Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.
DNA Res. 2012 Apr;19(2):165-77. doi: 10.1093/dnares/dss001. Epub 2012 Feb 14.
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.
从 51 个 cDNA 文库中获得了约 100 万个包含 125.3Mb 核苷酸的表达序列标签 (EST) 序列，这些文库是从小麦（Triticum aestivum）的各种组织和器官在各种条件下构建的，包括非生物胁迫和病原体挑战。使用内置脚本处理 EST 后，采用严格的参数进行组装，得到 37138 个 contigs 和 215199 个 singlets。在组装序列中，10.6%与公共数据库中的现有序列没有匹配。通过基因本体注释、挖掘转录因子、全长 cDNA 和 miRNA 靶标对小麦基因进行了功能表征。开发了一种生物信息学策略来发现我们的大型 EST 资源中的单核苷酸多态性 (SNP)，并报告了品种间和品种内 (同源) 的 SNP。进行数字基因表达以寻找组织特异性基因表达，并通过选择四个与生物胁迫相关的文库执行对应分析以识别共同和特定的基因表达。该组装和相关信息为功能基因组学的未来研究提供了一个框架。
