The genome of woodland strawberry (Fragaria vesca)
The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) an...
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| Tipo de recurso: | artículo |
| Fecha de publicación: | 2010 |
| País: | España |
| Institución: | Institut de Recerca i Tecnologia Agroalimentàries (IRTA) |
| Repositorio: | IRTA Pubpro. Open Digital Archive |
| OAI Identifier: | oai:repositori.irta.cat:20.500.12327/2979 |
| Acceso en línea: | http://hdl.handle.net/20.500.12327/2979 https://doi.org/10.1038/ng.740 |
| Access Level: | acceso abierto |
| Palabra clave: | 575 633 |
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The genome of woodland strawberry (Fragaria vesca)Shulaev, VladimirSargent, Daniel J.Crowhurst, Ross N.Mockler, Todd C.Folkerts, OttoDelcher, Arthur L.Jaiswal, PankajMockaitis, KeithanneListon, AaronMane, Shrinivasrao P.Burns, PaulDavis, Thomas M.Slovin, Janet P.Bassil, NahlaHellens, Roger P.Evans, CliveHarkins, TimKodira, ChinnappaDesany, BrianCrasta, Oswald R.Jensen, Roderick V.Allan, Andrew C.Michael, Todd P.Setubal, Joao CarlosCelton, Jean-MarcRees, D. Jasper G.Williams, Kelly P.Holt, Sarah H.Ruiz Rojas, Juan JairoChatterjee, MithuLiu, BoSilva, HermanMeisel, LeeAdato, AvitalFilichkin, Sergei A.Troggio, MichelaViola, RobertoAshman, Tia-LynnWang, HaoDharmawardhana, PalithaElser, JustinRaja, RajaniPriest, Henry D.Bryant Jr., Douglas W.Fox, Samuel E.Givan, Scott A.Wilhelm, Larry J.Naithani, SushmaChristoffels, AlanSalama, David Y.Carter, JadeLopez Girona, ElenaZdepski, AnnaWang, WenqinKerstetter, Randall A.Schwab, WilfriedKorban, Schuyler S.Davik, JahnMonfort, AmparoDenoyes-Rothan, BeatriceArús, PereMittler, RonFlinn, BarryAharoni, AsaphBennetzen, Jeffrey L.Salzberg, Steven L.Dickerman, Allan W.Velasco, RiccardoBorodovsky, MarkVeilleux, Richard E.Folta, Kevin M.575633The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.This work was supported by Roche and 454 Sequencing; the Virginia Bioinformatics Institute; the University of Florida Institute of Food and Agricultural Sciences (IFAS) Dean for Research; the University of Florida Strawberry Breeding Program; The Province of Trento, Italy (to R.V.); Driscoll’s Strawberry Associates; United States Department of Agriculture/Cooperative State Research, Education and Extension Service (USDA/CSREES) Hatch Project VA-135816 (to B.F.); Rutgers Busch Biomedical Funding (to T.P.M.); East Malling Trust (EMT) and Biotechnology and Biological Sciences Research Council (BBSRC) (to D.J.S. and E.L.G.); the Oregon State Agricultural Research Foundation #ARF4435 (to T.C.M.); the Oregon State Computational and Genome Biology Initiative (to T.C.M.); Oregon State University start-up fund (to P.J.); the Center for Genomics and Bioinformatics, supported in part by the METACyt Initiative of Indiana University (to K.M.); US National Institutes of Health (grant HG00783; to M.B.); USDA-CSREES National Research Initiative (NRI) Plant Genome Grant 2008-35300-04411 and New Hampshire Agricultural Experiment Station Project NH00535 (to T.M.D.); and USDA/ARS CRIS #1275- 21000-180-01R (to J.P.S.).info:eu-repo/semantics/publishedVersionNature ResearchProducció VegetalGenòmica i Biotecnologia202420242010info:eu-repo/semantics/article10application/pdfhttp://hdl.handle.net/20.500.12327/2979https://doi.org/10.1038/ng.740reponame:IRTA Pubpro. Open Digital Archiveinstname:Institut de Recerca i Tecnologia Agroalimentàries (IRTA)InglésNature GeneticsAttribution-NonCommercial-ShareAlike 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-sa/4.0/info:eu-repo/semantics/openAccessoai:repositori.irta.cat:20.500.12327/29792026-06-16T08:51:17Z |
| dc.title.none.fl_str_mv |
The genome of woodland strawberry (Fragaria vesca) |
| title |
The genome of woodland strawberry (Fragaria vesca) |
| spellingShingle |
The genome of woodland strawberry (Fragaria vesca) Shulaev, Vladimir 575 633 |
| title_short |
The genome of woodland strawberry (Fragaria vesca) |
| title_full |
The genome of woodland strawberry (Fragaria vesca) |
| title_fullStr |
The genome of woodland strawberry (Fragaria vesca) |
| title_full_unstemmed |
The genome of woodland strawberry (Fragaria vesca) |
| title_sort |
The genome of woodland strawberry (Fragaria vesca) |
| dc.creator.none.fl_str_mv |
Shulaev, Vladimir Sargent, Daniel J. Crowhurst, Ross N. Mockler, Todd C. Folkerts, Otto Delcher, Arthur L. Jaiswal, Pankaj Mockaitis, Keithanne Liston, Aaron Mane, Shrinivasrao P. Burns, Paul Davis, Thomas M. Slovin, Janet P. Bassil, Nahla Hellens, Roger P. Evans, Clive Harkins, Tim Kodira, Chinnappa Desany, Brian Crasta, Oswald R. Jensen, Roderick V. Allan, Andrew C. Michael, Todd P. Setubal, Joao Carlos Celton, Jean-Marc Rees, D. Jasper G. Williams, Kelly P. Holt, Sarah H. Ruiz Rojas, Juan Jairo Chatterjee, Mithu Liu, Bo Silva, Herman Meisel, Lee Adato, Avital Filichkin, Sergei A. Troggio, Michela Viola, Roberto Ashman, Tia-Lynn Wang, Hao Dharmawardhana, Palitha Elser, Justin Raja, Rajani Priest, Henry D. Bryant Jr., Douglas W. Fox, Samuel E. Givan, Scott A. Wilhelm, Larry J. Naithani, Sushma Christoffels, Alan Salama, David Y. Carter, Jade Lopez Girona, Elena Zdepski, Anna Wang, Wenqin Kerstetter, Randall A. Schwab, Wilfried Korban, Schuyler S. Davik, Jahn Monfort, Amparo Denoyes-Rothan, Beatrice Arús, Pere Mittler, Ron Flinn, Barry Aharoni, Asaph Bennetzen, Jeffrey L. Salzberg, Steven L. Dickerman, Allan W. Velasco, Riccardo Borodovsky, Mark Veilleux, Richard E. Folta, Kevin M. |
| author |
Shulaev, Vladimir |
| author_facet |
Shulaev, Vladimir Sargent, Daniel J. Crowhurst, Ross N. Mockler, Todd C. Folkerts, Otto Delcher, Arthur L. Jaiswal, Pankaj Mockaitis, Keithanne Liston, Aaron Mane, Shrinivasrao P. Burns, Paul Davis, Thomas M. Slovin, Janet P. Bassil, Nahla Hellens, Roger P. Evans, Clive Harkins, Tim Kodira, Chinnappa Desany, Brian Crasta, Oswald R. Jensen, Roderick V. Allan, Andrew C. Michael, Todd P. Setubal, Joao Carlos Celton, Jean-Marc Rees, D. Jasper G. Williams, Kelly P. Holt, Sarah H. Ruiz Rojas, Juan Jairo Chatterjee, Mithu Liu, Bo Silva, Herman Meisel, Lee Adato, Avital Filichkin, Sergei A. Troggio, Michela Viola, Roberto Ashman, Tia-Lynn Wang, Hao Dharmawardhana, Palitha Elser, Justin Raja, Rajani Priest, Henry D. Bryant Jr., Douglas W. Fox, Samuel E. Givan, Scott A. Wilhelm, Larry J. Naithani, Sushma Christoffels, Alan Salama, David Y. Carter, Jade Lopez Girona, Elena Zdepski, Anna Wang, Wenqin Kerstetter, Randall A. Schwab, Wilfried Korban, Schuyler S. Davik, Jahn Monfort, Amparo Denoyes-Rothan, Beatrice Arús, Pere Mittler, Ron Flinn, Barry Aharoni, Asaph Bennetzen, Jeffrey L. Salzberg, Steven L. Dickerman, Allan W. Velasco, Riccardo Borodovsky, Mark Veilleux, Richard E. Folta, Kevin M. |
| author_role |
author |
| author2 |
Sargent, Daniel J. Crowhurst, Ross N. Mockler, Todd C. Folkerts, Otto Delcher, Arthur L. Jaiswal, Pankaj Mockaitis, Keithanne Liston, Aaron Mane, Shrinivasrao P. Burns, Paul Davis, Thomas M. Slovin, Janet P. Bassil, Nahla Hellens, Roger P. Evans, Clive Harkins, Tim Kodira, Chinnappa Desany, Brian Crasta, Oswald R. Jensen, Roderick V. Allan, Andrew C. Michael, Todd P. Setubal, Joao Carlos Celton, Jean-Marc Rees, D. Jasper G. Williams, Kelly P. Holt, Sarah H. Ruiz Rojas, Juan Jairo Chatterjee, Mithu Liu, Bo Silva, Herman Meisel, Lee Adato, Avital Filichkin, Sergei A. Troggio, Michela Viola, Roberto Ashman, Tia-Lynn Wang, Hao Dharmawardhana, Palitha Elser, Justin Raja, Rajani Priest, Henry D. Bryant Jr., Douglas W. Fox, Samuel E. Givan, Scott A. Wilhelm, Larry J. Naithani, Sushma Christoffels, Alan Salama, David Y. Carter, Jade Lopez Girona, Elena Zdepski, Anna Wang, Wenqin Kerstetter, Randall A. Schwab, Wilfried Korban, Schuyler S. Davik, Jahn Monfort, Amparo Denoyes-Rothan, Beatrice Arús, Pere Mittler, Ron Flinn, Barry Aharoni, Asaph Bennetzen, Jeffrey L. Salzberg, Steven L. Dickerman, Allan W. Velasco, Riccardo Borodovsky, Mark Veilleux, Richard E. Folta, Kevin M. |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Producció Vegetal Genòmica i Biotecnologia |
| dc.subject.none.fl_str_mv |
575 633 |
| topic |
575 633 |
| description |
The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted. |
| publishDate |
2010 |
| dc.date.none.fl_str_mv |
2010 2024 2024 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/20.500.12327/2979 https://doi.org/10.1038/ng.740 |
| url |
http://hdl.handle.net/20.500.12327/2979 https://doi.org/10.1038/ng.740 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
Nature Genetics |
| dc.rights.none.fl_str_mv |
Attribution-NonCommercial-ShareAlike 4.0 International http://creativecommons.org/licenses/by-nc-sa/4.0/ info:eu-repo/semantics/openAccess |
| rights_invalid_str_mv |
Attribution-NonCommercial-ShareAlike 4.0 International http://creativecommons.org/licenses/by-nc-sa/4.0/ |
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openAccess |
| dc.format.none.fl_str_mv |
10 application/pdf |
| dc.publisher.none.fl_str_mv |
Nature Research |
| publisher.none.fl_str_mv |
Nature Research |
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reponame:IRTA Pubpro. Open Digital Archive instname:Institut de Recerca i Tecnologia Agroalimentàries (IRTA) |
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IRTA Pubpro. Open Digital Archive |
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15.300719 |