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This article in TPG

  1. Vol. 2 No. 1, p. 23-38
    unlockOPEN ACCESS
    Received: Nov 10, 2008
    Accepted: Feb 13, 2009

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Comparative Analysis and Functional Annotation of a Large Expressed Sequence Tag Collection of Apple

  1. Ksenija Gasic,
  2. Delkin O. Gonzalez,
  3. Jyothi Thimmapuram,
  4. Lei Liu,
  5. Mickael Malnoy,
  6. George Gong,
  7. Yuepeng Han,
  8. Lila O. Vodkin,
  9. Herb S. Aldwinckle,
  10. Natalie J. Carroll,
  11. Kathryn S. Orvis,
  12. Peter Goldsbrough,
  13. Sandra Clifton,
  14. Deana Pape,
  15. Lucinda Fulton,
  16. John Martin,
  17. Brenda Theising,
  18. Michael E. Wisniewski,
  19. Gennaro Fazio,
  20. Frank A. Feltus and
  21. Schuyler S. Korban 
  1. K. Gasic, Y. Han, and S.S. Korban, Dep. of Natural Resources and Environmental Sciences, Univ. of Illinois, 310 E.R. Madigan Bldg., 1201 W. Gregory Dr., Urbana, IL 61801; D.O. Gonzalez and L.O. Vodkin, Dep. of Crop Sciences, Univ. of Illinois, 384 E.R. Madigan Bldg., 1201 W. Gregory Dr., Urbana, IL 61801; J. Thimmapuram, L. Liu, and G. Gong, Biotechnology W.M. Keck Center, Univ. of Illinois, 354 E.R. Madigan Bldg., 1201 W. Gregory Dr., Urbana, IL 61801; M. Malnoy and H.S. Aldwinckle, Dep. of Plant Pathology, New York State Agricultural Experiment Station, Cornell Univ., 630 W. North St., Geneva, NY 14456; N.J. Carroll and K.S. Orvis, Dep. of Youth Development and Agricultural Education, Purdue Univ., West Lafayette, IN 47907; P. Goldsbrough, Dep. of Botany and Plant Pathology, Purdue Univ., West Lafayette, IN 47907; S. Clifton, D. Pape, L. Fulton, J. Martin, and B. Theising, Genome Sequencing Center, Washington Univ., School of Medicine, 4444 Forest Park Blvd., St. Louis, MO 63108; M.E. Wisniewski, USDA-ARS, Appalachian Fruit Research Station, 2217 Wiltshire Rd., Kearneysville, WV 25430; G. Fazio, USDA-ARS, Plant Genetic Resources Unit, 630 W. North St., Geneva, NY 14456; F.A. Feltus, Dep. of Genetics and Biochemistry, Clemson Univ., 302-C Biosystems Research Complex, 51 New Cherry Rd., Clemson, SC 29634. K. Gasic, present address: Dep. of Horticulture, Clemson Univ., 112BRC, 51 New Cherry Rd., Clemson, SC, 29634. M. Malnoy, present address: IASMA Research Center, Via E. Mach 1, San Michele all'Adige (TN), 38010, Italy. This work was funded by National Science Foundation Grant No. DBI-03-21701.


A total of 34 apple (Malus × domestica Borkh.) cDNA libraries were constructed from root, leaf, bud, shoot, flower, and fruit tissues, at various developmental stages and/or under biotic or abiotic stress conditions, and of several genotypes. From these libraries, 190,425 clones were partially sequenced from the 5′ end and 42,619 clones were sequenced from the 3′ end, and a total of 182,241 high-quality expressed sequence tags (ESTs) were obtained. These coalesced into 23,442 tentative contigs and 9843 singletons, for a total of 33,825 apple unigenes. Functional annotation of this unigene set revealed an even distribution of apple sequences among the three main gene ontology categories. Of ∼33,000 apple unigenes, 8437 (25%) had no detectable homologs (E >0.1) in the Arabidopsis genome. When the entire apple unigene set was compared with the entire citrus [Citrus sinensis (L.) Osbeck] unigene set and the poplar (Populus trichocarpa Torr. & Gray) predicted proteome, both members of the core eudicot and rosids clade, 13,521 of apple unigenes matched one or more sequences in citrus, while 25,817 had counterparts in the poplar protein database. Apple–Arabidopsis–citrus–poplar comparisons revealed closer evolutionary relationships between apple and poplar than with the other two species. Genes involved in basic metabolic pathways appear to be largely conserved among apple, citrus, poplar, and Arabidopsis.

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