Large‐scale analysis of the barley transcriptome based on expressed sequence tags

Abstract

SummaryTo 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 ethylenesignalling 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.

Spatiotemporal Profiling of Starch Biosynthesis and Degradation in the Developing Barley Grain

“…1,G and H). Amylose makes up around 20% of starch at the beginning of storage starch accumulation, and this pro-cDNA sequences of the relevant barley genes involved in the synthesis and degradation of starch were selected from EST databases (Zhang et al, 2004; http://compbio.dfci.harvard.edu) using already described sequences as references (Table I). The small subunit of AGPase in barley is encoded by Hv.AGP.S.1 and Hv.AGP.S.2 genes (Rö sti et al, 2006), abbreviated here as AGP-S1 and AGP-S2.…”

TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics

“…Large-scale EST and full-length cDNA collections of maize have also been used as resources to aid ongoing genome sequencing (Lai et al, 2004;Jia et al, 2006). ESTs of common wheat and barley (in the Pooideae subfamily) have been collected on a large scale to establish a comprehensive sequence resource for gene discovery and a reliable database of gene expression (Zhang et al, 2004;Mochida et al, 2006). Progress has now been made in both the barley and wheat genome sequencing projects, and full-length cDNA-related databases are expected to be key resources for genome annotation in these crops (Paux et al, 2008;Schulte et al, 2009).…”

A Set of Modular Binary Vectors for Transformation of Cereals

“…Assemblies of large EST datasets (approximately 855,000 ESTs for wheat [Triticum aestivum] and approximately 437,000 ESTs for barley [Hordeum vulgare]) provided important insight into the genome organization and led to in silico prediction of about 50,000 unique genes for wheat and barley, respectively (Zhang et al, 2004;Stein, 2007). Although bioinformatics, transcriptome analysis (Close et al, 2004;Druka et al, 2006;Zierold et al, 2005), transient overexpression, virus-induced gene silencing (VIGS; Lacomme et al, 2003), and transient-induced gene silencing (TIGS;Douchkov et al, 2005) have greatly extended the information on putative roles of genes, we are left with the major challenge of elucidating gene functions by modulation of their expression in planta.…”