Temporal coordination of probes associated with sucrose and starch metabolism pathways.

<p>The time of peak of rhythms in transcript levels of genes associated with sucrose and starch metabolism was identified in a schematic metabolic pathway. Each circle corresponds to a specific gene model. Metabolic pathways were colored according to the median of the phase of their constitutive genes. The time of peak of probes associated with starch and sucrose synthesis pathways was between ZT20 and ZT4, while the time of the peak of probes associate to sucrose and starch degradation was between ZT8 to ZT16. Genes that were not circadian (n. c.) were in gray. Rhythmic with a time of peak at ZT0 are in yellow, ZT4 in dark orange, ZT8 in red, ZT12 in blue, ZT16 in dark blue and ZT20 in light blue. Enzymes for sucrose synthesis are: (<b>1</b>) sucrose-phosphate synthase; (<b>2</b>) sucrose phosphatase; (<b>3</b>) sucrose synthase; (<b>4</b>) neutral invertase; (<b>5</b>) hexokinase; (<b>6</b>) fructokinase; (<b>7</b>) glucose-6-phosphate isomerase; (<b>8</b>) phosphoglucomutase; (<b>9</b>) UDP-glucose pyrophosphorylase <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071847#pone.0071847-Rohwer1" target="_blank">[75]</a>. Abbreviations: S6P – sucrose 6-phosphate; UDP-G - UDP-glucose; G1P – glucose 1-phosphate; G6P – glucose 6-phosphate; F6P – fructose 6-phosphate; ADP-G – ADP-glucose; 3P glycerate – 3-phospho glycerate.</p

Sense and antisense transcripts are modulated differently by the circadian clock.

<p>(<b>A</b>) Overlap between SAS that had their probes for sense transcripts (SS) considered circadian and SAS that had their probes for antisense transcripts (AS) considered circadian. (<b>B</b>) Distribution of Spearman's rank correlation coefficient (ρ) for each of all the 428 pairs of SS/AS (light blue) and only the 207 pairs of SS/AS that had at least one probe considered circadian (orange). If ρ >0.56, correlation is positive and significant. If ρ <−0.56, correlation is negative and significant. (<b>C to F</b>) Z-score normalized expression levels of SS (red) and AS (dark blue) for a gene that have (<b>C</b>) both SS and AS in the same phase (RuBisCo activase; SCBGLR1044D06.g,), (<b>D</b>) SS and AS in opposite phases (urease, SCSGLR1045A02.g), (<b>E</b>) AS peaking before SS (glucose 1-phosphate adenylyltransferase, SCVPCL6061A06.g) and (<b>F</b>) SS peaking before AS (violaxanthin de-epoxidase, SCVPHR1095C07.g). White boxes represent periods of subjective day and light grey boxes represent periods of subjective night.</p

Number of rhythmic probes in the sense direction (SS) and in the antisense direction (AS) considered expressed and rhythmic in the sugarcane dataset.

*<p>compared to the number of probes;</p>**<p>compared to number of probes expressed in ≤10 time points.</p

Time courses of probes associated with the perception of light.

<p>Z-score normalized time courses of rhythmic probes for sugarcane transcripts associated with the perception of light. Expression levels were measured using oligoarrays. Different probes for the same sugarcane genes are represented separately. (<b>A</b>) <i>PHYTOCHROME A</i> (Sc<i>PHYA</i>), (<b>B</b>) <i>ScPHYB</i>, (<b>C</b>) Sc<i>PHYC</i>, (<b>D</b>) <i>CRYPTOCHROME1</i> (Sc<i>CRY1</i>), (<b>E</b>) Sc<i>CRY2</i>, (<b>F</b>) <i>PHOTOTROPIN</i> (<i>ScPHOT</i>) (<b>G</b>) <i>ZEITLUPE</i> (<i>ZTL-1</i>), (<b>H</b>) <i>ZTL</i>-2, (<b>I</b>) Sc<i>UVR8</i>. White boxes represent periods of subjective day and light grey boxes represent periods of subjective night.</p

Identification of rhythmic sense and antisense transcripts in sugarcane.

<p>(<b>A</b>) Venn diagram showing the number of sense probes that were considered expressed and were considered rhythmic by three algorithms: JTK_CYCLE, COSOPT and Fisher's G-test. Probes identified as rhythmic in at least two algorithms were considered circadian. (<b>B</b>) Phase distribution of rhythmic sense probes. The phase of each rhythmic probe was estimated using JTK_CYCLE and binned in 6 groups, according to the time of their peak. (<b>C</b>) Venn diagram showing the number of antisense probes that were considered expressed and considered rhythmic by three algorithms: JTK_CYCLE, COSOPT and Fisher's G-test. (<b>D</b>) Phase distribution of circadian antisense probes.</p

Pathways regulated by the sugarcane circadian clock.

<p>The number of SS and AS probes considered circadian compared to the total number of transcripts expressed in the pathway (in parenthesis) and the phase of the circadian SS transcripts (median ± MAD).</p>*<p>two populations with distinct phases were detected.</p

Sugarcane has a high proportion of rhythmic probes associated with sucrose metabolism.

<p>The number of circadian probes and the total number of probes (in parenthesis) was determined for each enzyme model in different datasets and different methods of analysis. CJF: analysis using COSPOT, Fisher's G-test and JTK-CYCLE; C-CJF: Covington dataset; E-CJF: Edwards dataset; D: data taken from DIURNAL (<a href="http://diurnal.mocklerlab.org/" target="_blank">http://diurnal.mocklerlab.org/</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071847#pone.0071847-Mockler1" target="_blank">[76]</a>.</p>1<p>probes that peak at ZT0;</p>2<p>cells in red represent probes that peak at ZT8;</p>3<p>probes that peak at ZT16;</p>4<p>probes that peak at ZT20.</p