Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance
Background: Improvement of Citrus, 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 C...
| Main Authors: | , , , , , , , , , , , , , , , , , , , |
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| Format: | Artículo |
| Language: | Inglés |
| Published: |
2017
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| Online Access: | http://hdl.handle.net/20.500.11939/4578 |
| _version_ | 1855491779504111616 |
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| author | Terol, Javier Conesa, Ana Colmenero-Flores, José M. Cercós, Manuel Tadeo, Francisco R. Agustí, Javier Alos, Enriqueta Andres, Fernando Soler, Guillermo Brumos, Javier Iglesias, Domingo J. Gotz, Stefan Legaz, Francisco Argout, Xavier Courtois, Brigitte Ollitrault, Patrick Dossat, Carole Wincker, Patrick Morillon, Raphael Talón, Manuel |
| author_browse | Agustí, Javier Alos, Enriqueta Andres, Fernando Argout, Xavier Brumos, Javier Cercós, Manuel Colmenero-Flores, José M. Conesa, Ana Courtois, Brigitte Dossat, Carole Gotz, Stefan Iglesias, Domingo J. Legaz, Francisco Morillon, Raphael Ollitrault, Patrick Soler, Guillermo Tadeo, Francisco R. Talón, Manuel Terol, Javier Wincker, Patrick |
| author_facet | Terol, Javier Conesa, Ana Colmenero-Flores, José M. Cercós, Manuel Tadeo, Francisco R. Agustí, Javier Alos, Enriqueta Andres, Fernando Soler, Guillermo Brumos, Javier Iglesias, Domingo J. Gotz, Stefan Legaz, Francisco Argout, Xavier Courtois, Brigitte Ollitrault, Patrick Dossat, Carole Wincker, Patrick Morillon, Raphael Talón, Manuel |
| author_sort | Terol, Javier |
| collection | ReDivia |
| description | Background: Improvement of Citrus, 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 Citrus are improved fruit quality, higher yield and tolerance to environmental stresses, especially salinity. Results: A normalized full length and 9 standard cDNA libraries were generated, representing particular treatments and tissues from selected varieties ( Citrus clementina and C. sinensis) and rootstocks ( C. reshni, and C. sinenis x Poncirus trifoliata) 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 Citrus specific unigenes. The unigene set, composed of similar to 13000 putative different transcripts, including more than 5000 novel Citrus genes, was assigned with putative functions based on similarity, GO annotations and protein domains. Conclusion: Comparative genomics with Arabidopsis revealed the presence of putative conserved orthologs and single copy genes in Citrus 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 Citrus paralogs. Analysis of the Citrus 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 Citrus 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. |
| format | Artículo |
| id | ReDivia4578 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | ReDivia45782025-04-25T14:43:53Z Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance Terol, Javier Conesa, Ana Colmenero-Flores, José M. Cercós, Manuel Tadeo, Francisco R. Agustí, Javier Alos, Enriqueta Andres, Fernando Soler, Guillermo Brumos, Javier Iglesias, Domingo J. Gotz, Stefan Legaz, Francisco Argout, Xavier Courtois, Brigitte Ollitrault, Patrick Dossat, Carole Wincker, Patrick Morillon, Raphael Talón, Manuel Background: Improvement of Citrus, 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 Citrus are improved fruit quality, higher yield and tolerance to environmental stresses, especially salinity. Results: A normalized full length and 9 standard cDNA libraries were generated, representing particular treatments and tissues from selected varieties ( Citrus clementina and C. sinensis) and rootstocks ( C. reshni, and C. sinenis x Poncirus trifoliata) 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 Citrus specific unigenes. The unigene set, composed of similar to 13000 putative different transcripts, including more than 5000 novel Citrus genes, was assigned with putative functions based on similarity, GO annotations and protein domains. Conclusion: Comparative genomics with Arabidopsis revealed the presence of putative conserved orthologs and single copy genes in Citrus 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 Citrus paralogs. Analysis of the Citrus 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 Citrus 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. 2017-06-01T10:10:28Z 2017-06-01T10:10:28Z 2007 JAN 25 2007 article publishedVersion Terol, J., Conesa, Ana, Colmenero, J.M., Cercos, M., Tadeo, F., Agusti, J., Alos, E., Andres, F., Soler, Guillermo, Brumos, J., Iglesias, D.J., Gotz, Stefan, Legaz, F., Argout, X., Courtois, Brigitte, Ollitrault, P., Dossat, Carole, Wincker, P., Morillon, R., Talón, M. (2007). Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance. Bmc Genomics, 8, 31-31. 1471-2164 http://hdl.handle.net/20.500.11939/4578 10.1186/1471-2164-8-31 en openAccess Impreso |
| spellingShingle | Terol, Javier Conesa, Ana Colmenero-Flores, José M. Cercós, Manuel Tadeo, Francisco R. Agustí, Javier Alos, Enriqueta Andres, Fernando Soler, Guillermo Brumos, Javier Iglesias, Domingo J. Gotz, Stefan Legaz, Francisco Argout, Xavier Courtois, Brigitte Ollitrault, Patrick Dossat, Carole Wincker, Patrick Morillon, Raphael Talón, Manuel Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance |
| title | Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance |
| title_full | Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance |
| title_fullStr | Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance |
| title_full_unstemmed | Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance |
| title_short | Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance |
| title_sort | analysis of 13000 unique citrus clusters associated with fruit quality production and salinity tolerance |
| url | http://hdl.handle.net/20.500.11939/4578 |
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