Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation
Identifieur interne : 000F09 ( Main/Exploration ); précédent : 000F08; suivant : 000F10Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation
Auteurs : Ruben Parra [Espagne] ; Miguel A. Paredes [Espagne] ; Isabel M. Sanchez-Calle [Espagne] ; Maria C. Gomez-Jimenez [Espagne]Source :
- BMC Genomics [ 1471-2164 ] ; 2013.
Abstract
In fleshy fruit, abscission of fully ripe fruit is a process intimately linked to the ripening process. In many fruit-tree species, such as olive (
Roche-454 massive parallel pyrosequencing enabled us to generate 397,457 high-quality EST sequences, among which 199,075 were from ripe-fruit pericarp and 198,382 from AZ tissues. We assembled these sequences into 19,062 contigs, grouped as 17,048 isotigs. Using the read amounts for each annotated isotig (from a total of 15,671), we identified 7,756 transcripts. A comparative analysis of the transcription profiles conducted in ripe-fruit pericarp and AZ evidenced that 4,391 genes were differentially expressed genes (DEGs) in fruit and AZ. Functional categorization of the DEGs revealed that AZ tissue has an apparently higher response to external stimuli than does that of ripe fruit, revealing a higher expression of auxin-signaling genes, as well as lignin catabolic and biosynthetic pathway, aromatic amino acid biosynthetic pathway, isoprenoid biosynthetic pathway, protein amino acid dephosphorylation, amino acid transport, and photosynthesis. By contrast, fruit-enriched transcripts are involved in ATP synthesis coupled proton transport, glycolysis, and cell-wall organization. Furthermore, over 150 transcripts encoding putative transcription-factors (TFs) were identified (37 fruit TFs and 113 AZ TFs), of which we randomly selected eight genes and we confirmed their expression patterns using quantitative RT-PCR.
We generated a set of EST sequences from olive fruit at full ripening, and DEGs between two different olive tissues, ripe fruit and their AZ, were also identified. Regarding the cross-talk between fruit and AZ, using qRT-PCR, we confirmed a set of TF genes that were differentially expressed, revealing profiles of expression that have not previously been reported, this offering a promising beginning for studies on the different transcription regulation in such tissues.
The online version of this article (doi:10.1186/1471-2164-14-866) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/1471-2164-14-866
PubMed: 24320622
PubMed Central: 4046656
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation</title><author><name sortKey="Parra, Ruben" sort="Parra, Ruben" uniqKey="Parra R" first="Ruben" last="Parra">Ruben Parra</name><affiliation wicri:level="1"><nlm:aff id="Aff29">Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz, 06006 Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz</wicri:regionArea><wicri:noRegion>Badajoz</wicri:noRegion></affiliation></author><author><name sortKey="Paredes, Miguel A" sort="Paredes, Miguel A" uniqKey="Paredes M" first="Miguel A" last="Paredes">Miguel A. Paredes</name><affiliation wicri:level="1"><nlm:aff id="Aff29">Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz, 06006 Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz</wicri:regionArea><wicri:noRegion>Badajoz</wicri:noRegion></affiliation></author><author><name sortKey="Sanchez Calle, Isabel M" sort="Sanchez Calle, Isabel M" uniqKey="Sanchez Calle I" first="Isabel M" last="Sanchez-Calle">Isabel M. Sanchez-Calle</name><affiliation wicri:level="4"><nlm:aff id="Aff30">Department of Plant Physiology, University of Granada, Campus de Cartuja s/n, Granada, 18071 Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Physiology, University of Granada, Campus de Cartuja s/n, Granada</wicri:regionArea><orgName type="university">Université de Grenade</orgName><placeName><settlement type="city">Grenade (Espagne)</settlement><region nuts="2" type="region">Andalousie</region></placeName></affiliation></author><author><name sortKey="Gomez Jimenez, Maria C" sort="Gomez Jimenez, Maria C" uniqKey="Gomez Jimenez M" first="Maria C" last="Gomez-Jimenez">Maria C. Gomez-Jimenez</name><affiliation wicri:level="1"><nlm:aff id="Aff29">Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz, 06006 Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz</wicri:regionArea><wicri:noRegion>Badajoz</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24320622</idno><idno type="pmc">4046656</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046656</idno><idno type="RBID">PMC:4046656</idno><idno type="doi">10.1186/1471-2164-14-866</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000569</idno><idno type="wicri:Area/Pmc/Curation">000568</idno><idno type="wicri:Area/Pmc/Checkpoint">000B18</idno><idno type="wicri:Area/Ncbi/Merge">001531</idno><idno type="wicri:Area/Ncbi/Curation">001531</idno><idno type="wicri:Area/Ncbi/Checkpoint">001531</idno><idno type="wicri:Area/Main/Merge">000F13</idno><idno type="wicri:Area/Main/Curation">000F09</idno><idno type="wicri:Area/Main/Exploration">000F09</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation</title><author><name sortKey="Parra, Ruben" sort="Parra, Ruben" uniqKey="Parra R" first="Ruben" last="Parra">Ruben Parra</name><affiliation wicri:level="1"><nlm:aff id="Aff29">Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz, 06006 Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz</wicri:regionArea><wicri:noRegion>Badajoz</wicri:noRegion></affiliation></author><author><name sortKey="Paredes, Miguel A" sort="Paredes, Miguel A" uniqKey="Paredes M" first="Miguel A" last="Paredes">Miguel A. Paredes</name><affiliation wicri:level="1"><nlm:aff id="Aff29">Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz, 06006 Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz</wicri:regionArea><wicri:noRegion>Badajoz</wicri:noRegion></affiliation></author><author><name sortKey="Sanchez Calle, Isabel M" sort="Sanchez Calle, Isabel M" uniqKey="Sanchez Calle I" first="Isabel M" last="Sanchez-Calle">Isabel M. Sanchez-Calle</name><affiliation wicri:level="4"><nlm:aff id="Aff30">Department of Plant Physiology, University of Granada, Campus de Cartuja s/n, Granada, 18071 Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Physiology, University of Granada, Campus de Cartuja s/n, Granada</wicri:regionArea><orgName type="university">Université de Grenade</orgName><placeName><settlement type="city">Grenade (Espagne)</settlement><region nuts="2" type="region">Andalousie</region></placeName></affiliation></author><author><name sortKey="Gomez Jimenez, Maria C" sort="Gomez Jimenez, Maria C" uniqKey="Gomez Jimenez M" first="Maria C" last="Gomez-Jimenez">Maria C. Gomez-Jimenez</name><affiliation wicri:level="1"><nlm:aff id="Aff29">Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz, 06006 Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea>Department of Plant Physiology, University of Extremadura, Avda de Elvas s/n, Badajoz</wicri:regionArea><wicri:noRegion>Badajoz</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>In fleshy fruit, abscission of fully ripe fruit is a process intimately linked to the ripening process. In many fruit-tree species, such as olive (<italic>Olea europaea</italic> L. cv. Picual), there is a coupling of the full ripening and the activation of the abscission-zone (AZ). Although fully ripe fruit have marked physiological differences with respect to their AZs, dissimilarities in gene expression have not been thoroughly investigated. The present study examines the transcriptome of olive fruit and their AZ tissues at the last stage of ripening, monitored using mRNA-Seq.</p></sec><sec><title>Results</title><p>Roche-454 massive parallel pyrosequencing enabled us to generate 397,457 high-quality EST sequences, among which 199,075 were from ripe-fruit pericarp and 198,382 from AZ tissues. We assembled these sequences into 19,062 contigs, grouped as 17,048 isotigs. Using the read amounts for each annotated isotig (from a total of 15,671), we identified 7,756 transcripts. A comparative analysis of the transcription profiles conducted in ripe-fruit pericarp and AZ evidenced that 4,391 genes were differentially expressed genes (DEGs) in fruit and AZ. Functional categorization of the DEGs revealed that AZ tissue has an apparently higher response to external stimuli than does that of ripe fruit, revealing a higher expression of auxin-signaling genes, as well as lignin catabolic and biosynthetic pathway, aromatic amino acid biosynthetic pathway, isoprenoid biosynthetic pathway, protein amino acid dephosphorylation, amino acid transport, and photosynthesis. By contrast, fruit-enriched transcripts are involved in ATP synthesis coupled proton transport, glycolysis, and cell-wall organization. Furthermore, over 150 transcripts encoding putative transcription-factors (TFs) were identified (37 fruit TFs and 113 AZ TFs), of which we randomly selected eight genes and we confirmed their expression patterns using quantitative RT-PCR.</p></sec><sec><title>Conclusion</title><p>We generated a set of EST sequences from olive fruit at full ripening, and DEGs between two different olive tissues, ripe fruit and their AZ, were also identified. Regarding the cross-talk between fruit and AZ, using qRT-PCR, we confirmed a set of TF genes that were differentially expressed, revealing profiles of expression that have not previously been reported, this offering a promising beginning for studies on the different transcription regulation in such tissues.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/1471-2164-14-866) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Loureiro, J" uniqKey="Loureiro J">J Loureiro</name></author><author><name sortKey="Rodriguez, E" uniqKey="Rodriguez E">E Rodriguez</name></author><author><name sortKey="Costa, A" uniqKey="Costa A">A Costa</name></author><author><name sortKey="Santos, C" uniqKey="Santos C">C Santos</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Alagna, F" 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Jb" uniqKey="Wolf J">JB Wolf</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Gil Amado, Ja" uniqKey="Gil Amado J">JA Gil-Amado</name></author><author><name sortKey="Gomez Jimenez, Mc" uniqKey="Gomez Jimenez M">MC Gomez-Jimenez</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Espagne</li></country><region><li>Andalousie</li></region><settlement><li>Grenade (Espagne)</li></settlement><orgName><li>Université de Grenade</li></orgName></list><tree><country name="Espagne"><noRegion><name sortKey="Parra, Ruben" sort="Parra, Ruben" uniqKey="Parra R" first="Ruben" last="Parra">Ruben Parra</name></noRegion><name sortKey="Gomez Jimenez, Maria C" sort="Gomez Jimenez, Maria C" uniqKey="Gomez Jimenez M" first="Maria C" last="Gomez-Jimenez">Maria C. Gomez-Jimenez</name><name sortKey="Paredes, Miguel A" sort="Paredes, Miguel A" uniqKey="Paredes M" first="Miguel A" last="Paredes">Miguel A. Paredes</name><name sortKey="Sanchez Calle, Isabel M" sort="Sanchez Calle, Isabel M" uniqKey="Sanchez Calle I" first="Isabel M" last="Sanchez-Calle">Isabel M. Sanchez-Calle</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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