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Potato Expressed Sequence Tag Generation and Analysis using Standard and Unique cDNA Libraries
Authors:Barry Flinn  Charlotte Rothwell  Rebecca Griffiths  Martin Lägue  David DeKoeyer  Ravinder Sardana  Patrice Audy  Claudia Goyer  Xiu-Qing Li  Gefu Wang-Pruski  Sharon Regan
Institution:(1) Canadian Potato Genome Project, BioAtlantech Unit, 921 College Hill Road, Fredericton, New Brunswick, E3B 6Z9, Canada;(2) Potato Research Centre, Agriculture and Agri-Food Canada, 850 Lincoln Rd, P.O. Box 20280, Fredericton, New Brunswick, E3B 4Z7, Canada;(3) Department of Plant and Animal Sciences, Cox Institute, Nova Scotia Agricultural College, Box 550, Truro, Nova Scotia, B2N 5E3, Canada;(4) Department of Biology , Queen’s University, Kingston, Ontario, K7L 3N6, Canada
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. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users.
Keywords:common scab  EST  genomics  late blight  potato  tuber
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