An RNA-Seq-based reference transcriptome for Citrus
Previous RNA-Seq studies in citrus have been focused on physiological processes relevant to fruit quality and productivity of the major species, especially sweet orange. Less attention has been paid to vegetative or reproductive tissues, while most Citrus species have never been analysed. In this wo...
| Autores principales: | , , , |
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| Formato: | article |
| Lenguaje: | Inglés |
| Publicado: |
2017
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| Acceso en línea: | http://hdl.handle.net/20.500.11939/4581 https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12447 |
| _version_ | 1855032144612556800 |
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| author | Terol, Javier Tadeo, Francisco R. Ventimilla, Daniel Talón, Manuel |
| author_browse | Tadeo, Francisco R. Talón, Manuel Terol, Javier Ventimilla, Daniel |
| author_facet | Terol, Javier Tadeo, Francisco R. Ventimilla, Daniel Talón, Manuel |
| author_sort | Terol, Javier |
| collection | ReDivia |
| description | Previous RNA-Seq studies in citrus have been focused on physiological processes relevant to fruit quality and productivity of the major species, especially sweet orange. Less attention has been paid to vegetative or reproductive tissues, while most Citrus species have never been analysed. In this work, we characterized the transcriptome of vegetative and reproductive tissues from 12 Citrus species from all main phylogenetic groups. Our aims were to acquire a complete view of the citrus transcriptome landscape, to improve previous functional annotations and to obtain genetic markers associated with genes of agronomic interest. 28 samples were used for RNA-Seq analysis, obtained from 12 Citrus species: C.medica, C.aurantifolia, C.limon, C.bergamia, C.clementina, C.deliciosa, C.reshni, C.maxima, C.paradisi, C.aurantium, C.sinensis and Poncirus trifoliata. Four different organs were analysed: root, phloem, leaf and flower. A total of 3421 million Illumina reads were produced and mapped against the reference C.clementina genome sequence. Transcript discovery pipeline revealed 3326 new genes, the number of genes with alternative splicing was increased to 19739, and a total of 73797 transcripts were identified. Differential expression studies between the four tissues showed that gene expression is overall related to the physiological function of the specific organs above any other variable. Variants discovery analysis revealed the presence of indels and SNPs in genes associated with fruit quality and productivity. Pivotal pathways in citrus such as those of flavonoids, flavonols, ethylene and auxin were also analysed in detail. |
| format | article |
| id | ReDivia4581 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | ReDivia45812025-04-25T14:43:54Z An RNA-Seq-based reference transcriptome for Citrus Terol, Javier Tadeo, Francisco R. Ventimilla, Daniel Talón, Manuel Previous RNA-Seq studies in citrus have been focused on physiological processes relevant to fruit quality and productivity of the major species, especially sweet orange. Less attention has been paid to vegetative or reproductive tissues, while most Citrus species have never been analysed. In this work, we characterized the transcriptome of vegetative and reproductive tissues from 12 Citrus species from all main phylogenetic groups. Our aims were to acquire a complete view of the citrus transcriptome landscape, to improve previous functional annotations and to obtain genetic markers associated with genes of agronomic interest. 28 samples were used for RNA-Seq analysis, obtained from 12 Citrus species: C.medica, C.aurantifolia, C.limon, C.bergamia, C.clementina, C.deliciosa, C.reshni, C.maxima, C.paradisi, C.aurantium, C.sinensis and Poncirus trifoliata. Four different organs were analysed: root, phloem, leaf and flower. A total of 3421 million Illumina reads were produced and mapped against the reference C.clementina genome sequence. Transcript discovery pipeline revealed 3326 new genes, the number of genes with alternative splicing was increased to 19739, and a total of 73797 transcripts were identified. Differential expression studies between the four tissues showed that gene expression is overall related to the physiological function of the specific organs above any other variable. Variants discovery analysis revealed the presence of indels and SNPs in genes associated with fruit quality and productivity. Pivotal pathways in citrus such as those of flavonoids, flavonols, ethylene and auxin were also analysed in detail. 2017-06-01T10:10:28Z 2017-06-01T10:10:28Z 2016 MAR 2016 article publishedVersion Terol, J., Tadeo, F., Ventimilla, D. & Talon, M. (2016). An RNA-Seq-based reference transcriptome for Citrus. Plant Biotechnology Journal, 14(3), 938-950. 1467-7644 http://hdl.handle.net/20.500.11939/4581 10.1111/pbi.12447 https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12447 en openAccess Impreso |
| spellingShingle | Terol, Javier Tadeo, Francisco R. Ventimilla, Daniel Talón, Manuel An RNA-Seq-based reference transcriptome for Citrus |
| title | An RNA-Seq-based reference transcriptome for Citrus |
| title_full | An RNA-Seq-based reference transcriptome for Citrus |
| title_fullStr | An RNA-Seq-based reference transcriptome for Citrus |
| title_full_unstemmed | An RNA-Seq-based reference transcriptome for Citrus |
| title_short | An RNA-Seq-based reference transcriptome for Citrus |
| title_sort | rna seq based reference transcriptome for citrus |
| url | http://hdl.handle.net/20.500.11939/4581 https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12447 |
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