Journal Article

Comprehensive Functional Analyses of Expressed Sequence Tags in Common Wheat (<i>Triticum aestivum</i>)

Alagu Manickavelu, Kanako Kawaura, Kazuko Oishi, Tadasu Shin-I, Yuji Kohara, Nabila Yahiaoui, Beat Keller, Reina Abe, Ayako Suzuki, Taishi Nagayama, Kentaro Yano and Yasunari Ogihara

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 19, issue 2, pages 165-177
Published in print April 2012 | ISSN: 1340-2838
Published online February 2012 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dss001

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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.

Keywords: wheat; ESTs; annotation; transcription factors; miRNA; SNP; correspondence analysis

Journal Article.  6686 words.  Illustrated.

Subjects: Genetics and Genomics

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