The potato tuber transcriptome: analysis of 6077 expressed sequence tags

Abstract

This is the first report of the biosynthetic potential of a tuber storage organ investigated by expressed sequence tag sequencing. A cDNA library was generated from the mature tuber of field grown potato (Solanum tuberosum var. Kuras). Partial sequences obtained from 6077 clones were assembled into 828 clusters and 1533 singletons. The average read length was 592 bp, and 2254 clones were full length. 5717 clones showed homology to genes from other organisms. Genes involved in protein synthesis, protein destination and cell defense predominated in tuber compared to stolon, shoot and leaf organs. 1063 clones were unique to tuber. Transcripts of starch metabolizing enzymes showed similar relative levels in tuber and stolon. ß

Regulation of potato tuber sprouting

“…Other studies used large-scale sequencing technologies to generate expressed sequence tags (ESTs) from cDNA libraries specific for different potato tissues or developmental stages (Crookshanks et al 2001;Ronning et al 2003;Kloosterman et al 2008) together with a comparative bioinformatics analysis to identify genes associated with dormancy and sprouting. Ronning et al (2003) found genes involved in translation such as elongation factor EF1B-alpha and ribosomal proteins among the highest differentially expressed genes during sprouting, consistent with an increased cellular activity.…”

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.…”

“…Other proteins involved in defense responses were also identified, suggesting that protection against pests, other external stresses and reactive oxygen species are important in the maturing tuber. Proteinase inhibitors that are considered to assist in the protection against pest predation are highly expressed in mature tubers [16]; furthermore, they accumulate during tuber maturation and possibly facilitate protein accumulation by inhibiting protease activity [27]. Ascorbate peroxidase, identified as several isoforms, and dehydroascorbate reductase are involved in eliminating reactive oxygen species, protecting plant cells from oxidative stress [28].…”

Functional genomic resources for potato

“…To identify the expressed region of a genome, messenger RNA is isolated from the tissue of interest, converted to cDNA and random clones are partially sequenced from either the 5' end or 3' end by single-pass sequencing to generate ESTs. Various types of potato organs or tissues, representing different cultivars have been used to generate EST libraries (Crookshanks et al 2001;Li 2001;Ronning et al 2003;Flinn et al 2005) (Table 1). Most ESTs have come from tetraploid potato cultivars*Shepody (Flinn et al 2005;Li et al 2007), Bintje (Ronning et al 2003), Kennebec (Ronning et al 2003), Kuras (Crookshanks et al 2001), and Solara (Biemelt et al ESTs released to GenBank, http:// www.ncbi.nlm.nih.gov).…”

“…Meanwhile, many other resources are currently available that are relevant to the large-scale study of genes and determination of their functional relevance (functional genomics). These resources include expressed sequence tags (EST) (Crookshanks et al 2001;Ronning et al 2003;Flinn et al 2005;Rensink et al 2005a), Serial Analysis of Gene Expression (SAGE) (Velculescu et al 1995), gene microarrays (Kloosterman et al 2005;Rensink et al 2005b;Restrepo et al 2005), cDNA-based amplified restriction fragment length polymorphisms (cDNA-AFLP) (Bachem et al 1996), genetic maps with known genes (Chen et al 2001), and an activation-tagged mutant population (Regan et al 2006). With the establishment of these resources, we can expect accelerated discoveries in potato, and major advances in our understanding of potato growth and development.…”