Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags
Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags
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DOI：
10.1266/ggs.79.227
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发表时间：
2004-08-01
影响因子：
1.1
通讯作者：
Yamazaki, Y
中科院分区：
文献类型：
--
作者：
Ogihara, Y;Mochida, K;Yamazaki, Y
小麦的多倍体性质是植物的一个关键特征。全长互补DNA（cDNA）提供了可用于注释基因并提供这些基因及其产物的功能分析的重要信息。构建了小麦幼穗全长cDNA文库，从cDNA克隆的两端共获得24056个表达序列标签（expressedsequencetags，EST）。使用phrap方法将这些EST分组为3605个重叠群，代表来自三个基因组中的每一个的表达位点。使用BLAST，3605个重叠群被分成1902个基因簇，表明三个基因组的位点并不总是表达。将这些基因簇与小麦EST数据库（15964个基因簇）和水稻全长cDNA数据库（21447个基因簇）进行同源性搜索，发现四分之一的小麦全长cDNA是新的。使用拟南芥蛋白质数据库来检查这些基因簇的功能分类。将小麦cDNA的5 '-UTR区域中的GC含量与水稻的进行比较。其中43个基因（占小麦和水稻cDNA同源性的3.5%）在5 '-UTR区域具有不同的GC含量，表明小麦和水稻的育种行为不同。
The polyploid nature of wheat is a key characteristic of the plant. Full-length complementary DNAs (cDNAs) provide essential information that can be used to annotate the genes and provide a functional analysis of these genes and their products. We constructed a full-length cDNA library derived from young spikelets of common wheat, and obtained 24056 expressed sequence tags (ESTs) from both ends of the cDNA clones. These ESTs were grouped into 3605 contigs using the phrap method, representing expressed loci from each of the three genomes. Using BLAST, 3605 contigs were grouped into 1902 gene clusters, showing that loci of the three genomes are not always expressed. A homology search of these gene clusters against a wheat EST database (15964 gene clusters) and a rice full-length cDNA database (21447 gene clusters) revealed that a quarter of the wheat full-length cDNAs were novel. A protein database of Arabidopsis was used to examine the functional classification of these gene clusters. The GC-content in the 5'-UTR region of wheat cDNAs was compared to that of rice. Forty-three genes (3.5% of wheat cDNAs homologous to those of rice) possessed distinct GC-content in the 5'-UTR region, suggesting different breeding behaviors of wheat and rice.