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Published on January 23, 2003; 10.1104/pp.013581

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Received August 26, 2002
Returned for revision October 21, 2002
Accepted November 14, 2002

Comparative Analyses of Potato Expressed Sequence Tag Libraries

Catherine M. Ronning , Svetlana S. Stegalkina , Robert A. Ascenzi , Oleg Bougri , Amy L. Hart , Teresa R. Utterbach , Susan E. Vanaken , Steve B. Riedmuller , Joseph A. White , Jennifer Cho , Geo M. Pertea , Yuandan Lee , Svetlana Karamycheva , Razvan Sultana , Jennifer Tsai , John Quackenbush , Helen M. Griffiths , Silvia Restrepo , Christine D. Smart , William E. Fry , Rutger van der Hoeven , Steve Tanksley , Peifen Zhang , Hailing Jin , Miki L. Yamamoto , Barbara J. Baker , and C. Robin Buell *

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850 (C.M.R., S.S.S., R.A.A., O.B., A.L.H., T.R.U., S.E.V., St.B.R., J.A.W., J.C., G.M.P., Y.L., S.K., R.S., J.T., J.Q., C.R.B.); Departments of Plant Pathology (H.M.G., Si.R., C.D.S., W.E.F.) and Plant Breeding and Biometry (R.v.d.H., S.T.), Cornell University, Ithaca, New York 14853; and Plant Gene Expression Center and Department of Plant and Microbial Biology, University of California, Berkeley, and United States Department of Agriculture-Agricultural Research Service, 800 Buchanan Street, Albany, California 94710 (P.Z., H.J., M.L.Y., B.J.B.)

* Corresponding author; email: rbuell{at}tigr.org.

The cultivated potato (Solanum tuberosum) shares similar biology with other members of the Solanaceae, yet has features unique within the family, such as modified stems (stolons) that develop into edible tubers. To better understand potato biology, we have undertaken a survey of the potato transcriptome using expressed sequence tags (ESTs) from diverse tissues. A total of 61,940 ESTs were generated from aerial tissues, below-ground tissues, and tissues challenged with the late-blight pathogen (Phytophthora infestans). Clustering and assembly of these ESTs resulted in a total of 19,892 unique sequences with 8,741 tentative consensus sequences and 11,151 singleton ESTs. We were able to identify a putative function for 43.7% of these sequences. A number of sequences (48) were expressed throughout the libraries sampled, representing constitutively expressed sequences. Other sequences (13,068, 21%) were uniquely expressed and were detected only in a single library. Using hierarchal and k means clustering of the EST sequences, we were able to correlate changes in gene expression with major physiological events in potato biology. Using pair-wise comparisons of tuber-related tissues, we were able to associate genes with tuber initiation, dormancy, and sprouting. We also were able to identify a number of characterized as well as novel sequences that were unique to the incompatible interaction of late-blight pathogen, thereby providing a foundation for further understanding the mechanism of resistance.




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