TitleThe genome of woodland strawberry(Fragaria vesca).
Publication TypeJournal Article
Year of Publication2011
AuthorsShulaev, 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, JCarlos, Celton, J-M, D Rees, JG, Williams, KP, Holt, SH, Rojas, JJairo Ruiz, Chatterjee, M, Liu, B, Silva, H, Meisel, L, Adato, A, Filichkin, SA, Troggio, M, Viola, R, Ashman, T-L, 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, ELopez, 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
JournalNature genetics
Volume43
Pagination109-16
Date Published2011 Feb
ISSN1546-1718
KeywordsAlgorithms, Chloroplasts, Chromosome Mapping, Fluorescence, Fragaria, Gene Expression Profiling, Genes, Genetic, Genetic Linkage, Genome, In Situ Hybridization, Likelihood Functions, Models, Phylogeny, plant, Terminal Repeat Sequences, Transcription
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 × 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.