Potato Expressed Sequence Tag Generation and Analysis using Standard and Unique cDNA Libraries

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.

Long-Term Induction of Defense Gene Expression in Potato by Pseudomonas sp. LBUM223 and Streptomyces scabies

“…However, it could potentially contribute to controlling other diseases if pathogens are sensitive to the enhanced expression and production of the SA-related defense proteins under study. Although few studies on the defense responses induced by S. scabies in potato exist, focusing mostly on responses in individual tubers and not entire plant systems (16), there have been studies performed in A. thaliana plant systems. Interestingly, the inoculation of A. thaliana seedlings with S. scabies, after preinoculation with a nonpathogenic endophytic Streptomyces isolate, also induced an SA-related SAR response (23).…”

Proteomic analysis of the potato tuber life cycle

“…Studies at the transcript level using cDNA microarrays [7] and ESTs [14][15][16] have recently provided an overview of gene expression during tuber development and storage. Although the experimental conditions described in Kloosterman et al [7] were slightly different from the ones used in our experiment, the stages of early tuber growth designated 3a, 3b, 3c and 3d correspond approximately to the stages designated 5, 6, 7 and 8 by Kloosterman et al [7], respectively.…”

“…Two spots (3713, 3605) were matched to SGT1 or an EST similar to SGT1 protein of N. benthamiana, which has been shown to associate with a multiprotein complex involved in plant defense signaling [29,30]. Glycine-rich RNA binding protein transcripts are highly abundant in the stolons and also in the tubers in cold storage [14]. Recently they have been suggested to function as RNA chaperones in response to cold and other stresses [31,32].…”

Chromatin Structure and Physical Mapping of Chromosome 6 of Potato and Comparative Analyses With Tomato

“…Several molecular marker-based genetic linkage maps of diploid potato were developed (Bonierbale et al 1988;Gebhardt et al 1989Gebhardt et al , 1991Tanksley et al 1992;Jacobs et al 1995), including a 10,000-marker ultradense map that represents one of the densest genetic maps in any eukaryote (van Os et al 2006). Other resources for genomics research have also been developed, including expressed sequence tags (ESTs) (Ronning et al 2003;Flinn et al 2005), bacterial artificial chromosome (BAC) libraries Zhang et al 2003;Chen et al 2004), and BAC end sequences (Zhu et al 2008). An international potato genome sequencing consortium has been established recently (http:/ /potatogenome.net) that will make potato one of few major crop species whose genome will be sequenced using a BAC-by-BAC-based approach.…”