Comparative analyses of potato expressed sequence tag libraries.
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.
Ronning
Catherine M
CM
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
Stegalkina
Svetlana S
SS
Ascenzi
Robert A
RA
Bougri
Oleg
O
Hart
Amy L
AL
Utterbach
Teresa R
TR
Vanaken
Susan E
SE
Riedmuller
Steve B
SB
White
Joseph A
JA
Cho
Jennifer
J
Pertea
Geo M
GM
Lee
Yuandan
Y
Karamycheva
Svetlana
S
Sultana
Razvan
R
Tsai
Jennifer
J
Quackenbush
John
J
Griffiths
Helen M
HM
Restrepo
Silvia
S
Smart
Christine D
CD
Fry
William E
WE
Van Der Hoeven
Rutger
R
Tanksley
Steve
S
Zhang
Peifen
P
Jin
Hailing
H
Yamamoto
Miki L
ML
Baker
Barbara J
BJ
Buell
C Robin
CR
D016000:Cluster Analysis; D020224:Expressed Sequence Tags; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D007113:Immunity, Innate / Q000235:genetics; D018551:Solanum lycopersicum / Q000235:genetics; D010838:Phytophthora / Q000254:growth & development; D010935:Plant Diseases / Q000235:genetics / Q000382:microbiology; D018547:Plant Stems / Q000235:genetics / Q000254:growth & development; D011198:Solanum tuberosum / Q000235:genetics* / Q000254:growth & development / Q000382:microbiology