caa a22 4500 606208860 CHVBK 20210128101025.0 cr unu---uuuuu 210128e20150601xx s 000 0 eng 10.1007/s00425-015-2267-7 doi (NATIONALLICENCE)springer-10.1007/s00425-015-2267-7 High-throughput sequencing reveals differential expression of miRNAs in tomato inoculated with Phytophthora infestans [Elektronische Daten] [Yushi Luan, Jun Cui, Junmiao Zhai, Jie Li, Lu Han, Jun Meng] Main conclusion : The characterization and compare expression profiling of the miRNA transcriptome lay a solid foundation for unraveling the complex miRNA-mediated regulatory network in tomato resistance mechanisms against LB. MicroRNAs (miRNAs) are a class of small endogenous non-coding RNAs with 20-24nt. They have been identified in many plants with their diverse regulatory roles in biotic stresses. The knowledge, that miRNAs regulate late blight (LB), caused by Phytophthora infestans, is rather limited. In this study, we used miRNA-Seq to investigate the miRNA expression difference between the tomatoes treated with and without P. infestans. A total of 42,714,516 raw reads were generated from two small RNA libraries by high-throughput sequencing. Finally, 207 known miRNAs and 67 new miRNAs were obtained. The differential expression profile of miRNAs in tomato was further analyzed with twofold change (P value ≤0.01). A total of 70 miRNAs were manifested to change significantly in samples treated with P. infestans, including 50 down-regulated miRNAs and 20 up-regulated miRNAs. Moreover, a total of 73 target genes were acquired for 28 differentially expressed miRNAs by psRNATarget analysis. By enrichment pathway analysis of target genes, plant-pathogen interaction was the most highly relevant pathway which played an important role in disease defense. In addition, 30 miRNAs were selected for qRT-PCR to validate their expression patterns. The expression patterns for targets of miR6027, miR5300, miR476b, miR159a, miR164a and miRn13 were selectively examined, and the results showed that there was a negative correlation on the expression patterns between miRNAs and their targets. The targets have previously been reported to be related with plant immune and involved in plant-pathogen interaction pathway in this study, suggesting these miRNAs might act as regulators in process of tomato resistance against P. infestans. These discoveries will provide us useful information to explain tomato resistance mechanisms against LB. Springer-Verlag Berlin Heidelberg, 2015 Bioinformatics nationallicence Biotic stress nationallicence High-throughput sequencing nationallicence MicroRNA nationallicence Phytophthora nationallicence Tomato nationallicence BGI : Beijing Genomics Institute nationallicence CMV : Cucumber mosaic virus nationallicence Cs : Control samples nationallicence ETI : Effector-triggered immunity nationallicence GO : Gene Ontology nationallicence HR : Hypersensitive response nationallicence KEGG : Kyoto Encyclopedia of Genes and Genomes nationallicence LB : Late blight nationallicence MFE : Minimum free energy nationallicence MiRNA : MicroRNA nationallicence qRT-PCR : Reverse transcription-quantitative polymerase chain reaction nationallicence Rpi gene : Resistance genes against P. infestans nationallicence rRNA : Ribosomal RNA nationallicence snoRNA : Small nuclear RNA nationallicence snRNA : Small nuclear ribonucleic acids nationallicence TMV : Tobacco mosaic virus nationallicence ToMV : Tomato mosaic virus nationallicence tRNA : Transfer RNA nationallicence Ts : Treated samples nationallicence TuMV : Turnip mosaic virus nationallicence Luan Yushi School of Life Science and Biotechnology, Dalian University of Technology, 116024, Dalian, China aut Cui Jun School of Life Science and Biotechnology, Dalian University of Technology, 116024, Dalian, China aut Zhai Junmiao School of Life Science and Biotechnology, Dalian University of Technology, 116024, Dalian, China aut Li Jie School of Life Science and Biotechnology, Dalian University of Technology, 116024, Dalian, China aut Han Lu School of Life Science and Biotechnology, Dalian University of Technology, 116024, Dalian, China aut Meng Jun School of Computer Science and Technology, Dalian University of Technology, 116024, Dalian, China aut Planta Springer Berlin Heidelberg 241/6(2015-06-01), 1405-1416 0032-0935 241:6<1405 2015 241 425 https://doi.org/10.1007/s00425-015-2267-7 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00425-015-2267-7 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Luan Yushi School of Life Science and Biotechnology, Dalian University of Technology, 116024, Dalian, China aut NATIONALLICENCE 700 1- Cui Jun School of Life Science and Biotechnology, Dalian University of Technology, 116024, Dalian, China aut NATIONALLICENCE 700 1- Zhai Junmiao School of Life Science and Biotechnology, Dalian University of Technology, 116024, Dalian, China aut NATIONALLICENCE 700 1- Li Jie School of Life Science and Biotechnology, Dalian University of Technology, 116024, Dalian, China aut NATIONALLICENCE 700 1- Han Lu School of Life Science and Biotechnology, Dalian University of Technology, 116024, Dalian, China aut NATIONALLICENCE 700 1- Meng Jun School of Computer Science and Technology, Dalian University of Technology, 116024, Dalian, China aut NATIONALLICENCE 773 0- Planta Springer Berlin Heidelberg 241/6(2015-06-01), 1405-1416 0032-0935 241:6<1405 2015 241 425