Rubus Unigene v5.0

Overview
Analysis NameRubus Unigene v5.0
Unigene NameRubus Unigene v5.0
MethodCAP3
SourceGenbank Rubus ESTs (July 2012)
Date performed2013-01-03
Number of Reads3,055
Number of Contigs359
Number of Singlets1,734
OrganismsRubus sp.

This is the fifth version of the Rubus unigene. This build  used  ESTs from the genus Rubus in the NCBI dbEST database. The Rubus ESTs included in this assembly were downloaded on July 1, 2012.

Not all of the Rubus 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 (-p 90). The contigs from the assembly have been annotated by homology using BLASTX to the following protien datasets:  Swiss-Prot2, TrEMBL3TAIR Arabidopsis proteins4Prunus persica5Populus trichocarpa6, and Vitis vinifera7.

Processing Summary
Number of ESTs available 3,061
Number of ESTs available after filtering 3,055
Average Length 530
Number of Contigs(CAP3 Assembly, -p 90 ) 359
Average Length of Contigs 712
Number of Singlets 1,734
Number of Putative Unigenes 2,093


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 Rubus ESTs used for this assembly were downloaded on July 01, 2012

 

EST Libraries
Number of ESTs available 3,061
# of Species 3
# of Libraries 6
# of Tissues 4
# of Development Stages 3

 

View detailed chart of libraries.

 

Species
Rubus idaeus    327
Rubus idaeus subsp. strigosus    56
Rubus ulmifolius var. inermis x Rubus thyrsiger    2,678
 

 

Homology analysis

Homology was determined using the BLASTx algorithm for the Rubus Contigs against the Swiss-Prot, TrEMBLTAIR 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 data for Rubus contigs is available in Excel format can be downloaded from the Downloads link.

KEGG analysis

KEGG analysis of Rubus unigene v5.0 contigs

All Rubus 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 Rubus 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 Rubus unigene v5.0 contigs are available to be downloaded from the Downloads page.

Sequence information
Number of Sequences 359
Number of Sequences Having One Or More SSRs 91
Percentage of Sequences Having One Or More SSRs 25.34%
Total Number of SSRs Found 124  
Number of Motifs 58

Frequency of Motif Type

 

Motif Length Frequency Percentage Frequency
2bp 29 31.45%
3bp 63 50.81%
4bp 19 15.32%
5bp 3 2.42%

 

Contact us
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

 

Download data
Orignal EST sequences from NCBI (3,061 sequences) Rubus_est_NCBI_091212.fasta
Filtered and trimmed EST sequences (3,055 sequences) Rubus.trimmedESTs.fasta
Contigs from CAP3 assembly (359 contig sequences) Rubus.cap.contigs
Ace file from CAP3 assembly Rubus.cap.ace
SSRs found in contigs (with primer predictions) Rubus_ssrReport.xls

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

BLAST of contigs to UniProtKB/Swiss-Prot (47KB) Rubus_blastx_Swiss-Prot.xlsx
BLAST of contigs to UniProtKB/TrEMBL (49KB) Rubus_blastx_TrEMBL.xlsx
BLAST of contigs to TAIR10 Arabidopsis proteins (54KB) Rubus_blastx_TAIR10.xlsx
BLAST of contigs to Prunus persica (peach) v1.0 proteins (42KB) Rubus_blastx_peach.xlsx
BLAST of contigs to Vitis vinifera (grape) proteins (41KB) Rubus_blastx_grape.xlsx
BLAST of contigs to Populus trichocarpa (poplar) v2.0 proteins (42KB) Rubus_blastx_poplar.xlsx