Fragaria vesca Whole Genome v1.0 (build 8) Assembly & Annotation

The assembly and annotation files below are from the assembly as presented by the Shulaev, et. al 2010 strawberry genome paper. The assembly was constrcuted from 454, Illumina and Sanger reads using the Celera assembler and was assembled by Arthur Delcher at the University of Maryland.  The pseudomolecules are the final assembly (v1.0) of the chromosomal sequence. The pseudomolecule sequences were derived from ordered and oriented scaffolds.  The pseudomolecules, scaffolds used to construct the pseudomolecules, and low quality degenerate scaffolds (not used in construction of the pseudomolecules) are available for download.

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Ab Initio GeneMark Predictions
Ab initio GeneMark gene prediction were generated by Mark Borodovsky, Paul Burns and Alexandre Lomsadze (Georgia Institute of Technology, Atlanta, Georgia, USA) dated 10-12-2009. The ab initio predictions for Fragaria vesca were created using the new 2.51 version of the GeneMark-ES program¹ developed by Paul Burns. This program uses an iterative self-training algorithm to train a GMHMM gene model, which is used for gene prediction inside the iterative training as well as for the final prediction step. ^[1]Lomsadze A., Ter-Hovhannisyan V., Chernoff Y. and Borodovsky M. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Research, 2005, Vol. 33, No. 20, 6494-6506

Hybrid GeneMark Predictions
Hybrid GeneMark gene prediction were generated by Mark Borodovsky, Paul Burns and Alexandre Lomsadze (Georgia Institute of Technology, Atlanta, Georgia, USA) with EST data constraints released 16-11-2009. The ab initio predictions for Fragaria vesca were created using the new 2.51 version of the GeneMark-ES program¹ developed by Paul Burns. This program uses an iterative self-training algorithm to train a GMHMM gene model, which is used for gene prediction inside the iterative training as well as for the final prediction step. ^[1]Lomsadze A., Ter-Hovhannisyan V., Chernoff Y. and Borodovsky M. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Research, 2005, Vol. 33, No. 20, 6494-6506.

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The choloroplast genome was  constructed from Illumina reads and was annotated using DGMA by Aaron Liston at Oregon State University.

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Excel Reports
Best hit reports of blastp of Fragaria vesca genome v1.0 proteins versus various protein databases.  Results in Excel format.  These blast results are provided by the MainLab Bioinformatics group at Washington State University using protein sequences derived from the hybrid GeneMark gene models.

Uniref90 Alignments
Uniref90 release 15.6 consisting of 5,801,325 entries was obtained from the UniProt FTP site. NCBI Blast version 2.2.18 tblastn was used to compare the protein sequences against the Strawberry Genome Assembly version 8 scaffolds dynamically translated in all reading frames. Hits were divided into separate files with different significance levels.

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The Rosaceae family Conserved Orthlogous Set (COS) markers have been aligend to the F. vesca v1.0 scaffolds

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LTRs were identified using ltr_struc (McCarthy, E.M., and J.F. McDonald. 2003. LTR_STRUC: A novel search and identification program for LTR retrotransposons. Bioinformatics 19: 362-367) and LTRharvest (D. Ellinghaus, S. Kurtz, and U. Willhoeft. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 2008, 9:18).

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F. vesca EST were pre-clustered onto scaffolds and then assembled using MIRA.  Assembled clusters were then aligned to the scaffolds using GMAP. The single best match for each cluster was kept. The analysis was performed by Todd Mockler and Henry Priest at Oregon State University.

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Fragaria iinumae 454 contigs (assembly 21-07-2009) were mapped to the Fragaria vesca reference scaffolds. The F. iinumae contigs are generally short due to low coverage. 

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Gene indices were obtained from The Gene Index Project (http://compbio.dfci.harvard.edu/tgi/). The following plant species gene indices were obtained: Apple (Malus domestica) v1.0 7-8-08 (MdGI), Arabidopsis thaliana v13.0 6-16-06 (AGI), Beet (Beta vulgaris) v2.0 5-19-08 (BvGI), Brassica napus v3.1 5-31-08 (BnGI), Cotton (Gossypium) v9.0 6-14-08 (CGI), Grape (Vitis vinifera) v6.0 7-30-08 VvGI), Sunflower (Helianthus annuus) v5.0 (HaGI), Lettuce (Lactuca sativa) v3.0 7-2-08 (LsGI), Medicago truncatula v9.0 v7-16-08 (MtGI), Onion (Allium cepa) v2.0 (OnGI), Orange (Citrus sinensis) v1.0 6-25-08 (CsGI), Peach (Prunus persica) v1.0 6-29-08 (PrpeGI), Pepper (Capsicum annuum) v3.0 7-17-08 (CaGI), Pinus v7.0 7-23-08 (PGI), Soybean (Glycine max) v13.0 7-11-08 (GmGI), Sugar Cane (Saccharum officinarum) v2.2 (SoGI), and Tomato (Solanum lycopersicum) v12.0 7-15-08 (LGI). Gene indices were mapped to the genome sequence scaffolds and unassembled contigs using gmap version 2007-09-28 (http://www.gene.com/share/gmap/; and Watanabe, 2005).

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All assembly and annotation files are available for download by selecting the desired data type in the right-hand "Resources" side bar.  Each data type page will provide a description of the available files and links do download.