A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives
We produced a unique large dataset of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Wiley
2017
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/76382 |
| _version_ | 1855527195152220160 |
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| author | Sarah, Gautier Homa, Felix Pointet, Stéphanie Contreras, Sandy Sabot, François Nabholz, Benoit Santoni, Sylvain Sauné, Laure Ardisson, Morgane Chantret, Nathalie Sauvage, Christopher Tregear, James Jourda, Cyril Pot, David Vigouroux, Yves Chair, Hana Scarcelli, Nora Billot, Claire Yahiaoui, Nabila Bacilieri, Roberto Khadari, Bouchaib Boccara, Michel Barnaud, Adéline Péros, Jean-Pierre Labouisse, Jean-Pierre Pham, Jean-Louis David, Jacques Glémin, Sylvain Ruíz, Manuel |
| author_browse | Ardisson, Morgane Bacilieri, Roberto Barnaud, Adéline Billot, Claire Boccara, Michel Chair, Hana Chantret, Nathalie Contreras, Sandy David, Jacques Glémin, Sylvain Homa, Felix Jourda, Cyril Khadari, Bouchaib Labouisse, Jean-Pierre Nabholz, Benoit Pham, Jean-Louis Pointet, Stéphanie Pot, David Péros, Jean-Pierre Ruíz, Manuel Sabot, François Santoni, Sylvain Sarah, Gautier Sauné, Laure Sauvage, Christopher Scarcelli, Nora Tregear, James Vigouroux, Yves Yahiaoui, Nabila |
| author_facet | Sarah, Gautier Homa, Felix Pointet, Stéphanie Contreras, Sandy Sabot, François Nabholz, Benoit Santoni, Sylvain Sauné, Laure Ardisson, Morgane Chantret, Nathalie Sauvage, Christopher Tregear, James Jourda, Cyril Pot, David Vigouroux, Yves Chair, Hana Scarcelli, Nora Billot, Claire Yahiaoui, Nabila Bacilieri, Roberto Khadari, Bouchaib Boccara, Michel Barnaud, Adéline Péros, Jean-Pierre Labouisse, Jean-Pierre Pham, Jean-Louis David, Jacques Glémin, Sylvain Ruíz, Manuel |
| author_sort | Sarah, Gautier |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | We produced a unique large dataset of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum. We used the same protocol for the release of 26 new transcriptomes of crop plants and wild relatives, including still understudied crops such as yam, pearl millet and fonio. The species list has a wide taxonomic representation with the inclusion of 15 monocots and 11 eudicots. All contigs were annotated using BLAST, prot4EST, and Blast2GO. A strong originality of the dataset is that each crop is associated with close relative species, which will permit whole genome comparative evolutionary studies between crops and their wild related species. This large resource will thus serve research communities working on both crops and model organisms. All the data are available at http://arcad-bioinformatics.southgreen.fr/. |
| format | Journal Article |
| id | CGSpace76382 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace763822025-11-12T05:55:51Z A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives Sarah, Gautier Homa, Felix Pointet, Stéphanie Contreras, Sandy Sabot, François Nabholz, Benoit Santoni, Sylvain Sauné, Laure Ardisson, Morgane Chantret, Nathalie Sauvage, Christopher Tregear, James Jourda, Cyril Pot, David Vigouroux, Yves Chair, Hana Scarcelli, Nora Billot, Claire Yahiaoui, Nabila Bacilieri, Roberto Khadari, Bouchaib Boccara, Michel Barnaud, Adéline Péros, Jean-Pierre Labouisse, Jean-Pierre Pham, Jean-Louis David, Jacques Glémin, Sylvain Ruíz, Manuel rna sequence genomes wild plants plant genetic resources mapping secuencia de arn genomas plantas silvestres recursos genéticos vegetales We produced a unique large dataset of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum. We used the same protocol for the release of 26 new transcriptomes of crop plants and wild relatives, including still understudied crops such as yam, pearl millet and fonio. The species list has a wide taxonomic representation with the inclusion of 15 monocots and 11 eudicots. All contigs were annotated using BLAST, prot4EST, and Blast2GO. A strong originality of the dataset is that each crop is associated with close relative species, which will permit whole genome comparative evolutionary studies between crops and their wild related species. This large resource will thus serve research communities working on both crops and model organisms. All the data are available at http://arcad-bioinformatics.southgreen.fr/. 2017-05 2016-08-10T19:32:27Z 2016-08-10T19:32:27Z Journal Article https://hdl.handle.net/10568/76382 en Open Access application/pdf Wiley Sarah, Gautier; Homa, Felix; Pointet, Stéphanie; Contreras, Sandy; Sabot, François; Nabholz, Benoit; Santoni, Sylvain; Sauné, Laure; Ardisson, Morgane; Chantret, Nathalie; Sauvage, Christopher; Tregear, James; Jourda, Cyril; Pot, David; Vigouroux, Yves; Chair, Hana; Scarcelli, Nora; Billot, Claire; Yahiaoui, Nabila; Bacilieri, Roberto; Khadari, Bouchaib; Boccara, Michel; Barnaud, Adéline; Péros, Jean-Pierre; Labouisse, Jean-Pierre; Pham, Jean-Louis; David, Jacques; Glémin, Sylvain; Ruiz, Manuel. 2016. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Molecular Ecology Resources. Accepted Author Manuscript doi:10.1111/1755-0998.12587 |
| spellingShingle | rna sequence genomes wild plants plant genetic resources mapping secuencia de arn genomas plantas silvestres recursos genéticos vegetales Sarah, Gautier Homa, Felix Pointet, Stéphanie Contreras, Sandy Sabot, François Nabholz, Benoit Santoni, Sylvain Sauné, Laure Ardisson, Morgane Chantret, Nathalie Sauvage, Christopher Tregear, James Jourda, Cyril Pot, David Vigouroux, Yves Chair, Hana Scarcelli, Nora Billot, Claire Yahiaoui, Nabila Bacilieri, Roberto Khadari, Bouchaib Boccara, Michel Barnaud, Adéline Péros, Jean-Pierre Labouisse, Jean-Pierre Pham, Jean-Louis David, Jacques Glémin, Sylvain Ruíz, Manuel A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives |
| title | A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives |
| title_full | A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives |
| title_fullStr | A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives |
| title_full_unstemmed | A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives |
| title_short | A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives |
| title_sort | large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives |
| topic | rna sequence genomes wild plants plant genetic resources mapping secuencia de arn genomas plantas silvestres recursos genéticos vegetales |
| url | https://hdl.handle.net/10568/76382 |
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