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United States Department of Agriculture

Agricultural Research Service

Title: COMPARATIVE ANALYSES OF POTATO EXPRESSED SEQUENCE TAG LIBRARIES)

Author
item Ronning, Catherine
item Stegalkina, Svetlana
item Ascenzi, Robert
item Bougri, Oleg
item Hart, Amy
item Utterbach, Teresa
item Vanaken, Susan
item Riedmuller, Steve
item White, Joseph
item Cho, Jennifer
item Pertea, Geo
item Lee, Yuandan
item Karamycheva, Svetlana
item Sultana, Razvan
item Tsai, Jennifer
item Quackenbush, John
item Griffiths, Helen
item Restrepo, Silvia
item Smart, Christine
item Fry, William
item Van Der Hoeven, Rutger
item Tanksley, Steve
item Zhang, Peifen
item Jin, Hailing
item Yamamoto, Miki
item Baker, Barbara
item Buell, C. Robin

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/23/2003
Publication Date: 2/1/2003
Citation: RONNING, C.M., STEGALKINA, S.S., ASCENZI, R.A., BOUGRI, O., HART, A.L., UTTERBACH, T.R., VANAKEN, S.E., RIEDMULLER, S.B., WHITE, J.A., CHO, J., PERTEA, G.M., LEE, Y., KARAMYCHEVA, S., SULTANA, R., TSAI, J., QUACKENBUSH, J., GRIFFITHS, H.M., RESTREPO, S., SMART, C.D., FRY, W.E., VAN DER HOEVEN, R., TANKSLEY, S., ZHANG, P., JIN, H., YAMAMOTO, M.L., BAKER, B.J., BUELL, C. COMPARATIVE ANALYSES OF POTATO EXPRESSED SEQUENCE TAG LIBRARIES. PLANT PHYSIOLOGY. 2003. 131:419-429.

Interpretive Summary: 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. 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.

Technical Abstract: 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.

Last Modified: 8/24/2016
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