Malus Unigene v5.0

Analysis NameMalus Unigene v5.0
SourceGenbank Malus ESTs (July 2012)
Date performed2012-12-14

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

Not all of the Malus 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 against Swiss-Prot2, TrEMBL3, TAIR4 Arabidopsis proteins Prunus persica5, Populus trichocarpa6 and Vitis vinifera7.


Processing Summary
Number of ESTs available 334,190
Number of ESTs available after filtering 325,111
Average Length 488
Number of Contigs(CAP3 Assembly, -p 90 ) 25,525
Average Length of Contigs 885
Number of Singlets 60,918
Number of Putative Unigenes 86,443


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


EST Libraries
Number of ESTs available 334,190
# of Species 6
# of Libraries 150
# of Tissues 59
# of Development Stages 38


View detailed chart of libraries.


Malus hybrid rootstock   4,804
Malus prunifolia   150
Malus pumila   51
Malus sieboldii    1,210
Malus x domestica    323,020
Malus x domestica x Malus sieversii    4,955



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

Microsatellite Analysis

The type and frequency of simple sequence repeats in Malus unigene v5.0 contigs was determined using the 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 25,525
Number of Sequences Having One Or More SSRs 6,596
Percentage of Sequences Having One Or More SSRs 25.84%
Total Number of SSRs Found 9,084
Number of Motifs 478

Frequency of Motif Type

Motif Length Frequency Percentage Frequency
2bp 4098 45.11%
3bp 3289 36.21%
4bp 1321 14.54%
5bp 376 4.14%


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


Orignal EST sequences from NCBI (334,190 sequences) Malus_est_NCBI_091212.fasta
Filtered and trimmed EST sequences (325,111 sequences) Malus.trimmedESTs.fasta
Contigs from CAP3 assembly (25,525 contig sequences) Malus.cap.contigs
Ace file from CAP3 assembly Malus.cap.ace
SSRs found in contigs (with primer predictions) Malus_ssrReport.xls

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

BLAST of contigs to UniProtKB/Swiss-Prot (2.0MB) Malus_blastx_Swiss-Prot.xlsx
BLAST of contigs to UniProtKB/TrEMBL (2.7MB) Malus_blastx_TrEMBL.xlsx
BLAST of contigs to TAIR10 Arabidopsis proteins (2.7MB) Malus_blastx_TAIR10.xlsx
BLAST of contigs to Prunus persica (peach) v1.0 proteins (2.3MB) Malus_blastx_peach.xlsx
BLAST of contigs to Vitis vinifera (grape) proteins (2.2MB) Malus_blastx_grape.xlsx
BLAST of contigs to Populus trichocarpa (poplar) v2.0 proteins (2.3MB) Malus_blastx_poplar.xlsx



KEGG analysis of Malus unigene v5.0 contigs

All Malus unigene v5.0 contigs were uploaded to the KEGG / KASS server at 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.