Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance
Identifieur interne : 000154 ( France/Analysis ); précédent : 000153; suivant : 000155Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance
Auteurs : Javier Terol [Espagne] ; Ana Conesa [Espagne] ; Jose M. Colmenero [Espagne] ; Manuel Cercos [Espagne] ; Francisco Tadeo [Espagne] ; Javier Agustí [Espagne] ; Enriqueta Al S [Espagne] ; Fernando Andres [Espagne] ; Guillermo Soler [Espagne] ; Javier Brumos [Espagne] ; Domingo J. Iglesias [Espagne] ; Stefan Götz [Espagne] ; Francisco Legaz [Espagne] ; Xavier Argout [France] ; Brigitte Courtois [France] ; Patrick Ollitrault [France] ; Carole Dossat [France] ; Patrick Wincker [France] ; Raphael Morillon [France] ; Manuel Talon [Espagne]Source :
- BMC Genomics [ 1471-2164 ] ; 2007.
Abstract
Improvement of
A normalized full length and 9 standard cDNA libraries were generated, representing particular treatments and tissues from selected varieties (
Comparative genomics with Arabidopsis revealed the presence of putative conserved orthologs and single copy genes in
Url:
DOI: 10.1186/1471-2164-8-31
PubMed: 17254327
PubMed Central: 1796867
Affiliations:
- Espagne, France
- Communauté valencienne, Languedoc-Roussillon, Occitanie (région administrative), Île-de-France
- Evry, Montpellier
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000972
- to stream Pmc, to step Curation: 000971
- to stream Pmc, to step Checkpoint: 001127
- to stream Ncbi, to step Merge: 000659
- to stream Ncbi, to step Curation: 000659
- to stream Ncbi, to step Checkpoint: 000659
- to stream Main, to step Merge: 002420
- to stream Main, to step Curation: 002337
- to stream Main, to step Exploration: 002337
- to stream France, to step Extraction: 000154
Links to Exploration step
PMC:1796867Le document en format XML
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clusters associated with fruit quality, production and salinity tolerance</title>
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<author><name sortKey="Talon, Manuel" sort="Talon, Manuel" uniqKey="Talon M" first="Manuel" last="Talon">Manuel Talon</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Analysis of 13000 unique <italic>Citrus </italic>
clusters associated with fruit quality, production and salinity tolerance</title>
<author><name sortKey="Terol, Javier" sort="Terol, Javier" uniqKey="Terol J" first="Javier" last="Terol">Javier Terol</name>
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<author><name sortKey="Conesa, Ana" sort="Conesa, Ana" uniqKey="Conesa A" first="Ana" last="Conesa">Ana Conesa</name>
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<author><name sortKey="Colmenero, Jose M" sort="Colmenero, Jose M" uniqKey="Colmenero J" first="Jose M" last="Colmenero">Jose M. Colmenero</name>
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<author><name sortKey="Cercos, Manuel" sort="Cercos, Manuel" uniqKey="Cercos M" first="Manuel" last="Cercos">Manuel Cercos</name>
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<author><name sortKey="Tadeo, Francisco" sort="Tadeo, Francisco" uniqKey="Tadeo F" first="Francisco" last="Tadeo">Francisco Tadeo</name>
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<country xml:lang="fr">Espagne</country>
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<author><name sortKey="Agusti, Javier" sort="Agusti, Javier" uniqKey="Agusti J" first="Javier" last="Agustí">Javier Agustí</name>
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<country xml:lang="fr">Espagne</country>
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<country xml:lang="fr">Espagne</country>
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</affiliation>
</author>
<author><name sortKey="Soler, Guillermo" sort="Soler, Guillermo" uniqKey="Soler G" first="Guillermo" last="Soler">Guillermo Soler</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias. Carretera Moncada – Náquera, Km. 4.5 Moncada (Valencia) E46113, Spain</nlm:aff>
<country xml:lang="fr">Espagne</country>
<wicri:regionArea>Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias. Carretera Moncada – Náquera, Km. 4.5 Moncada (Valencia) E46113</wicri:regionArea>
<placeName><region nuts="2" type="communauté">Communauté valencienne</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Brumos, Javier" sort="Brumos, Javier" uniqKey="Brumos J" first="Javier" last="Brumos">Javier Brumos</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias. Carretera Moncada – Náquera, Km. 4.5 Moncada (Valencia) E46113, Spain</nlm:aff>
<country xml:lang="fr">Espagne</country>
<wicri:regionArea>Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias. Carretera Moncada – Náquera, Km. 4.5 Moncada (Valencia) E46113</wicri:regionArea>
<placeName><region nuts="2" type="communauté">Communauté valencienne</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Iglesias, Domingo J" sort="Iglesias, Domingo J" uniqKey="Iglesias D" first="Domingo J" last="Iglesias">Domingo J. Iglesias</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias. Carretera Moncada – Náquera, Km. 4.5 Moncada (Valencia) E46113, Spain</nlm:aff>
<country xml:lang="fr">Espagne</country>
<wicri:regionArea>Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias. Carretera Moncada – Náquera, Km. 4.5 Moncada (Valencia) E46113</wicri:regionArea>
<placeName><region nuts="2" type="communauté">Communauté valencienne</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Gotz, Stefan" sort="Gotz, Stefan" uniqKey="Gotz S" first="Stefan" last="Götz">Stefan Götz</name>
<affiliation wicri:level="2"><nlm:aff id="I2">BET-ITACA, Universidad Politécnica de Valencia, Camino de Vera, s/n 46022 Valencia, Spain</nlm:aff>
<country xml:lang="fr">Espagne</country>
<wicri:regionArea>BET-ITACA, Universidad Politécnica de Valencia, Camino de Vera, s/n 46022 Valencia</wicri:regionArea>
<placeName><region nuts="2" type="communauté">Communauté valencienne</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Legaz, Francisco" sort="Legaz, Francisco" uniqKey="Legaz F" first="Francisco" last="Legaz">Francisco Legaz</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias. Carretera Moncada – Náquera, Km. 4.5 Moncada (Valencia) E46113, Spain</nlm:aff>
<country xml:lang="fr">Espagne</country>
<wicri:regionArea>Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias. Carretera Moncada – Náquera, Km. 4.5 Moncada (Valencia) E46113</wicri:regionArea>
<placeName><region nuts="2" type="communauté">Communauté valencienne</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Argout, Xavier" sort="Argout, Xavier" uniqKey="Argout X" first="Xavier" last="Argout">Xavier Argout</name>
<affiliation wicri:level="3"><nlm:aff id="I3">CIRAD AMIS, UMR PIA – Avenue Agropolis – TA 40/03 34398 Montpellier Cedex 5, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>CIRAD AMIS, UMR PIA – Avenue Agropolis – TA 40/03 34398 Montpellier Cedex 5</wicri:regionArea>
<placeName><region type="region" nuts="2">Occitanie (région administrative)</region>
<region type="old region" nuts="2">Languedoc-Roussillon</region>
<settlement type="city">Montpellier</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Courtois, Brigitte" sort="Courtois, Brigitte" uniqKey="Courtois B" first="Brigitte" last="Courtois">Brigitte Courtois</name>
<affiliation wicri:level="3"><nlm:aff id="I3">CIRAD AMIS, UMR PIA – Avenue Agropolis – TA 40/03 34398 Montpellier Cedex 5, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>CIRAD AMIS, UMR PIA – Avenue Agropolis – TA 40/03 34398 Montpellier Cedex 5</wicri:regionArea>
<placeName><region type="region" nuts="2">Occitanie (région administrative)</region>
<region type="old region" nuts="2">Languedoc-Roussillon</region>
<settlement type="city">Montpellier</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Ollitrault, Patrick" sort="Ollitrault, Patrick" uniqKey="Ollitrault P" first="Patrick" last="Ollitrault">Patrick Ollitrault</name>
<affiliation wicri:level="3"><nlm:aff id="I4">Genoscope-Centre National de Séquençage and Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-8030, 91000 Evry, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Genoscope-Centre National de Séquençage and Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-8030, 91000 Evry</wicri:regionArea>
<placeName><region type="region" nuts="2">Île-de-France</region>
<settlement type="city">Evry</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Dossat, Carole" sort="Dossat, Carole" uniqKey="Dossat C" first="Carole" last="Dossat">Carole Dossat</name>
<affiliation wicri:level="3"><nlm:aff id="I5">CIRAD FLHOR, UPR "Amélioration génétique d'espèces à multiplication végétative", Avenue Agropolis – TA 40/03 34398 Montpellier Cedex 5, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>CIRAD FLHOR, UPR "Amélioration génétique d'espèces à multiplication végétative", Avenue Agropolis – TA 40/03 34398 Montpellier Cedex 5</wicri:regionArea>
<placeName><region type="region" nuts="2">Occitanie (région administrative)</region>
<region type="old region" nuts="2">Languedoc-Roussillon</region>
<settlement type="city">Montpellier</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wincker, Patrick" sort="Wincker, Patrick" uniqKey="Wincker P" first="Patrick" last="Wincker">Patrick Wincker</name>
<affiliation wicri:level="3"><nlm:aff id="I5">CIRAD FLHOR, UPR "Amélioration génétique d'espèces à multiplication végétative", Avenue Agropolis – TA 40/03 34398 Montpellier Cedex 5, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>CIRAD FLHOR, UPR "Amélioration génétique d'espèces à multiplication végétative", Avenue Agropolis – TA 40/03 34398 Montpellier Cedex 5</wicri:regionArea>
<placeName><region type="region" nuts="2">Occitanie (région administrative)</region>
<region type="old region" nuts="2">Languedoc-Roussillon</region>
<settlement type="city">Montpellier</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Morillon, Raphael" sort="Morillon, Raphael" uniqKey="Morillon R" first="Raphael" last="Morillon">Raphael Morillon</name>
<affiliation wicri:level="3"><nlm:aff id="I4">Genoscope-Centre National de Séquençage and Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-8030, 91000 Evry, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>Genoscope-Centre National de Séquençage and Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-8030, 91000 Evry</wicri:regionArea>
<placeName><region type="region" nuts="2">Île-de-France</region>
<settlement type="city">Evry</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Talon, Manuel" sort="Talon, Manuel" uniqKey="Talon M" first="Manuel" last="Talon">Manuel Talon</name>
<affiliation wicri:level="2"><nlm:aff id="I1">Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias. Carretera Moncada – Náquera, Km. 4.5 Moncada (Valencia) E46113, Spain</nlm:aff>
<country xml:lang="fr">Espagne</country>
<wicri:regionArea>Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias. Carretera Moncada – Náquera, Km. 4.5 Moncada (Valencia) E46113</wicri:regionArea>
<placeName><region nuts="2" type="communauté">Communauté valencienne</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">BMC Genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2007">2007</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Improvement of <italic>Citrus</italic>
, the most economically important fruit crop in the world, is extremely slow and inherently costly because of the long-term nature of tree breeding and an unusual combination of reproductive characteristics. Aside from disease resistance, major commercial traits in <italic>Citrus </italic>
are improved fruit quality, higher yield and tolerance to environmental stresses, especially salinity.</p>
</sec>
<sec><title>Results</title>
<p>A normalized full length and 9 standard cDNA libraries were generated, representing particular treatments and tissues from selected varieties (<italic>Citrus clementina </italic>
and <italic>C. sinensis</italic>
) and rootstocks (<italic>C. reshni, and C. sinenis </italic>
× <italic>Poncirus trifoliata</italic>
) differing in fruit quality, resistance to abscission, and tolerance to salinity. The goal of this work was to provide a large expressed sequence tag (EST) collection enriched with transcripts related to these well appreciated agronomical traits. Towards this end, more than 54000 ESTs derived from these libraries were analyzed and annotated. Assembly of 52626 useful sequences generated 15664 putative transcription units distributed in 7120 contigs, and 8544 singletons. BLAST annotation produced significant hits for more than 80% of the hypothetical transcription units and suggested that 647 of these might be <italic>Citrus </italic>
specific unigenes. The unigene set, composed of ~13000 putative different transcripts, including more than 5000 novel <italic>Citrus </italic>
genes, was assigned with putative functions based on similarity, GO annotations and protein domains</p>
</sec>
<sec><title>Conclusion</title>
<p>Comparative genomics with Arabidopsis revealed the presence of putative conserved orthologs and single copy genes in <italic>Citrus </italic>
and also the occurrence of both gene duplication events and increased number of genes for specific pathways. In addition, phylogenetic analysis performed on the ammonium transporter family and glycosyl transferase family 20 suggested the existence of <italic>Citrus </italic>
paralogs. Analysis of the <italic>Citrus </italic>
gene space showed that the most important metabolic pathways known to affect fruit quality were represented in the unigene set. Overall, the similarity analyses indicated that the sequences of the genes belonging to these varieties and rootstocks were essentially identical, suggesting that the differential behaviour of these species cannot be attributed to major sequence divergences. This <italic>Citrus </italic>
EST assembly contributes both crucial information to discover genes of agronomical interest and tools for genetic and genomic analyses, such as the development of new markers and microarrays.</p>
</sec>
</div>
</front>
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</listBibl>
</div1>
</back>
</TEI>
<affiliations><list><country><li>Espagne</li>
<li>France</li>
</country>
<region><li>Communauté valencienne</li>
<li>Languedoc-Roussillon</li>
<li>Occitanie (région administrative)</li>
<li>Île-de-France</li>
</region>
<settlement><li>Evry</li>
<li>Montpellier</li>
</settlement>
</list>
<tree><country name="Espagne"><region name="Communauté valencienne"><name sortKey="Terol, Javier" sort="Terol, Javier" uniqKey="Terol J" first="Javier" last="Terol">Javier Terol</name>
</region>
<name sortKey="Agusti, Javier" sort="Agusti, Javier" uniqKey="Agusti J" first="Javier" last="Agustí">Javier Agustí</name>
<name sortKey="Al S, Enriqueta" sort="Al S, Enriqueta" uniqKey="Al S E" first="Enriqueta" last="Al S">Enriqueta Al S</name>
<name sortKey="Andres, Fernando" sort="Andres, Fernando" uniqKey="Andres F" first="Fernando" last="Andres">Fernando Andres</name>
<name sortKey="Brumos, Javier" sort="Brumos, Javier" uniqKey="Brumos J" first="Javier" last="Brumos">Javier Brumos</name>
<name sortKey="Cercos, Manuel" sort="Cercos, Manuel" uniqKey="Cercos M" first="Manuel" last="Cercos">Manuel Cercos</name>
<name sortKey="Colmenero, Jose M" sort="Colmenero, Jose M" uniqKey="Colmenero J" first="Jose M" last="Colmenero">Jose M. Colmenero</name>
<name sortKey="Conesa, Ana" sort="Conesa, Ana" uniqKey="Conesa A" first="Ana" last="Conesa">Ana Conesa</name>
<name sortKey="Gotz, Stefan" sort="Gotz, Stefan" uniqKey="Gotz S" first="Stefan" last="Götz">Stefan Götz</name>
<name sortKey="Iglesias, Domingo J" sort="Iglesias, Domingo J" uniqKey="Iglesias D" first="Domingo J" last="Iglesias">Domingo J. Iglesias</name>
<name sortKey="Legaz, Francisco" sort="Legaz, Francisco" uniqKey="Legaz F" first="Francisco" last="Legaz">Francisco Legaz</name>
<name sortKey="Soler, Guillermo" sort="Soler, Guillermo" uniqKey="Soler G" first="Guillermo" last="Soler">Guillermo Soler</name>
<name sortKey="Tadeo, Francisco" sort="Tadeo, Francisco" uniqKey="Tadeo F" first="Francisco" last="Tadeo">Francisco Tadeo</name>
<name sortKey="Talon, Manuel" sort="Talon, Manuel" uniqKey="Talon M" first="Manuel" last="Talon">Manuel Talon</name>
</country>
<country name="France"><region name="Occitanie (région administrative)"><name sortKey="Argout, Xavier" sort="Argout, Xavier" uniqKey="Argout X" first="Xavier" last="Argout">Xavier Argout</name>
</region>
<name sortKey="Courtois, Brigitte" sort="Courtois, Brigitte" uniqKey="Courtois B" first="Brigitte" last="Courtois">Brigitte Courtois</name>
<name sortKey="Dossat, Carole" sort="Dossat, Carole" uniqKey="Dossat C" first="Carole" last="Dossat">Carole Dossat</name>
<name sortKey="Morillon, Raphael" sort="Morillon, Raphael" uniqKey="Morillon R" first="Raphael" last="Morillon">Raphael Morillon</name>
<name sortKey="Ollitrault, Patrick" sort="Ollitrault, Patrick" uniqKey="Ollitrault P" first="Patrick" last="Ollitrault">Patrick Ollitrault</name>
<name sortKey="Wincker, Patrick" sort="Wincker, Patrick" uniqKey="Wincker P" first="Patrick" last="Wincker">Patrick Wincker</name>
</country>
</tree>
</affiliations>
</record>
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