Additional file 11: Figure S4. of Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice

Drought response phenotype of rice in the vegetative state. a The phenotypic effect of progressive drought on wild type rice (Oryza sativa cv. Ilmi) at the vegetative growth stage. b Decrease in soil water content during drought treatment. c The transcript levels of Dip1 and RbcS1 in the leaves of drought-treated and well-watered control plants over a time course of exposure to drought were measured by qRT-PCR analysis. Values shown are the means ± SD of three independent experiments and are presented relative to the results from the control. (TIF 17024 kb

Additional file 10: Tabular data 3. of Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice

List of drought responsive long noncoding RNAs (lncRNAs). (XLSX 529 kb

Additional file 5: Figure S3. of Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice

Differentially expressed transcripts were classified into 3 main GO categories: Biological processes, Cellular components and Molecular functions. (TIF 8355 kb

Additional file 3: Figure S2. of Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice

Heat Map of the differentially expressed coding (a) and noncoding genes (b) under drought conditions. (TIF 5474 kb

Additional file 1: Table S1. of Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice

Information about the RNA-seq data obtained by Illumina Hi-seq 2500 sequencing. (XLSX 12 kb

Additional file 6: Table S3. of Transcriptome profiling of drought responsive noncoding RNAs and their target genes in rice

List of miRNAs that are constitutive pattern of high expression and low expression level. 1 Bold in miRNAs ID, rice specific drought responsive miRNAs; 2 RPKM, Reads Per Kilobase of transcript per Million mapped reads; 3 C, control; 4 1d, drought treatment for 1 day; 5 2d, drought treatment for 2 days; 6 3d, drought treatment for 3 days; 7 log2 ratio, log2(drought treatment / control), 8 Red, up-regulation by drought; Blue, down-regulation by drought Abbreviations: At, Arabidopsis thaliana; Bd, Brachypodium distachyon; Gm, Glycine max; Hv, Hordeum vulgare; Mt, Medicago truncatula; Me, Manihot esculenta; Pv, Phaseolus vulgaris; Peu, Populus euphratica; Ptc, Populus trichocarpa; Ppe, Prunus persica; Pte: Populus tremula; Pto, Populus tomentosa; Td, Triticum dicoccoides; Tt, Triticum turgidum; Os, Oryza sativa; Vu, Vigna unguiculata; Zm, Zea mays [10, 15]. (XLSX 24 kb

Rhododendron sanctum Nakai

原著和名: ジングウツツジ科名: ツツジ科 = Ericaceae採集地: 静岡県 引佐郡 引佐町 渋川 (遠江 引佐郡 引佐町 渋川)採集日: 1960/5/29採集者: 萩庭丈壽整理番号: JH015479国立科学博物館整理番号: TNS-VS-96547

Image_1_A Nitrogen Molecular Sensing System, Comprised of the ALLANTOINASE and UREIDE PERMEASE 1 Genes, Can Be Used to Monitor N Status in Rice.PDF

<p>Nitrogen (N) is an essential nutrient for plant growth and development, but its concentration in the soil is often insufficient for optimal crop production. Consequently, improving N utilization in crops is considered as a major target in agricultural biotechnology. However, much remains to be learnt about crop N metabolism for application. In this study, we have developed a molecular sensor system to monitor the N status in rice (Oryza sativa). We first examined the role of the ureide, allantoin, which is catabolized into allantoin-derived metabolites and used as an N source under low N conditions. The expression levels of two genes involved in ureide metabolism, ALLANTOINASE (OsALN) and UREIDE PERMEASE 1 (OsUPS1), were highly responsive to the N status. OsALN was rapidly up-regulated under low N conditions, whereas OsUPS1 was up-regulated under high N conditions. Taking advantage of the responses of these two genes to N status, we generated transgenic rice plants harboring the molecular N sensors, proALN::ALN-LUC2 and proUPS1::UPS1-LUC2, comprising the gene promoters driving expression of the luciferase reporter. We observed that expression of the transgenes mimicked transcriptional regulation of the endogenous OsALN and OsUPS1 genes in response to exogenous N status. Importantly, the molecular N sensors showed similar levels of specificity to nitrate and ammonium, from which we infer their sensing abilities. Transgenic rice plants expressing the proUPS1::UPS1-LUC2 sensor showed strong luminescence under high exogenous N conditions (>1 mM), whereas transgenic plants expressing the proALN::ALN-LUC2 sensor showed strong luminescence under low exogenous N conditions (<0.1 mM). High exogenous N (>1 mM) substantially increased internal ammonium and nitrate levels, whereas low exogenous N (<0.1 mM) had no effect on internal ammonium and nitrate levels, indicating the luminescence signals of molecular sensors reflect internal N status in rice. Thus, proALN::ALN-LUC2 and proUPS1::UPS1-LUC2 represent N molecular sensors that operate over a physiological and developmental range in rice.</p

Restoration of root growth inhibition phenotype by complementation.

<p>Col-0, <i>coi1-1</i> heterozygote, and complemented T3 homozygous lines were grown vertically on MS media containing 50 µM MeJA (left) or without MeJA (right). The asterisk indicates <i>coi1-1</i> homozygote which was tested by PCR and <i>Xcm</i>I enzyme digestion.</p

Summary of the Y2H assay of OsJAZs.

1<p>The strength of each interaction was rated as strong (+++), medium (++), weak (+) or undetectable (−), as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052802#pone.0052802.s004" target="_blank">Figure S4</a>.</p>2<p>OsCOI1a(N475Y) is a point mutant in which asparagine at 475 has been changed to tyrosine.</p>3<p>OsCOI2(H391Y) is a point mutant in which histidine at 391 has been changed to tyrosine.</p>4<p>OsCOI2(F91Y) is a point mutant in which phenylalanine at 91 has been changed to tyrosine.</p>5<p>OsCOI2(N477Y) is a point mutant in which asparagine at 477 has been changed to tyrosine.</p>6<p>OsCOI2(F91Y, H391Y, N477Y) is a point mutant in which each amino acid at there position has been changed to tyrosine.</p>7<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052802#pone.0052802-Seo1" target="_blank">[21]</a>.</p