Pyrus Unigene v5.0

Overview
Analysis NamePyrus Unigene v5.0
Unigene NamePyrus Unigene v5.0
MethodCAP3
SourceGenbank Pyrus ESTs (July 2012)
Date performed2013-01-03
Number of Reads1,760
Number of Contigs259
Number of Singlets964
OrganismsPyrus spp.

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

Not all of the Pyrus 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 1,868
Number of ESTs available after filtering 1,760
Average Length 442
Number of Contigs(CAP3 Assembly, -p 90 ) 259
Average Length of Contigs 524
Number of Singlets 964
Number of Putative Unigenes 1,223


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

 

EST Libraries
Number of ESTs available 1,868
# of Species 5
# of Libraries 37
# of Tissues 11
# of Development Stages 16

 

View detailed chart of libraries.

Species
Pyrus communis    450
Pyrus communis x Pyrus ussuriensis   82
Pyrus pyrifolia 699
Pyrus pyrifolia var. culta    1
Pyrus x bretschneideri 636
 

 

Homology

Homology was determined using the BLASTx algorithm for the Pyrus 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 Pyrus in Excel spreadsheet can be downloaded from the Downloads.

KEGG

KEGG analysis of Pyrus unigene v5.0 contigs

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

Sequence information
Number of Sequences 259
Number of Sequences Having One Or More SSRs 41
Percentage of Sequences Having One Or More SSRs 15.83%
Total Number of SSRs Found 53
Number of Motifs 32

Frequency of Motif Type

Motif Length Frequency Percentage Frequency
2bp 24 45.28%
3bp 19 35.85%
4bp 10 18.87%

 

Contact
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 (1,868 sequences) Pyrus_est_NCBI_091212.fasta
Filtered and trimmed EST sequences (1,760 sequences) Pyrus.trimmedESTs.fasta
Contigs from CAP3 assembly (259 contig sequences) Pyrus.cap.contigs
Ace file from CAP3 assembly Pyrus.cap.ace
SSRs found in contigs (with primer predictions) Pyrus_ssrReport.xls

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

BLAST of contigs to UniProtKB/Swiss-Prot (29KB) Pyrus_blastx_Swiss-Prot.xlsx
BLAST of contigs to UniProtKB/TrEMBL (31KB) Pyrus_blastx_TrEMBL.xlsx
BLAST of contigs to TAIR10 Arabidopsis proteins (34KB) Pyrus_blastx_TAIR10.xlsx
BLAST of contigs to Prunus persica (peach) v1.0 proteins (27KB) Pyrus_blastx_peach.xlsx
BLAST of contigs to Vitis vinifera (grape) proteins (26KB) Pyrus_blastx_grape.xlsx
BLAST of contigs to Populus trichocarpa (poplar) v2.0 proteins (27KB) Pyrus_blastx_poplar.xlsx