Analysis of transcriptome data in the red flour beetle, Tribolium castaneum
Analysis of transcriptome data in the red flour beetle, Tribolium castaneum
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DOI：
10.1016/j.ibmb.2007.09.008
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发表时间：
2008-04-01
影响因子：
3.8
通讯作者：
Gibbs, Richard A.
中科院分区：
文献类型：
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作者：
Park, Yoonseong;Aikins, Jamie;Gibbs, Richard A.
赤拟谷盗（Tribolium castaneum）是一种世界性的鞘翅目仓储物害虫，其全基因组序列已被测定。为了便于对该基因组进行准确的注释和详细的功能分析，我们整理和分析了所有可用的表达序列标签（EST）数据。原始数据包括61，228个EST，其中10，704个来自NCBI，另外50，524个来自我们实验室产生的32，544个克隆。这些序列是从代表六个不同组织或阶段的cDNA文库中收集的，即：整个胚胎、整个幼虫、幼虫后肠和马氏管、幼虫脂肪体和尸体、成虫卵巢和成虫头部。61，228个序列的组装分解成12，269个簇（代表单个基因的重叠EST组），其中10，134个映射到16，422个GLEAN基因模型（即官方Tribolium基因列表）中的6463个（39%）。大约1600个簇（总数的39%）缺乏相应的GLEAN模型，尽管与基因组高度匹配，这表明相当数量的转录序列被基因预测程序遗漏或被GLEAN删除。我们保守估计，目前的EST集代表超过7500个转录单位。爱思唯尔有限公司出版
The whole genome sequence of Tribolium castaneum, a worldwide coleopteran pest of stored products, has recently been determined. In order to facilitate accurate annotation and detailed functional analysis of this genome, we have compiled and analyzed all available expressed sequence tag (EST) data. The raw data consist of 61,228 ESTs, including 10,704 obtained from NCBI and an additional 50,524 derived from 32,544 clones generated in our laboratories. These sequences were amassed from cDNA libraries representing six different tissues or stages, namely: whole embryos, whole larvae, larval hindguts and Malpighian tubules, larval fat bodies and carcasses, adult ovaries, and adult heads. Assembly of the 61,228 sequences collapsed into 12,269 clusters (groups of overlapping ESTs representing single genes), of which 10,134 mapped onto 6463 (39%) of the 16,422 GLEAN gene models (i.e. official Tribolium gene list). Approximately 1600 clusters (39% of the total) lack corresponding GLEAN models, despite high matches to the genome, suggesting that a considerable number of transcribed sequences were missed by the gene prediction programs or were removed by GLEAN. We conservatively estimate that the current EST set represents more than 7500 transcription units. Published by Elsevier Ltd.