Quantitative comparison of cDNA-AFLP, microarrays, and genechip expression data in Saccharomyces cerevisiae

Reijans, Martin; Lascaris, Romeo; Groeneger, Antoinette Oude; Wittenberg, Alexander H. J.; Wesselink, Erik; Oeveren, Jan van; Wit, Elzo de; Boorsma, André; Voetdijk, B M; Spek, Hans van der; Grivell, Leslie A.; Simons, Guus

doi:10.1016/s0888-7543(03)00179-4

Cited by 80 publications

(54 citation statements)

References 27 publications

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“…In this study, we used a new variant of cDNA-AFLP technology to analyze differences in gene expression between two ecotypes of the marine snail Littorina saxatilis , considered an example of incomplete ecological and sympatric speciation. The experimental reproducibility obtained in this work for the cDNA-AFLP technique is in agreement with previous studies using this technology [11,59-61]. Since a pooling strategy has shown previously similar efficiency to the individual strategy for gene expression comparisons [62], we analyzed pools of 10 individuals (5 males and 5 females) with the aim of reducing individual effects, thus increasing the power to detect differences between ecotypes.…”

Section: Discussionsupporting

confidence: 88%

Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis

Martínez‐Fernández

Bernatchez²,

Rolán‐Alvarez

et al. 2010

BMC Evol Biol

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BackgroundIn the past 40 years, there has been increasing acceptance that variation in levels of gene expression represents a major source of evolutionary novelty. Gene expression divergence is therefore likely to be involved in the emergence of incipient species, namely, in a context of adaptive radiation. In this study, a genome-wide expression profiling approach (cDNA-AFLP), validated by quantitative real-time polymerase chain reaction (qPCR) were used to get insights into the role of differential gene expression on the ecological adaptation of the marine snail Littorina saxatilis. This gastropod displays two sympatric ecotypes (RB and SU) which are becoming one of the best studied systems for ecological speciation.ResultsAmong the 99 transcripts shared between ecotypes, 12.12% showed significant differential expression. At least 4% of these transcripts still displayed significant differences after correction for multiple tests, highlighting that gene expression can differ considerably between subpopulations adapted to alternative habitats in the face of gene flow. One of the transcripts identified was Cytochrome c Oxidase subunit I (COI). In addition, 6 possible reference genes were validated to normalize and confirm this result using qPCR. α-Tubulin and histone H3.3 showed the more stable expression levels, being therefore chosen as the best option for normalization. The qPCR analysis confirmed a higher COI expression in SU individuals.ConclusionsAt least 4% of the transcriptome studied is being differentially expressed between ecotypes living in alternative habitats, even when gene flow is still substantial between ecotypes. We could identify a candidate transcript of such ecotype differentiation: Cytochrome c Oxidase Subunit I (COI), a mitochondrial gene involved in energy metabolism. Quantitative PCR was used to confirm the differences found in COI and its over-expression in the SU ecotype. Interestingly, COI is involved in the oxidative phosphorylation, suggesting an enhanced mitochondrial gene expression (or increased number of mitochondria) to improve energy supply in the ecotype subjected to the strongest wave action.

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Section: Discussionsupporting

confidence: 88%

Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis

Martínez‐Fernández

Bernatchez²,

Rolán‐Alvarez

et al. 2010

BMC Evol Biol

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“…This PCR-based technique combines a high sensitivity with a high specificity, allowing detection of rarely expressed genes and distinction between homologous genes (Bachem et al 1998;Reijans et al 2003). Since the first introduction of cDNA-AFLP to profile genes involved in potato tuber development (Bachem et al 1996), more than 50 papers have been published on different biological processes using this platform.…”

Section: Introductionmentioning

confidence: 99%

Tomato defense to the powdery mildew fungus: differences in expression of genes in susceptible, monogenic- and polygenic resistance responses are mainly in timing

Bai²,

Jacobsen³

et al. 2006

Plant Mol Biol

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Oidium neolycopersici is a causal agent of tomato powdery mildew. In this paper, gene expression profiles were investigated of susceptible, monogenicand polygenic resistant tomato genotypes in response to O. neolycopersici infection by using cDNA-AFLP. Around 30,000 TDFs (Transcript Derived Fragments), representing~22% of the transcriptome based on in silico estimation, were identified and 887 TDFs were differentially expressed (DE-TDFs) upon inoculation with O. neolycopersici spores. Forty-two percent of the identified DE-TDFs were detected in both the compatible and incompatible interactions, a subset of these were studied for their temporal patterns. All of these common induced DE-TDFs displayed an expression peak at 7 days post incoluation in monogenic resistant response but sustained up-regulation in the susceptible and the polygenic resistant response. While more than half of these common DE-TDFs showed earlier timing in incompatible interactions compared to compatible interaction. Only 2% of the identified DE-TDFs were specific to either the monogenic or the polygenic resistant response. By annotation of the 230 sequenced DE-TDFs we found that 34% of the corresponding transcripts were known to be involved in plant defense, whereas the other transcripts played general roles in signal transduction (11%), regulation (24%), protein synthesis and degradation (11%), energy metabolism (12%) including photosynthesis, photorespiration and respiration.

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“…Since its first application on potato tuber development, several modifications of this technique have improved its validity and advantages over other fingerprinting techniques and DNA chip-based approaches [18][19][20]. In most cases, it has been employed for surveying transcriptional changes in host plants during interactions with fungi, bacteria, nematode or environmental stimuli [21][22][23][24][25][26][27][28][29].…”

Section: Discussionmentioning

confidence: 99%

Sinorhizobium meliloti nifA mutant induces different gene expression profile from wild type in Alfalfa nodules

Gong

Zhu

et al. 2006

Cell Res

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Quantitative comparison of cDNA-AFLP, microarrays, and genechip expression data in Saccharomyces cerevisiae

Cited by 80 publications

References 27 publications

Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis

Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis

Tomato defense to the powdery mildew fungus: differences in expression of genes in susceptible, monogenic- and polygenic resistance responses are mainly in timing

Sinorhizobium meliloti nifA mutant induces different gene expression profile from wild type in Alfalfa nodules

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