The Drosophila gene collection:: Identification of putative full-length cDNAs for 70% of D-melanogaster genes
The Drosophila gene collection:: Identification of putative full-length cDNAs for 70% of D-melanogaster genes
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DOI：
10.1101/gr.269102
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发表时间：
2002-08-01
期刊：
影响因子：
7
通讯作者：
Rubin, GM
中科院分区：
文献类型：
--
作者：
Stapleton, M;Liao, GC;Rubin, GM
全长非冗余cDNA克隆的收集是功能基因组学的关键试剂。获得这些资源的第一步是生成cDNA文库并进行单次测序，这些文库中包含大量的全长克隆。第一个版本的果蝇基因收集版本1 （DGCr1）是从代表不同组织、发育阶段和培养的S2细胞系的六个文库中产生的。来自这些文库的近80,000个随机5‘表达序列标签（5’表达序列标签[ESTs]）被分解成一组5849个非冗余的cdna，相当于果蝇13474个预测基因中的40%。为了获得代表剩余基因的cDNA克隆，我们从两个先前存在的文库和三个新文库中额外生成了157,835个S' ESTs。一个新的文库来自于成人睾丸，我们以前没有利用这种组织进行基因发现；从0-22 h胚胎和成人头中获得了两个新的帽捕获归一化文库。利用带注释的D. melanogaster基因组序列，我们将est与基因组进行比对聚类。进一步分析DGCr1中尚未被cDNA克隆所代表的重叠基因簇，并选择推定的全长克隆纳入新的DGC。DGC （DGCr2）的第二次发布包含5061个额外的克隆，将收集的cdna扩展到10,910个，代表了果蝇中预测基因的约70%。
Collections of full-length nonredundant cDNA clones are critical reagents for functional genomics. The first step toward these resources is the generation and single-pass sequencing of cDNA libraries that contain a high proportion of full-length clones. The first release of the Drosophila Gene Collection Release 1 (DGCr1) was produced from six libraries representing various tissues, developmental stages, and the Cultured S2 cell line. Nearly 80,000 random 5' expressed sequence tags (5' expressed sequence tags [ESTs]from these libraries were collapsed into a nonredundant set of 5849 cDNAs, corresponding to similar to40% of the 13,474 predicted genes in Drosophila. To obtain cDNA clones representing the remaining genes, we have generated an additional 157,835 S' ESTs from two previously existing and three new libraries. One new library is derived from adult testis, a tissue we previously did not exploit for gene discovery; two new cap-trapped normalized libraries are derived from 0-22-h embryos and adult heads. Taking advantage of the annotated D. melanogaster genome sequence, we clustered the ESTs by aligning them to the genome. Clusters that overlap genes not already represented by cDNA clones in the DGCr1 were analyzed further, and putative full-length clones were selected for inclusion in the new DGC. This second release of the DGC (DGCr2) contains 5061 additional clones, extending the collection to 10,910 cDNAs representing >70% of the predicted genes in Drosophila.