Comprehensive Functional Analyses of Expressed Sequence Tags in Common Wheat (Triticum aestivum)
Autor: | Alagu Manickavelu, Kanako Kawaura, Yasunari Ogihara, Beat Keller, Kazuko Oishi, Taishi Nagayama, Reina Abe, Kentaro Yano, Tadasu Shin-I, Yuji Kohara, Ayako Suzuki, Nabila Yahiaoui |
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Přispěvatelé: | University of Zurich, Ogihara, Y |
Jazyk: | angličtina |
Rok vydání: | 2012 |
Předmět: |
DNA
Complementary SNP Biology 580 Plants (Botany) Genes Plant Polymorphism Single Nucleotide correspondence analysis 10126 Department of Plant and Microbial Biology 1311 Genetics Gene Expression Regulation Plant Complementary DNA wheat transcription factors Databases Genetic Genetics 1312 Molecular Biology Genomic library Common wheat Molecular Biology Triticum miRNA Gene Library Expressed Sequence Tags Expressed sequence tag cDNA library ESTs Gene Expression Profiling food and beverages Computational Biology Molecular Sequence Annotation General Medicine Sequence Analysis DNA Full Papers Gene expression profiling annotation Functional genomics |
Zdroj: | DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes |
ISSN: | 1756-1663 1340-2838 |
Popis: | 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. |
Databáze: | OpenAIRE |
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