Reduced representation sequencing of plant stress transcriptomes

Kahl, Günter; Molina, Carlos I.; Rotter, Björn; Jüngling, Ruth; Frank, Anja; Krezdorn, Nico; Hoffmeier, Klaus; Winter, Peter

doi:10.1007/s13562-012-0129-y

Cited by 23 publications

(18 citation statements)

References 28 publications

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“…Bars represent means of two independent replicates ± standard error. wide field of applications (Bonaventure, 2010;Gilardoni et al, 2010;Sharbel et al, 2010;Gilardoni et al, 2011;Molina et al, 2011;Kahl et al, 2012;Draffehn et al, 2013). To our knowledge, this is the first report on the use of HT-SuperSAGE to produce a digital gene-expression profiling in a nonmodel lepidopteran pest.…”

Section: Discussionmentioning

confidence: 93%

“…In this study, we have used HT‐SuperSAGE to quantify the expression of thousands of genes differentially regulated in the gut tissue of a Vip3Aa‐resistant strain of H. virescens . HT‐SuperSAGE, the result of combining an improved version of Serial Analysis Gene Expression with Next Generation Sequencing, has proven to be a valuable tag‐based transcriptome sequencing method in a wide field of applications (Bonaventure, ; Gilardoni et al ., ; Sharbel et al ., ; Gilardoni et al ., ; Molina et al ., ; Kahl et al ., ; Draffehn et al ., ). To our knowledge, this is the first report on the use of HT‐SuperSAGE to produce a digital gene‐expression profiling in a nonmodel lepidopteran pest.…”

Section: Discussionmentioning

confidence: 97%

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HT‐SuperSAGE of the gut tissue of a Vip3Aa‐resistant Heliothis virescens (Lepidoptera: Noctuidae) strain provides insights into the basis of resistance

et al. 2017

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Multitoxin Bt-crops expressing insecticidal toxins with different modes of action, for example, Cry and Vip, are expected to improve resistance management in target pests. While Cry1A resistance has been relatively well characterized in some insect species, this is not the case for Vip3A, for which no mechanism of resistance has yet been identified. Here we applied HT-SuperSAGE to analyze the transcriptome of the gut tissue of tobacco budworm Heliothis virescens (F.) laboratory-selected for Vip3Aa resistance. From a total of 1 324 252 sequence reads, 5 895 126-bp tags were obtained representing 17 751 nonsingleton unique transcripts (UniTags) from genetically similar Vip3Aa-resistant (Vip-Sel) and susceptible control (Vip-Unsel) strains. Differential expression was significant (≥2.5 fold or ≤0.4; P < 0.05) for 1989 sequences (11.2% of total UniTags), where 420 represented overexpressed (OE) and 1569 underexpressed (UE) genes in Vip-Sel. BLASTN searches mapped 419 UniTags to H. virescens sequence contigs, of which, 416 (106 OE and 310 UE) were unambiguously annotated to proteins in NCBI nonredundant protein databases. Gene Ontology distributed 345 of annotated UniTags in 14 functional categories with metabolism (including serine-type hydrolases) and translation/ribosome biogenesis being the most prevalent. A UniTag homologous to a particular member of the REsponse to PAThogen (REPAT) family was found among most overexpressed, while UniTags related to the putative Vip3Aa-binding ribosomal protein S2 (RpS2) were underexpressed. qRT-PCR of a subset of UniTags validated the HT-SuperSAGE data. This study is the first providing lepidopteran gut transcriptome associated with Vip3Aa resistance and a foundation for future attempts to elucidate the resistance mechanism.

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Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 97%

HT‐SuperSAGE of the gut tissue of a Vip3Aa‐resistant Heliothis virescens (Lepidoptera: Noctuidae) strain provides insights into the basis of resistance

et al. 2017

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“…Transcriptomic data was generated using the MACE technique (Kahl et al 2012). A particular feature of this technique is that only one sequence (tag) per cDNA molecule is generated, so normalization to the length of the respective transcript/gene model is not necessary.…”

Section: Macementioning

confidence: 99%

Interaction of roses with a biotrophic and a hemibiotrophic leaf pathogen leads to differences in defense transcriptome activation

et al. 2019

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Key message Transcriptomic analysis resulted in the upregulation of the genes related to common defense mechanisms for black spot and the downregulation of the genes related to photosynthesis and cell wall modification for powdery mildew. Abstract Plant pathogenic fungi successfully colonize their hosts by manipulating the host defense mechanisms, which is accompanied by major transcriptome changes in the host. To characterize compatible plant pathogen interactions at early stages of infection by the obligate biotrophic fungus Podosphaera pannosa, which causes powdery mildew, and the hemibiotrophic fungus Diplocarpon rosae, which causes black spot, we analyzed changes in the leaf transcriptome after the inoculation of detached rose leaves with each pathogen. In addition, we analyzed differences in the transcriptomic changes inflicted by both pathogens as a first step to characterize specific infection strategies. Transcriptomic changes were analyzed using next-generation sequencing based on the massive analysis of cDNA ends approach, which was validated using high-throughput qPCR. We identified a large number of differentially regulated genes. A common set of the differentially regulated genes comprised of pathogenesis-related (PR) genes, such as of PR10 homologs, chitinases and defense-related transcription factors, such as various WRKY genes, indicating a conserved but insufficient PTI [pathogen associated molecular pattern (PAMP) triggered immunity] reaction. Surprisingly, most of the differentially regulated genes were specific to the interactions with either P. pannosa or D. rosae. Specific regulation in response to D. rosae was detected for genes from the phenylpropanoid and flavonoid pathways and for individual PR genes, such as paralogs of PR1 and PR5, and other factors of the salicylic acid signaling pathway. Differently, inoculation with P. pannosa leads in addition to the general pathogen response to a downregulation of genes related to photosynthesis and cell wall modification.Keywords Black spot · Powdery mildew · MACE analysis · High-throughput qPCR · WRKY genes · PR genes Enzo Neu and Helena Sophia Domes have contributed equally to this work. Electronic supplementary materialThe online version of this article (https ://doi.

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“…With regard to phr, no information on differentially expressed genes leading to efficient (prehaustorial) resistance is available up to now. In this respect genome wide transcription profiling with, e.g., Massive Analysis of cDNA Ends (MACE, Kahl et al, 2012; Zawada et al, 2014; Nold-Petry et al, 2015) is well suited to detect differences in gene expression between T. monococcum accessions with different levels of resistance against leaf rust. The comparison of differentially expressed genes within the first 24 hai comprises the time after the germination of uredospores up to the beginning of the formation of the first haustoria within mesophyll cells of susceptible plants (Bolton et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

“…Consequently, much less sequences – resulting in lower costs – are required to obtain the same quantitative accuracy as RNA-seq. Moreover, the TrueQuant technology embedded in MACE ensures that the resulting quantitative data are free of a PCR bias (Kahl et al, 2012; Zawada et al, 2014; Nold-Petry et al, 2015). In order to get detailed information on the phr to P. Triticina , the following studies have been conducted (i), leaves of a T. monococcum accession showing phr and a susceptible T. boeoticum accession were inoculated with P. triticina isolates with different virulence patterns, (ii) these accessions were microscopically analyzed to detect the inhibition of fungal growth, phenolic compounds, hydrogen peroxide and reduced fluorescence of fungal cell walls by endochitinase activity, (iii) genome-wide transcription profiling of mRNA from leaves of resistant and susceptible accessions harvested within the first 24 h after infection was applied using MACE in order to detect differentially expressed genes, (iv) respective genes were assigned to Gene Ontology (GO) categories enabling a deeper insight into compatible and incompatible resistance reactions and explaining a large deal of the mechanisms underlying non-host resistance against leaf rust.…”

Section: Introductionmentioning

confidence: 99%

Microscopic and Molecular Characterization of the Prehaustorial Resistance against Wheat Leaf Rust (Puccinia triticina) in Einkorn (Triticum monococcum)

et al. 2016

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Puccinia triticina f. sp. tritici (Eriks.), the causal agent of leaf rust, causes substantial yield losses in wheat production. In wheat many major leaf rust resistance genes have been overcome by virulent races. In contrast, the prehaustorial resistance (phr) against wheat leaf rust detected in the diploid wheat Einkorn (Triticum monoccocum var. monococcum) accession PI272560 confers race-independent resistance against isolates virulent on accessions harboring resistance genes located on the A-genome of Triticum aestivum. Phr in PI272560 leads to abortion of fungal development during the formation of haustorial mother cells and to increased hydrogen peroxide concentration in comparison to the susceptible accession 36554 (Triticum boeoticum ssp. thaoudar var. reuteri). Increased peroxidase and endochitinase activity was detected in PI272560 within 6 h after inoculation (hai). Comparative transcriptome profiling using Massive Analysis of cDNA Ends (MACE) in infected and non-infected leaves detected 14220 differentially expressed tags in PI272560 and 15472 in accession 36554. Of these 2908 and 3004, respectively, could be assigned to Gene Ontology (GO) categories of which 463 were detected in both accessions and 311 were differentially expressed between the accessions. In accordance with the concept of non-host resistance in PI272560, genes with similarity to peroxidases, chitinases, β-1,3-glucanases and other pathogenesis-related genes were up-regulated within the first 8 hai, whereas up-regulation of such genes was delayed in 36554. Moreover, a Phosphoribulokinase gene contributing to non-host resistance in rice against stripe rust was exclusively expressed in the resistant accession PI272560. Gene expression underpinned physiological and phenotypic observations at the site of infection and are in accordance with the concept of non-host resistance.

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Reduced representation sequencing of plant stress transcriptomes

Cited by 23 publications

References 28 publications

HT‐SuperSAGE of the gut tissue of a Vip3Aa‐resistant Heliothis virescens (Lepidoptera: Noctuidae) strain provides insights into the basis of resistance

HT‐SuperSAGE of the gut tissue of a Vip3Aa‐resistant Heliothis virescens (Lepidoptera: Noctuidae) strain provides insights into the basis of resistance

Interaction of roses with a biotrophic and a hemibiotrophic leaf pathogen leads to differences in defense transcriptome activation

Microscopic and Molecular Characterization of the Prehaustorial Resistance against Wheat Leaf Rust (Puccinia triticina) in Einkorn (Triticum monococcum)

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