Use of a large-scale Triticeae expressed sequence tag resource to reveal gene expression profiles in hexaploid wheat (Triticum aestivumL.)

Abstract

Abstract:The US Wheat Genome Project, funded by the National Science Foundation, developed the first large public Triticeae expressed sequence tag (EST) resource. Altogether, 116 272 ESTs were produced, comprising 100 674 5′ ESTs and 15 598 3′ ESTs. These ESTs were derived from 42 cDNA libraries, which were created from hexaploid bread wheat (Triticum aestivum L.) and its close relatives, including diploid wheat (T. monococcum L. and Aegilops speltoides L.), tetraploid wheat (T. turgidum L.), and rye (Secale cereale L.), using tissues collected from various stages of plant growth and development and under diverse regimes of abiotic and biotic stress treatments. ESTs were assembled into 18 876 contigs and 23 034 singletons, or 41 910 wheat unigenes. Over 90% of the contigs contained fewer than 10 EST members, implying that the ESTs represented a diverse selection of genes and that genes expressed at low and moderate to high levels were well sampled. Statistical methods were used to study the correlation of gene expression patterns, based on the ESTs clustered in the1536 contigs that contained at least 10 5′ EST members and thus representing the most abundant genes expressed in wheat. Analysis further identified genes in wheat that were significantly upregulated (p < 0.05) in tissues under various abiotic stresses when compared with control tissues. Though the function annotation cannot be assigned for many of these genes, it is likely that they play a role associated with the stress response. This study predicted the possible functionality for 4% of total wheat unigenes, which leaves the remaining 96% with their functional roles and expression patterns largely unknown. Nonetheless, the EST data generated in this project provide a diverse and rich source for gene discovery in wheat.Key words: Expressed sequence tags, ESTs, gene expression profiles, wheat, Triticeae. Résumé :Le projet américain sur le génome du blé, financé par la « National Science Foundation », a développé la première grande collection publique d'EST chez les hordées. Au total, 116 272 EST ont été produits à partir de 42 Des analyses statistiques ont été employées pour étudier la corrélation entre les motifs d'expression génique en s'appuyant sur les EST compris au sein des 1 536 contigs qui comptaient au moins 10 EST en 5′ (ceux qui représentent vraisemblablement les gènes le plus fortement exprimés chez le blé). Des analyses ont également permis d'identifier des gènes dont l'expression était significativement plus élevée (p < 0,05) au sein de tissus ayant subi divers stress par rapport aux tissus témoins. Bien qu'on ne puisse assigner aucune fonction à plusieurs de ces gènes, il est probable qu'ils jouent un rôle dans la réponse aux stress. Cette étude a permis de prédire une fonction pour 4 % des unigènes chez le blé, ce qui laisse 96 % de gènes pour lesquels la fonction demeure largement inconnue. Néanmoins, les données produites sur les EST au cours de ce travail constituent une vaste et riche ressource pour la découverte de gènes chez le blé.

Analysis of expressed sequence tags from a single wheat cultivar facilitates interpretation of tandem mass spectrometry data and discrimination of gamma gliadin proteins that may play different functional roles in flour

“…To evaluate which EST databases were likely to contain the most accurate representation of Butte 86 gamma gliadin genes, contigs containing each Butte 86 gamma gliadin EST were identified in four publicly available EST assemblies (Additional File 1). The US Wheat Genome Project assembly [9,10] included 117,510 ESTs and 18,876 contigs. This assembly used Phrap with penalty-5, minmatch 50, minscore 100, thereby allowing any 2 sequences with at least 90% sequence similarity over 100 bases to form a contig.…”

Data mining for miRNAs and their targets in the Triticeae

“…The genomic DNA sequence of wheat is currently limited; wheat has the largest genome (~16 000 Mb) among major crop species and complete sequencing of the wheat genome appears to still be years away. However, there is a rich EST database derived from cDNA libraries of T. aestivum and related species which represents the effort of many laboratories (e.g., Chao et al 2006;Houde et al 2006;Mochida et al 2006). The conserved nature of miRNAs predicts that most of the mature miRNAs among the Triticeae genomes will be the same or very similar and will have a very high probability of targeting the same gene family members.…”

Patterns of differential gene expression in Brassica napus cultivars infected with Sclerotinia sclerotiorum

“…, 2004), soybean to Pseudomonas syringae (Zabala et al. , 2006) and wheat to various biotic and abiotic stresses (Chao et al. , 2006).…”