New cross talk between ROS, ABA and auxin controlling seed maturation and germination unraveled in APX6 deficient Arabidopsis seeds

<div><p>Successful execution of germination program greatly depends on the seeds’ oxidative homeostasis. We recently identified new roles for the H₂O₂-reducing enzyme ascorbate peroxidase 6 (APX6) in germination control and seeds’ stress tolerance. <i>APX6</i> replaces <i>APX1</i> as the dominant APX in dry seeds, and its loss-of-function results in reduced germination due to over accumulation of ROS and oxidative damage. Metabolic analyses in dry <i>apx6</i> seeds, revealed altered homeostasis of primary metabolites including accumulation of TCA cycle metabolites, ABA and auxin, supporting a novel role for APX6 in regulating cellular metabolism. Increased sensitivity of <i>apx6</i> mutants to ABA or IAA in germination assays indicated impaired perception of these signals. Relative suppression of <i>ABI3</i> and <i>ABI5</i> expression, and induction of <i>ABI4</i>, suggested the activation of a signaling route inhibiting germination in <i>apx6</i> seeds that is independent of ABI3. Here we provide additional evidence linking ABI4 with ABA- and auxin-controlled inhibition of germination and suggest a hypothetical model for the role of APX6 in the regulation of the crosstalk between these hormones and ROS.</p></div

Comparison of <i>de novo</i> assembly using Trinity and Velvet-oases programs.

*<p>Represents the number of contigs that at less 200 bp in length.</p>#<p>represents the result of TIGCL and Phrap for reduce the redundancy after Trinity with 25-mer assembly.</p

SNP statistical information based on mapping <i>C. frutescens</i> reads in reference to <i>C. annuum</i> contigs.

<p>SNP statistical information based on mapping <i>C. frutescens</i> reads in reference to <i>C. annuum</i> contigs.</p

The number of SSR in all unigenes and CDS.

<p>The blue bar represents SSR markers in all unigenes, and the red bar represents SSR markers in CDS.</p

Illustrated the partly distribution (ratio of alignment/short no less than 0.8) of homologous length and aligned length.

<p>The X axis represents the ratio is length of pepper EST/unigene length, the Y axis is represents the ratio of alignment length/shorter between pepper EST and unigene.</p

Identity new transcripts (genes) on the capsaicinoids biosynthetic pathway.

<p>Identity new transcripts (genes) on the capsaicinoids biosynthetic pathway.</p

Size distribution of the unigenes and CDS.

<p>The blue and red bars indicate unigene and CDS, respectively.</p

<em>De Novo</em> Transcriptome Assembly in Chili Pepper (<em>Capsicum frutescens</em>) to Identify Genes Involved in the Biosynthesis of Capsaicinoids

<div><p>The capsaicinoids are a group of compounds produced by chili pepper fruits and are used widely in many fields, especially in medical purposes. The capsaicinoid biosynthetic pathway has not yet been established clearly. To understand more knowledge in biosynthesis of capsaicinoids, we applied RNA-seq for the mixture of placenta and pericarp of pungent pepper (<em>Capsicum frutescens</em> L.). We have assessed the effect of various assembly parameters using different assembly software, and obtained one of the best strategies for <em>de novo</em> assembly of transcriptome data. We obtained a total 54,045 high-quality unigenes (transcripts) using Trinity software. About 92.65% of unigenes showed similarity to the public protein sequences, genome of potato and tomato and pepper (<em>C. annuum</em>) ESTs databases. Our results predicted 3 new structural genes (DHAD, TD, PAT), which filled gaps of the capsaicinoid biosynthetic pathway predicted by Mazourek, and revealed new candidate genes involved in capsaicinoid biosynthesis based on KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. A significant number of SSR (Simple Sequence Repeat) and SNP (Single Nucleotide Polymorphism) markers were predicted in <em>C. frutescens</em> and <em>C. annuum</em> sequences, which will be helpful in the identification of polymorphisms within chili pepper populations. These data will provide new insights to the pathway of capsaicinoid biosynthesis and subsequent research of chili peppers. In addition, our strategy of <em>de novo</em> transcriptome assembly is applicable to a wide range of similar studies.</p> </div

The results of annotation on unigenes by different databases.

<p>Note:</p>1<p>presents the unigenes annotated by whole protein sequences using blastx,</p>2<p>presents the unigenes annotated by whole genome using blat.</p

The clusters revealed by the voxel-wise linear regression model.

<p>In these clusters, the gray matter volume (vertical axis) correlated negatively with the normalized reaction time cost (horizontal axis, calculated as follow: (rt_incongruent-rt_congruent)/rt_neutral.</p