Fragaria Unigene v5.0

Overview
Analysis NameFragaria Unigene v5.0
Unigene NameFragaria Unigene v5.0
MethodCAP3
SourceGenbank Fragaria ESTs (July 2012)
Date performed2012-12-19
Number of Reads55,513
Number of Contigs6,226
Number of Singlets12,008
OrganismsFragaria vesca

This is the fifth version of the Fragaria unigene. This build was used many sequencing projects around the world are depositing ESTs from the genus Fragaria in the NCBI dbEST database. The Fragaria ESTs included in this assembly were downloaded on July 1, 2012.

Not all of the Fragaria ESTs are of high quality. To filter, we crossmatched the public sequences against NCBI's UniVec database and used the BLAST sequence similarity algorithm to remove species-specific chloroplast, mitochondrial, tRNA, and rRNA sequences. To reduce redundancy and create longer transcripts we assembled these ESTs using the CAP31 program. The final assembly has been annotated by BLAST sequence similarity searching agaist Swiss-Prot2,TrEMBL3,TAIR4Arabidopsis proteinsPrunus persica5,Populus trichocarpa6 and Vitis vinifera7.

Processing Summary
Number of ESTs available 58,295
Number of ESTs available after filtering 55,513
Average Length 627
Number of Contigs(CAP3 Assembly, -p 90 ) 6,226
Average Length of Contigs 952
Number of Singlets 12,008
Number of Putative Unigenes 18,234


References

  1. Huan, X. and Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome Research, 9, 868-877.
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990) Basic local alignment search tool. J Mol Biol. 215(3):403-10.
  3. Boeckmann B., Bairoch A., Apweiler R., Blatter M.-C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., Pilbout S., and Sneider M. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research. 31:365-370.
  4. Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P. (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gate way to Arabidopsis biology, research materials and community. Nucleic Acids Research. 31(1):224-8.
  5. http://services.appliedgenomics.org/projects/drupomics/
  6. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). (2006) Science. Sep 15; 313(5793):1596-604
  7. French-Italian Public Consortium for Grapevine Genome Characterization.(2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. Sep 27; 449(7161):463-7.
Library Information
The Fragaria ESTs used for this assembly were downloaded on July 01, 2012

 

EST Libraries
Number of ESTs available 58,295
# of Species 4
# of Libraries 54
# of Tissues 20
# of Development Stages 14

View detailed chart of libraries.

Species
Fragaria chiloensis 137
Fragaria vesca 44,979
Fragaria vesca subsp. vesca 2,824
Fragaria x ananassa 10,354
 

 

Homology

Homology was determined using the BLASTx algorithm for the Fragaria Contigs and Singlets vs. the Swiss-Prot , TrEMBL,TAIR Arabidopsis proteins,Prunus persica, Populus trichocarpa and Vitis vinifera proteins. Only matches with an E-value of 1.0 e-6 or better were recorded. Swiss-Prot is a curated protein database with a high level of annotation and a minimal level of redundancy, and TrEMBL is a computer-annotated supplement of Swiss-Prot that contains all the translations of TrEMBL nucleotide sequence entries not yet integrated in Swiss-Prot. Homology of Fragaria in Excel spreadsheet can be downloaded from the Downloads.

KEGG

KEGG analysis of Fragaria unigene v5.0 contigs

All Fragaria unigene v5.0 contigs were uploaded to the KEGG / KASS server at http://www.genome.jp/kaas-bin/kaas_main. The SBH (single-directional best hit) method was selected under the category "Assignment method". All other settings were defaults. Results were downloaded in the heir.tar.gz heirarchy file and uploaded to the website.

 

 

Microsatellite Analysis

The type and frequency of simple sequence repeats in Fragaria unigene v5.0 contigs was determined using the MainLabssr.pl program.For these searches, SSRs are defined as dinucleotides repeated at least 5 times, trinucleotides repeated at least 4 times, tetranucleotides repeated at least 3 times, or pentanucleotides repeated at least 3 times. The SSRs of Fragaria unigene v5.0 contigs are available to be downloaded from the Downloads.

Sequence information
Number of Sequences 6,226
Number of Sequences Having One Or More SSRs 1,853
Percentage of Sequences Having One Or More SSRs 29.76%
Total Number of SSRs Found 2,556
Number of Motifs 251

Frequency of Motif Type

Motif Length Frequency Percentage Frequency
2bp 801 31.33%
3bp 1379 53.95%
4bp 281 10.99%
5bp 95 3.72%

 

Contact
Contact Details
Name Main, Dorrie
Lab Department of Horticulture
Organization Washington State University
Address 45 Johnson Hall, Pullman, WA 99164
Telephone 509-335-2774
Fax 509-335-8690
Email dorrie@wsu.edu

 

Downloads
Orignal EST sequences from NCBI (58,295 sequences) Fragaria_est_NCBI_091212.fasta
Filtered and trimmed EST sequences (55,513 sequences) Fragaria.trimmedESTs.fasta
Contigs from CAP3 assembly (6,226 contig sequences) Fragaria.cap.contigs
Ace file from CAP3 assembly Fragaria.cap.ace
SSRs found in contigs (with primer predictions) Fragaria_ssrReport.xls

Fragaria unigene v5.0 contigs blastx vs protein databases. Best hit reports in Excel

BLAST of contigs to UniProtKB/Swiss-Prot (586KB) Fragaria_blastx_Swiss-Prot.xlsx
BLAST of contigs to UniProtKB/TrEMBL(685KB) Fragaria_blastx_TrEMBL.xlsx
BLAST of contigs to TAIR10 Arabidopsis proteins(767KB) Fragaria_blastx_TAIR10.xlsx
BLAST of contigs to Prunus persica (peach) v1.0 proteins(594KB) Fragaria_blastx_peach.xlsx
BLAST of contigs to Vitis vinifera (grape) proteins(577KB) Fragaria_blastx_grape.xlsx
BLAST of contigs to Populus trichocarpa (poplar) v2.0 proteins (601KB) Fragaria_blastx_poplar.xlsx