halleri_transcript_modified_lyrataJGI_ERCC_2_CBF2_Virus3981_Ahg

The reference transcriptome sequences file of Arabidopsis halleri subsp. gemmifer

Heatmap of all expressed genes.

<p>Gene expression was calculated using log-transformed RPKM values. Gene expression data were rearranged according to artificial data. The color palette was that of the topo.colors package of R software and shows data in 12 steps. Correlation coefficients are listed in order of gene (high, A). Genes with log values of ≤0.1 were used as blanks (1090 genes).</p

Expression patterns of <i>timing of CAB expression 1</i> (<i>TOC1</i>) and <i>late elongated hypocotyl</i> (<i>LHY</i>).

<p><i>Arabidopsis thaliana</i> gene data were collected from the diurnal database. Registered data from the diurnal database for every 4 hours from 6:00 to 2:00, we used the data of <i>A</i>. <i>thaliana</i> in the overlaped time with tomato; diamonds, triangles, circles, and x marks indicate expression patterns of <i>Sl_LHY1</i>, <i>Sl_TOC1</i>, <i>At_CCA1</i>, and <i>At_TOC1</i>. Black and red lines indicate genes of tomato and <i>A</i>. <i>thaliana</i>, respectively.</p

Supplemental Data. Shirakawa et al. (2014). Plant Cell 10.1105/tpc.114.129874_Microarray data of Col_vs_syp22

Microarray data of Col_vs_syp22

Statistical analysis of hormone pathway-related genes.

<p>Statistical analysis of hormone pathway-related genes.</p

Comparison of hormone pathway-related genes in tomato and <i>Arabidopsis thaliana</i>.

<p>Temporal expression data for <i>A</i>. <i>thaliana</i> were collected from the diurnal database (<a href="http://diurnal.mocklerlab.org/" target="_blank">http://diurnal.mocklerlab.org/</a>) using LDHC data. <i>AAO3</i>, <i>ACS1</i>, <i>ACO1</i>, <i>EIN2</i>, <i>ERF1</i>, <i>PDF1</i>, <i>CTR1</i>, <i>PDF1</i>, <i>NDR1</i>, <i>EDR1</i>, <i>NPR1</i>, <i>LOX</i>, <i>OPR1</i>, <i>WRKY51</i>, <i>JAI1</i>, and <i>VSP</i> of <i>A</i>. <i>thaliana</i> were not temporally expressed. Gene IDs of <i>A</i>. <i>thaliana</i> are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143412#pone.0143412.s001" target="_blank">S1 Table</a>. <i>A</i>. <i>thaliana</i> genes indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143412#pone.0143412.g005" target="_blank">Fig 5</a> that were not registered with the diurnal database were excluded from analyses. The diamond-shape (blue line) and circle-shape (red line) indicate expression patterns of <i>A</i>. <i>thaliana</i> and tomato, respectively. Asterisks indicate temporally expressed genes in tomato. (A) Abscisic acid pathway, (B) Ethylene pathway, (C) Salicylic acid pathway, and (D) Jasmonic acid pathway.</p

Overview of prediction plant hormone pathway responses.

<p>Abscisic acid (ABA), ethylene (ET), salicylic acid (SA), and jasmonic acid (JA) are representative plant hormones and are known to respond to various stimuli. Orange and blue boxes show representative hormone-related genes with homology to those in <i>Arabidopsis thaliana</i> (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143412#pone.0143412.s001" target="_blank">S1 Table</a>). Orange boxes indicate biosynthetic products; blue boxes indicate genes that suppress hormone pathways. Asterisks (*) indicate temporally expressed genes with <i>p</i>-values of <0.05 and false discovery rate values of <0.05. ABA pathway: SDR, short-chain dehydrogenase/reductase; ABA3, abscisic acid deficient 3; ET pathway: ACO1, 1-aminocyclopropane-1-carboxylate oxidase; ACS1, arabidopsis cysteine synthase 1; EIN2, ethylene insensitive 2; PDF1, plant defensin 1; CTR1, constitutive triple response 1; ERF4, ethylene response factor4; SA pathway: PAL, phenylalanine ammonia-lyase; SID2, salicylic acid induction deficient 2; EDR1, enhanced disease resistance 1; NPR1, nonexpressor of pathogenesis-related genes 1; JA pathway: AOC, allene oxide cyclase; VSP, vegetative storage protein; JAL1, jasmonate resistance long hypocotyl 1. WRKY is a transcription factor.</p

Expression levels of hormone-related tomato genes in the sunlight type factory and under LL conditions.

<p>The diamond-shape (blue line) and the circle-shape (red line) indicate expression patterns under LL conditions and in the sunlight type plant factory, respectively. Asterisks (*) indicate temporally expressed hormone-related genes in the sunlight-type plant factory. Temporal expression of hormone-related tomato genes was abolished under LL conditions. (A) Abscisic acid pathway, (B) ethylene pathway, (C) salicylic acid pathway, and (D) jasmonic acid pathway.</p

Environmental conditions in a sunlight-type plant factory.

<p>Environmental conditions in Matsuyama, Japan, on January 6^th–8^th, 2014. Measured values were recorded from instruments installed in the plant factory. Temperature was calculated as the average of two measurements. Temperature (black line), relative humidity (black broken line), solar radiation (gray bar), and precipitation (light gray bar) are presented in 10-minute intervals. The arrows show experimental periods, and daily measurements were recorded between 14:00 and 14:00.</p

Expression levels of opening–closing stomata-related genes.

<p>Gene data for <i>Arabidopsis thaliana</i> was collected from the TAIR database (<a href="http://www.arabidopsis.org/" target="_blank">http://www.arabidopsis.org/</a>), and relationships between ABI1 and stomata-related genes were elucidated using STRING software (Ver. 9.1). Because registered data from the diurnal database for every 4 hours from 6:00 to 2:00, we used the data of <i>A</i>. <i>thaliana</i> in the overlaped time with tomato. Expression patterns of <i>A</i>. <i>thaliana</i> genes were collected from the diurnal database using LDHC data (<i>At_OST1</i>, AT4G33950; <i>At_ABI1</i>, AT4G26080; <i>At_SLAC1</i>, AT1G12480). Homologous tomato genes were identified using the Homolog search systems in Pytozome and NCBI databases. Diamonds, triangles, circles, and x marks indicate expression patterns of <i>OST1</i>, <i>ABI1</i>, <i>PP2CA</i>, and <i>SLAC1</i>, respectively; <i>At_PP2CA</i> was not registered with the diurnal database. (A) Stomata-related genes of tomato and (B) stomata-related genes of <i>A</i>. <i>thaliana</i>.</p