title: Comprehensive functional analyses of expressed sequence tags in common wheat (Triticum aestivum).
abstract: About 1 million expressed sequence tag (EST) sequences comprising 125.3 Mb nucleotides were accreted from 51 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including abiotic stresses and pathogen challenges in common wheat (Triticum aestivum). Expressed sequence tags were assembled with stringent parameters after processing with inbuild scripts, resulting in 37,138 contigs and 215,199 singlets. In the assembled sequences, 10.6% presented no matches with existing sequences in public databases. Functional characterization of wheat unigenes by gene ontology annotation, mining transcription factors, full-length cDNA, and miRNA targeting sites were carried out. A bioinformatics strategy was developed to discover single-nucleotide polymorphisms (SNPs) within our large EST resource and reported the SNPs between and within (homoeologous) cultivars. Digital gene expression was performed to find the tissue-specific gene expression, and correspondence analysis was executed to identify common and specific gene expression by selecting four biotic stress-related libraries. The assembly and associated information cater a framework for future investigation in functional genomics.
authors.affiliation: Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.
authors.forename: Alagu
authors.initials: A
authors.lastname: Manickavelu
authors.forename: Kanako
authors.initials: K
authors.lastname: Kawaura
authors.forename: Kazuko
authors.initials: K
authors.lastname: Oishi
authors.forename: Tadasu
authors.initials: T
authors.lastname: Shin-I
authors.forename: Yuji
authors.initials: Y
authors.lastname: Kohara
authors.forename: Nabila
authors.initials: N
authors.lastname: Yahiaoui
authors.forename: Beat
authors.initials: B
authors.lastname: Keller
authors.forename: Reina
authors.initials: R
authors.lastname: Abe
authors.forename: Ayako
authors.initials: A
authors.lastname: Suzuki
authors.forename: Taishi
authors.initials: T
authors.lastname: Nagayama
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yano
authors.forename: Yasunari
authors.initials: Y
authors.lastname: Ogihara
mesh_terms: D019295:Computational Biology / Q000379:methods; D018076:DNA, Complementary / Q000302:isolation & purification; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods; D014908:Triticum / Q000235:genetics* / Q000254:growth & development
chemical_list: D018076:DNA, Complementary