title: Comparative analyses of potato expressed sequence tag libraries.
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.
authors.affiliation: The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
authors.forename: Catherine M
authors.initials: CM
authors.lastname: Ronning
authors.forename: Svetlana S
authors.initials: SS
authors.lastname: Stegalkina
authors.forename: Robert A
authors.initials: RA
authors.lastname: Ascenzi
authors.forename: Oleg
authors.initials: O
authors.lastname: Bougri
authors.forename: Amy L
authors.initials: AL
authors.lastname: Hart
authors.forename: Teresa R
authors.initials: TR
authors.lastname: Utterbach
authors.forename: Susan E
authors.initials: SE
authors.lastname: Vanaken
authors.forename: Steve B
authors.initials: SB
authors.lastname: Riedmuller
authors.forename: Joseph A
authors.initials: JA
authors.lastname: White
authors.forename: Jennifer
authors.initials: J
authors.lastname: Cho
authors.forename: Geo M
authors.initials: GM
authors.lastname: Pertea
authors.forename: Yuandan
authors.initials: Y
authors.lastname: Lee
authors.forename: Svetlana
authors.initials: S
authors.lastname: Karamycheva
authors.forename: Razvan
authors.initials: R
authors.lastname: Sultana
authors.forename: Jennifer
authors.initials: J
authors.lastname: Tsai
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
authors.forename: Helen M
authors.initials: HM
authors.lastname: Griffiths
authors.forename: Silvia
authors.initials: S
authors.lastname: Restrepo
authors.forename: Christine D
authors.initials: CD
authors.lastname: Smart
authors.forename: William E
authors.initials: WE
authors.lastname: Fry
authors.forename: Rutger
authors.initials: R
authors.lastname: Van Der Hoeven
authors.forename: Steve
authors.initials: S
authors.lastname: Tanksley
authors.forename: Peifen
authors.initials: P
authors.lastname: Zhang
authors.forename: Hailing
authors.initials: H
authors.lastname: Jin
authors.forename: Miki L
authors.initials: ML
authors.lastname: Yamamoto
authors.forename: Barbara J
authors.initials: BJ
authors.lastname: Baker
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
mesh_terms: 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