Abstract
To help develop an understanding of the genes that govern the developmental characteristics of the potato (Solanum tuberosum), as well as the genes associated with responses to specified pathogens and storage conditions, The Canadian Potato Genome Project (CPGP) carried out 5′ end sequencing of regular, normalized and full-length cDNA libraries of the Shepody potato cultivar, generating over 66,600 expressed sequence tags (ESTs). Libraries sequenced represented tuber developmental stages, pathogen-challenged tubers, as well as leaf, floral developmental stages, suspension cultured cells and roots. All libraries analysed to date have contributed unique sequences, with the normalized libraries high on the list. In addition, a low molecular weight library has enhanced the 3′ ends of our sequence assemblies. Using the combined assembly dataset, unique tuber developmental, cold storage and pathogen-challenged sequences have been identified. A comparison of the ESTs specific to the pathogen-challenged tuber and foliar libraries revealed minimal overlap between these libraries. Mixed assemblies using over 189,000 potato EST sequences from CPGP and The Institute for Genomics Research (TIGR) has revealed common sequences, as well as CPGP- and TIGR-unique sequences.
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References
S.F. Altschul W. Gish W. Miller E.W. Myers D.J. Lipman (1990) ArticleTitleBasic local alignment search tool J. Mol. Biol. 215 403–410 Occurrence Handle10.1006/jmbi.1990.9999 Occurrence Handle2231712
N.J.G. Appeldoorn S.M. Bruijn Particlede E.A.M. Koot-Gronsveld R.G.F. Visser D. Vreugdenhil L.H.W. Plas Particlevan der (1997) ArticleTitleDevelopmental changes of enzymes involved in conversion of sucrose to hexose-phosphate during early tuberization of potato Planta 202 220–226 Occurrence Handle10.1007/s004250050122
C. Bachem R. Hoeven Particlevan der J. Lucker R. Oomen E. Casarini E. Jacobsen R. Visser (2000) ArticleTitleFunctional genomic analysis of potato tuber life-cycle Pot. Res. 43 297–312
K. Beyer A. Binder T. Boller M. Collinge (2001) ArticleTitleIdentification of potato genes induced during colonization by Phytophthora infestans Mol. Plant Pathol. 2 125–134 Occurrence Handle10.1046/j.1364-3703.2001.00059.x
M.F. Bonaldo G. Lennon M.B. Soares (1996) ArticleTitleNormalization and subtraction: two approaches to facilitate gene discovery Genome Res. 6 791–806 Occurrence Handle8889548
K. Bouchek-Mechiche L. Gardan P. Normand B. Jouan (2000) ArticleTitleDNA relatedness among strains of Streptomyces pathogenic to potato in France: description of three new species, S. europaeiscabiei sp. nov. and S. stelliscabiei sp. nov. associated with common scab, and S. reticuliscabiei sp. nov. associated with netted scab Int. J. Syst. Evol. Microbiol 50 91–99 Occurrence Handle10826791
S. Chang J. Puryear J. Cairney (1993) ArticleTitleA simple and efficient method for isolating RNA from pine trees Plant Mol. Biol. Rep. 11 113–116
D. Choi B.L. Ward R.M. Bostock (1992) ArticleTitleDifferential induction and suppression of potato 3-hydroxy- 3-methylglutaryl coenzyme A reductase genes in response to Phytophthora infestans and to its elicitor arachidonic acid Plant Cell 4 1333–1344
L. Corsi R. Avallone E. Geminiani F. Cosenza I. Venturini M. Baraldi (2004) ArticleTitlePeripheral benzodiazepine receptors in potatoes (Solanum tuberosum) Biochem. Biophys. Res. Commun. 313 62–66 Occurrence Handle10.1016/j.bbrc.2003.11.089 Occurrence Handle14672698
M. Crookshanks J. Emmersen K.G. Welinder K.L. Nielsen (2001) ArticleTitleThe potato transcriptome: analysis of 6077 expressed sequence tags FEBS Lett. 506 123–126 Occurrence Handle10.1016/S0014-5793(01)02888-5 Occurrence Handle11591384
R. Ehness M. Ecker D.E. Godt T. Roitsch (1997) ArticleTitleGlucose and stress independently regulate source and sink metabolism and defense mechanisms via signal transduction pathways involving protein phosphorylation Plant Cell 9 1825–1841 Occurrence Handle10.1105/tpc.9.10.1825 Occurrence Handle12237349
B. Ewing P. Green (1998) ArticleTitleBase-calling of automated sequencer traces using phred. II. Error probabilities Genome Res. 8 186–194 Occurrence Handle9521922
B. Ewing L. Hillier M.C. Wendl P. Green (1998) ArticleTitleBase␣calling of automated sequencer traces using phred I. Accuracy assessment Genome Res. 8 175–185 Occurrence Handle9521921
O. Faivre-Rampant L. Cardle D. Marshall R. Viola M.A. Taylor (2004) ArticleTitleChanges in gene expression during meristem activation processes in Solanum tuberosum with a focus on the regulation of an auxin response factor gene J. Exp. Bot. 55 613–622 Occurrence Handle10.1093/jxb/erh075 Occurrence Handle14966214
A.R. Fernie L. Willmitzer (2001) ArticleTitleMolecular and biochemical triggers of potato tuber development Plant Physiol. 127 1459–1465 Occurrence Handle10.1104/pp.127.4.1459 Occurrence Handle11743089
A.R. Fernie E. Tauberger A. Lytovchenko U. Roessner L. Willmitzer R.N. Trethewey (2002) ArticleTitleAntisense repression of cytosolic phosphoglucomutase in potato (Solanum tuberosum) results in severe growth retardation, reduction in tuber number and altered carbon metabolism Planta 214 510–520 Occurrence Handle10.1007/s004250100644 Occurrence Handle11925034
W.E. Fry S.B. Goodwin (1997) ArticleTitleResurgence of the Irish potato famine fungus Bioscience 47 363–371
P. Geigenberger M. Hajirezaei M. Geiger U. Deiting U. Sonnewald M. Stitt (1998) ArticleTitleOverexpression of pyrophosphatase leads to increased sucrose degradation and starch synthesis, increased activities of enzymes for sucrose–starch interconversions, and increased levels of nucleotides in growing potato tubers Planta 205 428–437 Occurrence Handle10.1007/s004250050340 Occurrence Handle9640668
D.E. Godt T. Roitsch (1997) ArticleTitleRegulation and tissue-specific distribution of mRNAs for three extracellular invertase isoenzymes of tomato suggests an important function in establishing and maintaining sink metabolism Plant Physiol. 115 273–282 Occurrence Handle10.1104/pp.115.1.273 Occurrence Handle9306701
M.R. Hajirezaei Y. Takahata R.N. Trethewey L. Willmitzer U. Sonnewald (2000) ArticleTitleImpact of elevated cytosolic and apoplastic invertase activity on carbon metabolism during potato tuber development J. Exp. Bot. 51 439–445 Occurrence Handle10.1093/jexbot/51.suppl_1.439 Occurrence Handle10938852
A.O. Jackson C.B. Taylor (1996) ArticleTitlePlant–microbe interactions: life and death at the interface Plant Cell 8 1651–1668 Occurrence Handle10.1105/tpc.8.10.1651 Occurrence Handle12239356
J.H. Lange (2004) ArticleTitleA study of apple trees exposed to the fungicide azoxystrobin and mixture interactions with surfactants Int. J. Environ. Stud. 61 173–187 Occurrence Handle10.1080/0020723022000042277
P. Lindemann A. Koch B. Degenhardt G. Hause B. Grimm V. Papadopoulos (2004) ArticleTitleA novel Arabidopsis thaliana protein is a functional peripheral-type benzodiazepine receptor Plant Cell Physiol. 45 723–733 Occurrence Handle10.1093/pcp/pch088 Occurrence Handle15215507
E.A. Madrid A.M. Laxalt V. Beligni L. Lamattina (1999) ArticleTitlePartial characterization of potato F0F1-ATPase gamma-subunit cDNA and its regulation during fungal infection and elicitor treatment Physiol. Plant. 105 304–311 Occurrence Handle10.1034/j.1399-3054.1999.105216.x
E. Nakane K. Kawakita N. Doke H. Yoshioka (2003) ArticleTitleElicitation of primary and secondary metabolism during defense in the potato J. Gen. Plant Pathol. 69 378–384 Occurrence Handle10.1007/s10327-003-0075-6
O.M. Olanya D.H. Lambert S.B. Johnson J.D. Dwyer (2002) ArticleTitleAssessment of the impact of mid-season late blight infection on disease development and yield of potato variety Russet Norkotah in Maine Int. J. Pest Manage. 48 139–146 Occurrence Handle10.1080/09670870110102594
C.M. Ronning S.S. Stegalkina R.A. Ascenzi O. Bougri A.L. Hart T.R. Utterbach S.E. Vanaken S.B. Riedmuller J.A. White J. Cho G.M. Pertea Y. Lee S. Karamycheva R. Sultana J. Tsai J. Quackenbush H.M. Griffiths S. Restrepo C.D. Smart W.E. Fry R. Hoeven Particlevan der S. Tanksley P. Zhang H. Jin M.L. Yamamoto B.J. Baker C.R. Buell (2003) ArticleTitleComparative analyses of potato expressed sequence tag libraries Plant Physiol. 131 419–429 Occurrence Handle10.1104/pp.013581 Occurrence Handle12586867
B. Ros F. Thümmler G. Wenzel (2004) ArticleTitleAnalysis of differentially expressed genes in a susceptible and moderately resistant potato cultivar upon Phytophthora infestans infection Mol. Plant Pathol. 5 191–201 Occurrence Handle10.1111/j.1364-3703.2004.00221.x
M.B. Soares M.F. Bonaldo P. Jelene L. Su L. Lawton A. Efstratiadis (1994) ArticleTitleConstruction and characterization of a normalized cDNA library Proc. Natl. Acad. Sci. USA 91 9228–9232 Occurrence Handle7937745
J.R. Sowokinos (2001) ArticleTitleBiochemical and molecular control of cold-induced sweetening in potatoes Am. J. Pot. Res. 78 221–236
J.C. Suttle (2004) ArticleTitlePhysiological regulation of potato tuber dormancy Amer. J. of Pot. Res. 81 253–262
D. Takemoto H. Maeda H. Yoshioka N. Doke K. Kawakita (1999) ArticleTitleEffect of cytochalasin D on defense responses of potato tuber discs treated with hyphal wall components of Phytophthora infestans Plant Sci. 141 219–226 Occurrence Handle10.1016/S0168-9452(98)00238-6
J. Berkel Particlevan F. Salamini C. Gebhardt (1994) ArticleTitleTranscripts accumulating during cold storage of potato (Solanum tuberosum L.) tubers are sequence related to stress-responsive genes Plant. Physiol. 104 445–452 Occurrence Handle10.1104/pp.104.2.445 Occurrence Handle7909163
R. Hoeven Particlevan der C. Ronning J. Giovannoni G. Martin S. Tanksley (2002) ArticleTitleDeductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing Plant Cell 14 1441–1456 Occurrence Handle10.1105/tpc.010478 Occurrence Handle12119366
G. Wang-Pruski J. Nowak (2004) ArticleTitlePotato after-cooking darkening Am. J. Pot. Res. 81 7–16
J. Wildmann (1988) ArticleTitleIncrease of natural benzodiazepines in wheat and potato during germination Biochem. Biophys. Res. Commun. 157 1436–1443 Occurrence Handle10.1016/S0006-291X(88)81036-2 Occurrence Handle2849941
X. Xu D. Vreugdenhil A.A.M. Lammeren Particlevan (1998) ArticleTitleCell division and cell enlargement during potato tuber formation J. Exp. Bot. 49 573–582 Occurrence Handle10.1093/jexbot/49.320.573
R. Zrenner M. Salanoubat L. Willmitzer U. Sonnewald (1995) ArticleTitleEvidence of the crucial role of sucrose synthase for sink strength using transgenic potato plants Plant J. 7 97–107 Occurrence Handle10.1046/j.1365-313X.1995.07010097.x Occurrence Handle7894514
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Flinn, B., Rothwell, C., Griffiths, R. et al. Potato Expressed Sequence Tag Generation and Analysis using Standard and Unique cDNA Libraries. Plant Mol Biol 59, 407–433 (2005). https://doi.org/10.1007/s11103-005-0185-y
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DOI: https://doi.org/10.1007/s11103-005-0185-y