Journal article
Large-scale analysis of the barley transcriptome based on expressed sequence tags
The Plant Journal, Vol.40(2), pp.276-290
2004
Abstract
To provide resources for barley genomics, 110,981 expressed sequence tags (ESTs) were generated from 22 cDNA libraries representing tissues at various developmental stages. This EST collection corresponds to approximately one-third of the 380,000 publicly available barley ESTs. Clustering and assembly resulted in 14,151 tentative consensi (TCs) and 11 073 singletons, altogether representing 25 224 putatively unique sequences. Of these, 17.5% showed no significant similarity to other barley ESTs present in dbEST. More than 41% of all barley genes are supposed to belong to multigene families and approximately 4% of the barley genes undergo alternative splicing. Based on the functional annotation of the set of unique sequences, the functional category 'Energy' was further analysed to reveal tissue- and stage-specific differences in gene expression. Hierarchical clustering of 362 differentially expressed TCs resulted in the identification of seven major clusters. The clusters reflect biochemical pathways predominantly activated in specific tissues and at various developmental stages. During seed germination glycolysis could be identified as the most predominant biochemical pathway. Germination-specific glycolysis is characterized by the coordinated expression of phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxykinase, whose antagonistic actions possibly regulate the flux of amino acids into protein biosynthesis and gluconeogenesis respectively. The expression of defence-related and antioxidant genes during germination might be controlled by the ethylene-signalling pathway as concluded from the coordinated expression of those genes and the transcription factors (TF) EIN3 and EREBPG. Moreover, because of their predominant expression in germinating seeds, TF of the AP2 and MYB type are presumably major regulators of germination.
Details
- Title
- Large-scale analysis of the barley transcriptome based on expressed sequence tags
- Authors/Creators
- H. Zhang (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)N. Sreenivasulu (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)W. Weschke (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)N. Stein (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)S. Rudd (Author/Creator) - MIPS/IBI, Institut für Bioinformatik, GSF Forschungszentrum für Umwelt und Gesundheit, D‐85764 Neuherberg, GermanyV. Radchuk (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)E. Potokina (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)U. Scholz (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)P. Schweizer (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)U. Zierold (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)P. Langridge (Author/Creator) - Australian Centre for Plant Functional GenomicsR.K. Varshney (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)U. Wobus (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)A. Graner (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
- Publication Details
- The Plant Journal, Vol.40(2), pp.276-290
- Publisher
- Blackwell Publishing
- Identifiers
- 991005545995307891
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Plant Sciences
- ESI research areas
- Plant & Animal Science