance estimation approach to identify genes suited for normalization, applied to bladder, and colon cancer data-sets, Cancer Research, 64, 5245, 10.1158/0008-5472.CAN-04-0496 Aslam, 2022, Recent insights into signaling responses to cope drought stress in rice, Rice Science, 29, 105, 10.1016/j.rsci.2021.08.001 Bai, 2018, Plant behaviour under combined stress: Tomato responses to combined salinity and pathogen stress, The Plant Journal, 93, 781, 10.1111/tpj.13800 Barsalobres-Cavallari, 2009, Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions, BMC Molecular Biology, 10, 1, 10.1186/1471-2199-10-1 Biondi, 2018, Ecology, worldwide spread, and management of the invasive South American tomato pinworm, Tuta absoluta: Past, present, and future, Annual Review of Entomology, 63, 239, 10.1146/annurev-ento-031616-034933 Bustin, 2013, The need for transparency and good practices in the qPCR literature, Nature Methods, 10, 1063, 10.1038/nmeth.2697 Bustin, 2004, Pitfalls of quantitative real-time reverse transcription polymerase chain reaction, Journal of Biomolecular Techniques, 15, 155 Cassol, 2016, Identification of reference genes for quantitative RT-PCR analysis of microRNAs and mRNAs in castor bean (Ricinus communis L.) under drought stress, Plant Physiology and Biochemistry, 106, 101, 10.1016/j.plaphy.2016.02.024 Cheng, 2017, Genome-wide identification and evaluation of reference genes for quantitative RT-PCR analysis during tomato fruit development, Frontiers in Plant Science, 8 Coker, 2003, Selection of candidate housekeeping controls in tomato plants using EST data, BioTechniques, 35, 740, 10.2144/03354st04 Czechowski, 2005, Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis, Plant Physiology, 139, 5, 10.1104/pp.105.063743 Dekkers, 2012, Identification of reference genes for RT-qPCR expression analysis in Arabidopsis and tomato seeds, Plant and Cell Physiology, 53, 28, 10.1093/pcp/pcr113 Du, 2013 Eisenberg, 2013, Human housekeeping genes, revisited, Trends in Genetics, 29, 569, 10.1016/j.tig.2013.05.010 Expósito-Rodríguez, 2008, Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process, BMC Plant Biology, 8, 131, 10.1186/1471-2229-8-131 Fodor, 1991, Light-directed, spatially addressable parallel chemical synthesis, Science, 251, 767, 10.1126/science.1990438 Gachon, 2004, Real-time PCR: What relevance to plant studies?, Journal of Experimental Botany, 55, 1445, 10.1093/jxb/erh181 Gao, 2018, Transcriptome-wide identification of optimal reference genes for expression analysis of Pyropia yezoensis responses to abiotic stress, BMC Genomics, 19, 251, 10.1186/s12864-018-4643-8 Gerszberg, 2017, Tomato tolerance to abiotic stress: A review of most often engineered target sequences, Plant Growth Regulation, 83, 175, 10.1007/s10725-017-0251-x Gibson, 1996, A novel method for real time quantitative RT-PCR, Genome Research, 6, 995, 10.1101/gr.6.10.995 Gong, 2016, LbCML38 and LbRH52, two reference genes derived from RNA-Seq data suitable for assessing gene expression in Lycium barbarum L, Scientific Reports, 6, 10.1038/srep37031 González-Aguilera, 2016, Selection of reference genes for quantitative real-time RT-PCR studies in tomato fruit of the genotype MT-Rg1, Frontiers in Plant Science, 7, 10.3389/fpls.2016.01386 Gutierrez, 2008, Towards a systematic validation of references in real-time RT-PCR, The Plant Cell, 20, 1734, 10.1105/tpc.108.059774 Habib, 2021, Down-regulation of SlGRAS10 in tomato confers abiotic stress tolerance, Genes, 12, 623, 10.3390/genes12050623 Hoagland, 1950, The water-culture method for growing plants without soil, California Agricultural Experiment Station Circular, 347, 1 Hruz, 2011, RefGenes: Identification of reliable and condition specific reference genes for RT-qPCR data normalization, BMC Genomics, 12, 156, 10.1186/1471-2164-12-156 Huang, 2019, Genome-wide identification and evaluation of new reference genes for gene expression analysis under temperature and salinity stresses in Ciona savignyi, Frontiers in Genetics, 10, 71, 10.3389/fgene.2019.00071 Huggett, 2005, Real-time RT-PCR normalisation; strategies and considerations, Genes and Immunity, 6, 279, 10.1038/sj.gene.6364190 Huggett, 2006, Normalization, 83 Jahan, 2021, Melatonin-mediated photosynthetic performance of tomato seedlings under high-temperature stress, Plant Physiology and Biochemistry, 167, 309, 10.1016/j.plaphy.2021.08.002 Lacerda, 2015, Reference gene selection for qPCR analysis in tomato-bipartite begomovirus interaction and validation in additional tomato-virus pathosystems, PLoS ONE, 10, 10.1371/journal.pone.0136820 Li, 2021, Selection of reference genes for gene expression analysis in Liriodendron hybrids’ somatic embryogenesis and germinative tissues, Scientific Reports, 11 Lima, 2020, Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data, Briefings in Bioinformatics, 21, 1164, 10.1093/bib/bbz058 Lin, 2018, Effect of exogenous H2S and H2O2 on the physiological characteristics of processing tomato seedlings under NaCl stress, Acta Agriculturae Boreali-Sinica, 22, 159 Long, 2011, Identification and validation of internal control genes for gene expression in wheat leaves infected by strip rust, International Journal of Plant Breeding & Genetics, 5, 255, 10.3923/ijpbg.2011.255.267 Løvdal, 2009, Reference gene selection for quantitative real-time PCR normalization in tomato subjected to nitrogen, cold, and light stress, Analytical Biochemistry, 387, 238, 10.1016/j.ab.2009.01.024 Lyndon, 1992, Plant and organ development, Plant Molecular Biology, 19, 51, 10.1007/BF00015606 Mandal, 2009, Salicylic acid-induced resistance to Fusarium oxysporum f. sp. lycopersici in tomato, Plant Physiology and Biochemistry, 47, 642, 10.1016/j.plaphy.2009.03.001 Martins, 2016, Selection of reliable reference genes for RT-qPCR analysis during developmental stages and abiotic stress in Setaria viridis, Scientific Report, 6 Mascia, 2010, Evaluation of reference genes for quantitative reverse-transcription polymerase chain reaction normalization in infected tomato plants, Molecular Plant Pathology, 11, 805, 10.1111/j.1364-3703.2010.00646.x Mele, 2003, Expression profiling of plant development, Genome Biology, 4, 215, 10.1186/gb-2003-4-5-215 Müller, 2015, Genome-wide identification and validation of reference genes in infected tomato leaves for quantitative RT-PCR analyses, PLoS ONE, 10, 10.1371/journal.pone.0136499 Nemeskéri, 2019, Physiological responses of selected vegetable crop species to water stress, Agronomy, 9, 447, 10.3390/agronomy9080447 Pfaffl, 2004, Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper- Excel-based tool using pair-wise correlations, Biotechnology Letters, 26, 509, 10.1023/B:BILE.0000019559.84305.47 Pombo, 2017, Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato–Pseudomonas pathosystem, Scientific Report, 7 Redman, 2001, Fitness costs of jasmonic acid-induced defense in tomato, Lycopersicon esculentum, Oecologia, 126, 380, 10.1007/s004420000522 Reid, 2006, An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development, BMC Plant Biology, 6, 27, 10.1186/1471-2229-6-27 Rezzonico, 2018, Expression of tomato reference genes using established primer sets: Stability across experimental set-ups, Journal of Phytopathology, 166, 123, 10.1111/jph.12668 Rivas, 2005, Molecular interactions between tomato and the leaf mold pathogen Cladosporium fulvum, Annual Review of Phytopathology, 43, 395, 10.1146/annurev.phyto.43.040204.140224 Shinozaki, 2003, Cell signalling and gene regulation. Global analyses of signal transduction and gene expression profiles, Current Opinion in Plant Biology, 6, 405, 10.1016/S1369-5266(03)00093-1 Shinozaki, 2007, Gene networks involved in drought stress response and tolerance, Journal of Experimental Botany, 58, 221, 10.1093/jxb/erl164 Silver, 2006, Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR, BMC Molecular and Cell Biology, 7, 33, 10.1186/1471-2199-7-33 Sims, 2014, Sequencing depth and coverage: Key considerations in genomic analyses, Nature Reviews Genetics, 15, 121, 10.1038/nrg3642 Smitha, 2019, Genome wide search to identify reference genes candidates for gene expression analysis in Gossypium hirsutum, BMC Plant Biology, 19, 405, 10.1186/s12870-019-1988-3 Sun, 2010, Comparative transcriptomic profiling of a salt-tolerant wild tomato species and a salt-sensitive tomato cultivar, Plant and Cell Physiology, 6, 997, 10.1093/pcp/pcq056 Tang, 2017, Selection and validation of reference genes for RT-qPCR analysis in potato under abiotic stress, Plant Methods, 13, 85, 10.1186/s13007-017-0238-7 Tong, 2021, Determination of reliable reference genes for gene expression studies in Chinese chive (Allium tuberosum) based on the transcriptome profiling, Scientific Reports, 11, 10.1038/s41598-021-95849-z Vandesompele, 2002, Accurate normalization of real-time quantitative RT-PCR data by geo-metric averaging of multiple internal control genes, Genome Biology, 3, 34, 10.1186/gb-2002-3-7-research0034 Vinogradov, 2004, Compactness of human housekeeping genes: Selection for economy or genomic design?, Trends in Genetics, 20, 248, 10.1016/j.tig.2004.03.006 Vogelstein, 1999, Digital PCR, Proceedings of the National Academy of Sciences of the United States of America, 96, 9236, 10.1073/pnas.96.16.9236 Wan, 2010, Selection of appropriate reference genes for gene expression studies by quantitative real-time polymerase chain reaction in cucumber, Analytical Biochemistry, 399, 257, 10.1016/j.ab.2009.12.008 Wang, 1989, Quantitation of mRNA by the polymerase chain reaction, Proceedings of the National Academy of Sciences of the United States of America, 86, 9717, 10.1073/pnas.86.24.9717 Wang, 2022, The network centered on ICEs play roles in plant cold tolerance, growth and development, Planta, 255, 81, 10.1007/s00425-022-03858-7 Wang, 2009, RNA-Seq: A revolutionary tool for transcriptomics, Nature Reviews Genetics, 10, 57, 10.1038/nrg2484 Wieczorek, 2013, Assessment of reference gene stability influenced by extremely divergent disease symptoms in Solanum lycopersicum L, Journal of Virological Methods, 194, 161, 10.1016/j.jviromet.2013.08.010 Wong, 2005, Real-time PCR for mRNA quantitation, Biotechniques, 39, 75, 10.2144/05391RV01 Wu, 2021, Selection and validation of candidate reference genes for gene expression analysis by RT-qPCR in Rubus, International Journal of Molecular Sciences, 22 Xie, 2012, miRDeepFinder: A miRNA analysis tool for deep sequencing of plant small RNAs, Plant Molecular Biology, 80, 75, 10.1007/s11103-012-9885-2 Yang, 2021, Identification and validation of reference genes for gene expression analysis in Schima superba, Genes (Basel), 12, 732, 10.3390/genes12050732 Yin, 2021, Reference gene selection for miRNA and mRNA normalization in potato in response to potato virus Y, Molecular and Cellular Probes, 55, 10.1016/j.mcp.2020.101691 Zhang, 2021, Evaluation validation of a qPCR curve analysis method and conventional approaches, BMC Genomics, 22, 680, 10.1186/s12864-021-07986-4 Zhang, 2020, Selection of the reference gene for expression normalization in Papaver somniferum L. under abiotic stress and hormone treatment, Genes (Basel), 11, 124, 10.3390/genes11020124 Zhao, 2017, Genome-wide constitutively expressed gene analysis and new reference gene selection based on transcriptome data: A case study from poplar/canker disease interaction, Frontiers in Plant Science, 8, 10.3389/fpls.2017.01876 Zhou, 2017, Using RNA-seq data to select reference genes for normalizing gene expression in apple roots, The Public Library of Science, 12 Zhu, 2021, Expression stability of internal reference gene in response to Trichoderma polysporum infection in Avena fatua L, Current Genetics, 67, 909, 10.1007/s00294-021-01200-4