Transcriptional Reprogramming of Wheat and the Hemibiotrophic Pathogen <i>Septoria tritici</i> during Two Phases of the Compatible Interaction

<div><p>The disease septoria leaf blotch of wheat, caused by fungal pathogen <i>Septoria tritici</i>, is of worldwide concern. The fungus exhibits a hemibiotrophic lifestyle, with a long symptomless, biotrophic phase followed by a sudden transition to necrotrophy associated with host necrosis. Little is known about the systematic interaction between fungal pathogenicity and host responses at specific growth stages and the factors triggering the transition. In order to gain some insights into global transcriptome alterations in both host and pathogen during the two phases of the compatible interaction, disease transition was monitored using pathogenesis-related gene markers and H₂O₂ signature prior to RNA-Seq. Transcriptome analysis revealed that the slow symptomless growth was accompanied by minor metabolic responses and slightly suppressed defences in the host, whereas necrotrophic growth was associated with enhanced host responses involving energy metabolism, transport, signalling, defence and oxidative stress as well as a decrease in photosynthesis. The fungus expresses distinct classes of stage-specific genes encoding potential effectors, probably first suppressing plant defence responses/facilitating the symptomless growth and later triggering life style transition and inducing host necrosis/facilitating the necrotrophic growth. Transport, signalling, anti-oxidative stress mechanisms and apoplastic nutrient acquisition play important roles in the entire infection process of <i>S. tritici</i>. Our findings uncover systematic <i>S. tritici</i>-induced expression profiles of wheat related to specific fungal infection strategies and provide a transcriptome resource for studying both hosts and pathogens in plant-Dothideomycete interactions. </p></div

Overview of sequencing transcriptome data from wheat leaves.

<p>Overview of sequencing transcriptome data from wheat leaves.</p

Functional category distribution in the ten expression clusters of fungal transcripts.

<p>The fungal transcripts were identified from <i>S. tritici</i>-infected wheat at 4, 10 and 13 dai. Expression level of the transcripts was calculated by log₂FPKM. Histogram representation of the category distribution is expressed as percentage of the amount of transcripts belonging to the cluster. Transcripts coding for unknown products were included in the analysis. The clusters fall into three groups (A, B and C) based on the major profiling over the time course.</p

Heat map visualization of differentially expressed wheat transcripts.

<p>The plant transcripts are mainly involved in primary metabolism, signalling, transport and stress and defence in response to <i>S. tritici</i>. Differential expression patterns are based on the log₂ fold changes of transcript abundance in <i>S. tritici</i>-infected wheat <i>versus</i> controls at 4, 10 and 13 dai.</p

Principal component analysis of the transcriptome data.

<p>Principal components (PCs) 1, 2 and 3 account for 73.9, 11.6 and 7% of the variance, respectively. C₄, control at 4 dai; C₁₀, control at 10 dai; C₁₃, control at 13 dai; I₄, S. <i>tritici</i>-infected wheat at 4 dai; I₁₀, S. <i>tritici</i>-infected wheat at 10 dai; I₁₃, S. <i>tritici</i>-infected wheat at 13 dai.</p

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

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

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

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

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