37 research outputs found

    Building the sugarcane genome for biotechnology and identifying evolutionary trends

    Get PDF

    Rhythmic probes associated with sugar storage.

    No full text
    <p>Z-score normalized time courses of rhythmic probes for transcripts associated with sugar storage pathways were separated into (<b>A</b>) sucrose synthesis (light green); (<b>B</b>) sucrose degradation (dark green); (<b>C</b>) starch synthesis (dark red); (<b>D</b>) starch degradation (cyan); (<b>E</b>) starch branching (red); and starch debranching (light blue). White boxes represent periods of subjective day and light grey boxes represent periods of subjective night.</p

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

    No full text
    <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.

    No full text
    <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

    Proportion of rhythmic probes in different plant species using different algorithms.

    No full text
    1<p>Khan et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071847#pone.0071847-Khan1" target="_blank">[18]</a>;</p>2<p>Filichkin et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071847#pone.0071847-Filichkin2" target="_blank">[17]</a>;</p>3<p>Covington and Harmer <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071847#pone.0071847-Covington2" target="_blank">[39]</a>;</p>4<p>Edwards et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071847#pone.0071847-Edwards1" target="_blank">[20]</a>;</p>5<p>estimated.</p

    Time courses of probes associated with the perception of light.

    No full text
    <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.

    No full text
    <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

    Time courses of probes associated with the central oscillator.

    No full text
    <p>Z-score normalized time courses of rhythmic probes for sense sugarcane transcripts associated with the central oscillator. (<b>A–H</b>) Expression levels were measured using oligoarrays. Different probes for the same sugarcane genes are represented separately. Lighter lines indicate probes for antisense transcripts expression of the gene. (<b>I</b>) Expression levels were measured using RT-qPCR, using an arrhythmic GAPDH as reference. (<b>A</b>) <i>CIRCADIAN ASSOCIATED1</i> (<i>ScCCA1</i>), (<b>B</b>) <i>TIME OF CHLOROPHYLL A/B BINDING PROTEIN EXPRESSION (ScTOC1</i>), (<b>C</b>) <i>GIGANTEA</i> (<i>ScGI</i>), (<b>D</b>) <i>PSEUDO-RESPONSE REGULATOR3</i> (<i>ScPRR3</i>), (<b>E</b>) <i>ScPRR59</i>, (<b>F</b>) <i>Sc</i>PRR7, (<b>G</b>) <i>FIONA (ScFIO)</i>, (<b>H</b>) <i>EARLY-FLOWERING3</i> (Sc<i>ELF3</i>), and (<b>I</b>) <i>LUX ARRHYTHMO</i> (<i>ScLUX</i>). White boxes represent periods of subjective day and light grey boxes represent periods of subjective night.</p

    Pathways regulated by the sugarcane circadian clock.

    No full text
    <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
    corecore