The genome of woodland strawberry (Fragaria vesca)

Vladimir Shulaev; Daniel J. Sargent; Ross N. Crowhurst; Todd C. Mockler; Otto Folkerts; Arthur L. Delcher; Pankaj Jaiswal; Keithanne Mockaitis; Aaron Liston; Shrinivasrao P. Mane; Paul Burns; Thomas M. Davis; Janet P. Slovin; Nahla Bassil; Roger P. Hellens; Clive Evans; Tim Harkins; Chinnappa Kodira; Brian Desany; Oswald R. Crasta; Roderick V. Jensen; Andrew C. Allan; Todd P. Michael; Joao Carlos Setubal; Jean Marc Celton; D. Jasper G. Rees; Kelly P. Williams; Sarah H. Holt; Juan Jairo Ruiz Rojas; Mithu Chatterjee; Bo Liu; Herman Silva; Lee Meisel; Avital Adato; Sergei A. Filichkin; Michela Troggio; Roberto Viola; Tia Lynn Ashman; Hao Wang; Palitha Dharmawardhana; Justin Elser; Rajani Raja; Henry D. Priest; Douglas W. Bryant; Samuel E. Fox; Scott A. Givan; Larry J. Wilhelm; Sushma Naithani; Alan Christoffels; David Y. Salama; Jade Carter; Elena Lopez Girona; Anna Zdepski; Wenqin Wang; Randall A. Kerstetter; Wilfried Schwab; Schuyler S. Korban; Jahn Davik; Amparo Monfort; Beatrice Denoyes-Rothan; Pere Arus; Ron Mittler; Barry Flinn; Asaph Aharoni; Jeffrey L. Bennetzen; Steven L. Salzberg; Allan W. Dickerman; Riccardo Velasco; Mark Borodovsky; Richard E. Veilleux; Kevin M. Folta

doi:10.1038/ng.740

The genome of woodland strawberry (Fragaria vesca)

Vladimir Shulaev, Daniel J. Sargent, Ross N. Crowhurst, Todd C. Mockler, Otto Folkerts, Arthur L. Delcher, Pankaj Jaiswal, Keithanne Mockaitis, Aaron Liston, Shrinivasrao P. Mane, Paul Burns, Thomas M. Davis, Janet P. Slovin, Nahla Bassil, Roger P. Hellens, Clive Evans, Tim Harkins, Chinnappa Kodira, Brian Desany, Oswald R. CrastaRoderick V. Jensen, Andrew C. Allan, Todd P. Michael, Joao Carlos Setubal, Jean Marc Celton, D. Jasper G. Rees, Kelly P. Williams, Sarah H. Holt, Juan Jairo Ruiz Rojas, Mithu Chatterjee, Bo Liu, Herman Silva, Lee Meisel, Avital Adato, Sergei A. Filichkin, Michela Troggio, Roberto Viola, Tia Lynn Ashman, Hao Wang, Palitha Dharmawardhana, Justin Elser, Rajani Raja, Henry D. Priest, Douglas W. Bryant, Samuel E. Fox, Scott A. Givan, Larry J. Wilhelm, Sushma Naithani, Alan Christoffels, David Y. Salama, Jade Carter, Elena Lopez Girona, Anna Zdepski, Wenqin Wang, Randall A. Kerstetter, Wilfried Schwab, Schuyler S. Korban, Jahn Davik, Amparo Monfort, Beatrice Denoyes-Rothan, Pere Arus, Ron Mittler, Barry Flinn, Asaph Aharoni, Jeffrey L. Bennetzen, Steven L. Salzberg, Allan W. Dickerman, Riccardo Velasco, Mark Borodovsky, Richard E. Veilleux, Kevin M. Folta

Research output: Contribution to journal › Article › peer-review

Abstract

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 Ã- 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.

Original language	English (US)
Pages (from-to)	109-116
Number of pages	8
Journal	Nature Genetics
Volume	43
Issue number	2
DOIs	https://doi.org/10.1038/ng.740
State	Published - Feb 2011
Externally published	Yes

ASJC Scopus subject areas

Genetics

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10.1038/ng.740

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Shulaev, V., Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S. P., Burns, P., Davis, T. M., Slovin, J. P., Bassil, N., Hellens, R. P., Evans, C., Harkins, T., Kodira, C., Desany, B., ... Folta, K. M. (2011). The genome of woodland strawberry (Fragaria vesca). Nature Genetics, 43(2), 109-116. https://doi.org/10.1038/ng.740

Shulaev, V, Sargent, DJ, Crowhurst, RN, Mockler, TC, Folkerts, O, Delcher, AL, Jaiswal, P, Mockaitis, K, Liston, A, Mane, SP, Burns, P, Davis, TM, Slovin, JP, Bassil, N, Hellens, RP, Evans, C, Harkins, T, Kodira, C, Desany, B, Crasta, OR, Jensen, RV, Allan, AC, Michael, TP, Setubal, JC, Celton, JM, Rees, DJG, Williams, KP, Holt, SH, Rojas, JJR, Chatterjee, M, Liu, B, Silva, H, Meisel, L, Adato, A, Filichkin, SA, Troggio, M, Viola, R, Ashman, TL, Wang, H, Dharmawardhana, P, Elser, J, Raja, R, Priest, HD, Bryant, DW, Fox, SE, Givan, SA, Wilhelm, LJ, Naithani, S, Christoffels, A, Salama, DY, Carter, J, Girona, EL, Zdepski, A, Wang, W, Kerstetter, RA, Schwab, W, Korban, SS, Davik, J, Monfort, A, Denoyes-Rothan, B, Arus, P, Mittler, R, Flinn, B, Aharoni, A, Bennetzen, JL, Salzberg, SL, Dickerman, AW, Velasco, R, Borodovsky, M, Veilleux, RE & Folta, KM 2011, 'The genome of woodland strawberry (Fragaria vesca)', Nature Genetics, vol. 43, no. 2, pp. 109-116. https://doi.org/10.1038/ng.740

@article{ca9be213ca3a434397ceaaa8ce7cfa11,

title = "The genome of woodland strawberry (Fragaria vesca)",

abstract = "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 {\~A}- 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.",

author = "Vladimir Shulaev and Sargent, {Daniel J.} and Crowhurst, {Ross N.} and Mockler, {Todd C.} and Otto Folkerts and Delcher, {Arthur L.} and Pankaj Jaiswal and Keithanne Mockaitis and Aaron Liston and Mane, {Shrinivasrao P.} and Paul Burns and Davis, {Thomas M.} and Slovin, {Janet P.} and Nahla Bassil and Hellens, {Roger P.} and Clive Evans and Tim Harkins and Chinnappa Kodira and Brian Desany and Crasta, {Oswald R.} and Jensen, {Roderick V.} and Allan, {Andrew C.} and Michael, {Todd P.} and Setubal, {Joao Carlos} and Celton, {Jean Marc} and Rees, {D. Jasper G.} and Williams, {Kelly P.} and Holt, {Sarah H.} and Rojas, {Juan Jairo Ruiz} and Mithu Chatterjee and Bo Liu and Herman Silva and Lee Meisel and Avital Adato and Filichkin, {Sergei A.} and Michela Troggio and Roberto Viola and Ashman, {Tia Lynn} and Hao Wang and Palitha Dharmawardhana and Justin Elser and Rajani Raja and Priest, {Henry D.} and Bryant, {Douglas W.} and Fox, {Samuel E.} and Givan, {Scott A.} and Wilhelm, {Larry J.} and Sushma Naithani and Alan Christoffels and Salama, {David Y.} and Jade Carter and Girona, {Elena Lopez} and Anna Zdepski and Wenqin Wang and Kerstetter, {Randall A.} and Wilfried Schwab and Korban, {Schuyler S.} and Jahn Davik and Amparo Monfort and Beatrice Denoyes-Rothan and Pere Arus and Ron Mittler and Barry Flinn and Asaph Aharoni and Bennetzen, {Jeffrey L.} and Salzberg, {Steven L.} and Dickerman, {Allan W.} and Riccardo Velasco and Mark Borodovsky and Veilleux, {Richard E.} and Folta, {Kevin M.}",

note = "Funding Information: 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{\textquoteright}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.).",

year = "2011",

month = feb,

doi = "10.1038/ng.740",

language = "English (US)",

volume = "43",

pages = "109--116",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group",

number = "2",

}

TY - JOUR

T1 - The genome of woodland strawberry (Fragaria vesca)

AU - Shulaev, Vladimir

AU - Sargent, Daniel J.

AU - Crowhurst, Ross N.

AU - Mockler, Todd C.

AU - Folkerts, Otto

AU - Delcher, Arthur L.

AU - Jaiswal, Pankaj

AU - Mockaitis, Keithanne

AU - Liston, Aaron

AU - Mane, Shrinivasrao P.

AU - Burns, Paul

AU - Davis, Thomas M.

AU - Slovin, Janet P.

AU - Bassil, Nahla

AU - Hellens, Roger P.

AU - Evans, Clive

AU - Harkins, Tim

AU - Kodira, Chinnappa

AU - Desany, Brian

AU - Crasta, Oswald R.

AU - Jensen, Roderick V.

AU - Allan, Andrew C.

AU - Michael, Todd P.

AU - Setubal, Joao Carlos

AU - Celton, Jean Marc

AU - Rees, D. Jasper G.

AU - Williams, Kelly P.

AU - Holt, Sarah H.

AU - Rojas, Juan Jairo Ruiz

AU - Chatterjee, Mithu

AU - Liu, Bo

AU - Silva, Herman

AU - Meisel, Lee

AU - Adato, Avital

AU - Filichkin, Sergei A.

AU - Troggio, Michela

AU - Viola, Roberto

AU - Ashman, Tia Lynn

AU - Wang, Hao

AU - Dharmawardhana, Palitha

AU - Elser, Justin

AU - Raja, Rajani

AU - Priest, Henry D.

AU - Bryant, Douglas W.

AU - Fox, Samuel E.

AU - Givan, Scott A.

AU - Wilhelm, Larry J.

AU - Naithani, Sushma

AU - Christoffels, Alan

AU - Salama, David Y.

AU - Carter, Jade

AU - Girona, Elena Lopez

AU - Zdepski, Anna

AU - Wang, Wenqin

AU - Kerstetter, Randall A.

AU - Schwab, Wilfried

AU - Korban, Schuyler S.

AU - Davik, Jahn

AU - Monfort, Amparo

AU - Denoyes-Rothan, Beatrice

AU - Arus, Pere

AU - Mittler, Ron

AU - Flinn, Barry

AU - Aharoni, Asaph

AU - Bennetzen, Jeffrey L.

AU - Salzberg, Steven L.

AU - Dickerman, Allan W.

AU - Velasco, Riccardo

AU - Borodovsky, Mark

AU - Veilleux, Richard E.

AU - Folta, Kevin M.

N1 - Funding Information: 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.).

PY - 2011/2

Y1 - 2011/2

N2 - 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 Ã- 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.

AB - 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 Ã- 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.

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DO - 10.1038/ng.740

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JO - Nature Genetics

JF - Nature Genetics

IS - 2

ER -

The genome of woodland strawberry (Fragaria vesca)

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