The Apple EST Project.

Large-scale single-pass sequencing of clones, randomly picked from cDNA libraries, is a very powerful approach in gene discovery and for providing a description of the transcriptional activity of a tissue.  Expressed sequenced tags (ESTs) are the most widely sequenced nucleotide entities from plant genomes as they provide robust sequence resources that can be exploited for gene discovery, genome annotation, and comparative genomics.  In this public apple EST project, a total of 34 cDNA libraries, either normalized or primary, were constructed from bud (dormant and active), shoot (dormant and active), root, flower (five stages of development), fruit (five stages of development), insect-challenged (leaf roller), and pathogen-challenged (apple scab, fire blight, Phytophthora) tissues.  A total of seven high-quality fruit apple cultivars along with five apple rootstocks (influencing tree growth habit and architecture) at different stages of development were also used.  Over 180,000 EST clones have been subjected to 5’ end sequencing, and over 145,000 EST sequences have been generated.  Analysis of these sequences revealed tentative consensus sequences and singletons representing over 42,000 unigenes.  The selected unigene set has been subjected to 3’ end sequencing.  A user-friendly apple EST project database has been established (http://titan.biotec.uiuc.edu/apple /apple.shtml), and linked to the Rosaceae Genome database (http://www.genome.clemson.edu/gdr/).  As part of an educational component of this project, we have established an on-line educational module (http://www.four-h.purdue.edu/apple_genomics/) for teaching genomics to high school educators and students using the apple as a teaching tool.  This module consists of seven animations, including tree growth, genome organization, chromosomes, genes, DNA and RNA, cDNA libraries, and microarrays.   This project was funded by NSF- Plant Genome Program project #9872565.