Use of Robust-Long Serial Analysis of Gene Expression to Identify Novel Fungal and Plant Genes Involved in Host-Pathogen Interactions

Gowda, Malali; Reddyvari-Channarayappa, Venu; Jia, Yulin; Stahlberg, Eric; Pampanwar, Vishal; Soderlund, Carol; Wang, Guoliang

doi:10.1385/1-59259-966-4:131

Cited by 7 publications

(6 citation statements)

References 15 publications

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“…Each FL-cDNA was equally divided into three portions (3#, mid, and 5#). The distinct sense and antisense tags from the three RL-SAGE libraries were mapped to the FL-cDNAs using the SAGEspy program (Gowda et al, 2006b). The number of hits and the percent of tags are shown on the top of each category.…”

Section: Significant Reduction Of the Matching Rate Of The R And S LImentioning

confidence: 99%

“…The SAGEspy program developed at the Ohio Supercomputer Center (http://www.osc. edu/research/bioinformatics/sagespy/index.shtml) and analysis tools at the Magnaporthe Grisea Oryza Sativa database (http://www.mgosdb.org/sage; Gowda et al, 2006b) were used to isolate ditags, individual tags, and distinct tags. The RL-SAGE tags from the C, R, and S libraries were submitted to the National Center for Biotechnology Information (GEO accession no.…”

Section: Isolation Of Ditags and Individual Tagsmentioning

confidence: 99%

“…Although many laboratories have tried to adopt SAGE and LongSAGE methodologies in the past, most failed to make quality libraries for sequencing due to the inherent technical difficulties in concatemer cloning. The improved LongSAGE method, called robust-long (RL) SAGE, significantly increased the cloning efficiency of concatemers and insert size (Gowda et al, 2004;Gowda et al, 2006bGowda et al, , 2006cGowda and Wang, 2007). Recently, we developed a new method, called robust analysis of 5#-transcript ends in which cloning steps are eliminated and a conventional sequencing method is replaced by 454 pyrosequencing methods (Gowda et al, 2006a).…”

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confidence: 99%

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Magnaporthe griseaInfection Triggers RNA Variation and Antisense Transcript Expression in Rice

Gowda

Venu

et al. 2007

Plant Physiology

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Rice blast disease, caused by the fungal pathogen Magnaporthe grisea, is an excellent model system to study plant-fungal interactions and host defense responses. In this study, comprehensive analysis of the rice (Oryza sativa) transcriptome after M. grisea infection was conducted using robust-long serial analysis of gene expression. A total of 83,382 distinct 21-bp robust-long serial analysis of gene expression tags were identified from 627,262 individual tags isolated from the resistant (R), susceptible (S), and control (C) libraries. Sequence analysis revealed that the tags in the R and S libraries had a significant reduced matching rate to the rice genomic and expressed sequences in comparison to the C library. The high level of one-nucleotide mismatches of the R and S library tags was due to nucleotide conversions. The A-to-G and U-to-C nucleotide conversions were the most predominant types, which were induced in the M. grisea-infected plants. Reverse transcription-polymerase chain reaction analysis showed that expression of the adenine deaminase and cytidine deaminase genes was highly induced after inoculation. In addition, many antisense transcripts were induced in infected plants and expression of four antisense transcripts was confirmed by strand-specific reverse transcription-polymerase chain reaction. These results demonstrate that there is a series of dynamic and complex transcript modifications and changes in the rice transcriptome at the M. grisea early infection stages.

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Section: Significant Reduction Of the Matching Rate Of The R And S LImentioning

confidence: 99%

Section: Isolation Of Ditags and Individual Tagsmentioning

confidence: 99%

mentioning

confidence: 99%

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Magnaporthe griseaInfection Triggers RNA Variation and Antisense Transcript Expression in Rice

Gowda

Venu

et al. 2007

Plant Physiology

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“…Modified versions producing longer tags of 21 bp for LongSAGE [54] or even 26 bp for SuperSAGE [55] have thus been introduced. LongSAGE has been successfully used, for example, to identify novel fungal and plant genes involved in host-pathogen interactions [56,57]. Even so, the extension of SAGE tags to the 3 1 cDNA end is still often necessary to unambiguously identify the matching RNA [58].…”

Section: Disadvantagesmentioning

confidence: 99%

Genetic approaches to study plant responses to environmental stresses

Moustafa¹,

Cross²

2018

Preprint

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Abstract:The assessment of gene expression levels is an important step toward elucidating gene functions temporally and spatially. Decades ago, typical studies were focusing on a few genes individually, whereas now researchers are able to examine whole genomes at once. The upgrade of throughput levels aided the introduction of systems biology approaches whereby cell functional networks can be scrutinized in their entireties to unravel potential functional interacting components. The birth of systems biology goes hand-in-hand with huge technological advancements and enables a fairly rapid detection of all transcripts in studied biological samples. Even so, earlier technologies that were restricted to probing single genes or a subset of genes still have their place in research laboratories. The objective here is to highlight key approaches used in gene expression analysis in plant responses to environmental stresses, or, more generally, any other condition of interest. Northern blots, RNase protection assays, and qPCR are described for their targeted detection of one or a few transcripts at a once. Differential display and serial analysis of gene expression represent non-targeted methods to evaluate expression changes of a significant number of gene transcripts. Finally, microarrays and RNA-seq (next-generation sequencing) contribute to the ultimate goal of identifying and quantifying all transcripts in a cell under conditions or stages of study. Recent examples of applications as well as principles, advantages, and drawbacks of each method are contrasted. We also suggest replacing the term "Next-Generation Sequencing (NGS)" with another less confusing synonym such as "RNA-seq", "high throughput sequencing", or "massively parallel sequencing" to avoid confusion with any future sequencing technologies.

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“…Modified versions producing longer tags of 21 bp for LongSAGE [ 54 ] or even 26 bp for SuperSAGE [ 55 ] have thus been introduced. LongSAGE has been successfully used, for example, to identify novel fungal and plant genes involved in host–pathogen interactions [ 56 , 57 ]. Even so, the extension of SAGE tags to the 3′ cDNA end is still often necessary to unambiguously identify the matching RNA [ 58 ].…”

Section: Serial Analysis Of Gene Expression (Sage)mentioning

confidence: 99%

Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview

Moustafa

Cross

2016

Biology

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The assessment of gene expression levels is an important step toward elucidating gene functions temporally and spatially. Decades ago, typical studies were focusing on a few genes individually, whereas now researchers are able to examine whole genomes at once. The upgrade of throughput levels aided the introduction of systems biology approaches whereby cell functional networks can be scrutinized in their entireties to unravel potential functional interacting components. The birth of systems biology goes hand-in-hand with huge technological advancements and enables a fairly rapid detection of all transcripts in studied biological samples. Even so, earlier technologies that were restricted to probing single genes or a subset of genes still have their place in research laboratories. The objective here is to highlight key approaches used in gene expression analysis in plant responses to environmental stresses, or, more generally, any other condition of interest. Northern blots, RNase protection assays, and qPCR are described for their targeted detection of one or a few transcripts at a once. Differential display and serial analysis of gene expression represent non-targeted methods to evaluate expression changes of a significant number of gene transcripts. Finally, microarrays and RNA-seq (next-generation sequencing) contribute to the ultimate goal of identifying and quantifying all transcripts in a cell under conditions or stages of study. Recent examples of applications as well as principles, advantages, and drawbacks of each method are contrasted. We also suggest replacing the term “Next-Generation Sequencing (NGS)” with another less confusing synonym such as “RNA-seq”, “high throughput sequencing”, or “massively parallel sequencing” to avoid confusion with any future sequencing technologies.

show abstract

Use of Robust-Long Serial Analysis of Gene Expression to Identify Novel Fungal and Plant Genes Involved in Host-Pathogen Interactions

Cited by 7 publications

References 15 publications

Magnaporthe griseaInfection Triggers RNA Variation and Antisense Transcript Expression in Rice

Magnaporthe griseaInfection Triggers RNA Variation and Antisense Transcript Expression in Rice

Genetic approaches to study plant responses to environmental stresses

Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview

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