Prunus Unigene v5.0

Overview
Analysis NamePrunus Unigene v5.0
Unigene NamePrunus Unigene v5.0
MethodCAP3
SourceGenbank Prunus ESTs (July 2012)
Date performed2013-01-03
Number of Reads106,148
Number of Contigs10,934
Number of Singlets22,957
OrganismsPrunus persica

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

Not all of the Prunus 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 proteins, Populus trichocarpa5 and Vitis vinifera6.

Processing Summary
Number of ESTs available 110,806
Number of ESTs available after filtering 106,148
Average Length 589
Number of Contigs(CAP3 Assembly, -p 90 ) 10,934
Average Length of Contigs 972
Number of Singlets 22,957
Number of Putative Unigenes 33,891


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. 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
  6. 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 Prunus ESTs used for this assembly were downloaded on July 01, 2012

 

EST Libraries
Number of ESTs available 110,806
# of Species 8
# of Libraries 63
# of Tissues 23
# of Development Stages 24

 

View detailed chart of libraries.

 

Species
Prunus armeniaca    15,105
Prunus avium    6,035
Prunus avium x P. cerasus x P. canescens    89
Prunus cerasus    1,255
Prunus domestica    54
Prunus dulcis    3,864
Prunus mume    4,589
Prunus persica    79,815
 

 

Homology

Homology was determined using the BLASTx algorithm for the Prunus Contigs and Singlets vs. the Swiss-Prot , TrEMBL,TAIR Arabidopsis proteins,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 Prunus in Excel spreadsheet can be downloaded from the Downloads.

KEGG

KEGG analysis of Prunus unigene v5.0 contigs

All Prunus 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 Prunus 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 Malus unigene v5.0 contigs are available to be downloaded from the Downloads.

Sequence information
Number of Sequences 10,934
Number of Sequences Having One Or More SSRs 3,448
Percentage of Sequences Having One Or More SSRs 31.53%
Total Number of SSRs Found 4,944
Number of Motifs 426

Frequency of Motif Type

Motif Length Frequency Percentage Frequency
2bp 2061    41.69%
3bp 1752     35.44%
4bp 822    16.63%
5bp 309    6.25%

 

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 (110,806 sequences) Prunus_est_NCBI_091212.fasta
Filtered and trimmed EST sequences (106,148 sequences) Prunus.trimmedESTs.fasta
Contigs from CAP3 assembly (972 contig sequences) Prunus.cap.contigs
Ace file from CAP3 assembly Prunus.cap.ace
SSRs found in contigs (with primer predictions) Prunus_ssrReport.xls

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

BLAST of contigs to UniProtKB/Swiss-Prot (964KB) Prunus_blastx_Swiss-Prot.xlsx
BLAST of contigs to UniProtKB/TrEMBL (1.2MB) Prunus_blastx_TrEMBL.xlsx
BLAST of contigs to TAIR10 Arabidopsis proteins (1.3MB) Prunus_blastx_TAIR10.xlsx
BLAST of contigs to Prunus persica (peach) v1.0 proteins (1.1MB) Prunus_blastx_peach.xlsx
BLAST of contigs to Vitis vinifera (grape) proteins (1008KB) Prunus_blastx_grape.xlsx
BLAST of contigs to Populus trichocarpa (poplar) v2.0 proteins (1.1MB) Prunus_blastx_poplar.xlsx