First published online January 23, 2003; 10.1104/pp.013581
Plant Physiol, February 2003, Vol. 131, pp. 419-429
Comparative Analyses of Potato Expressed Sequence Tag
Libraries1
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.)
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.
1
This work was supported by the National Science
Foundation Plant Genome Research Program (grant no. DBI-9975866 to
B.J.B.).
*
Corresponding author; e-mail rbuell{at}tigr.org; fax
301-838-0208.
© 2003 American Society of Plant Biologists
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