Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes
Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes
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DOI：
10.1152/physiolgenomics.00121.2005
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发表时间：
2006-03-13
影响因子：
4.6
通讯作者：
Pang, CP
中科院分区：
文献类型：
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作者：
Choy, KW;Wang, CC;Pang, CP
为了补充妊娠早期人眼的c DNA文库，并发现与早期眼发育相关的候选基因，我们以9~14周新鲜解剖的人眼球为材料，构建了人胎眼早期c DNA文库。从未扩增和非归一化文库中共分离并测序了15,809个克隆。我们筛选了11,246个高质量的EST，最终识别出5,534个非冗余簇。其中，有4010个基因(72%)与人类蛋白质数据库(EnSembl)中的基因匹配。其余28%(1,524)对应于潜在的新EST或以前未识别的EST。我们使用BLASTX将我们的EST数据与八种生物进行比较，发现高比例基因的共同表达：线虫(26%)、秀丽线虫(27%)、冈比亚按蚊(37%)、黑腹果蝇(32%)、黑腹果蝇(42%)、红鳍河豚(49%)、褐毛鼠(52%)和小鼠(59%)。然而，在发育早期眼中表达的基因中有48%(2,680个)与当前NEIBank人眼的cdna数据不一致。此外，我们的EST中还存在8个已知的视网膜疾病基因。其中6个(COL11A1、BBS5、PDE6B、OAT、VMD2和PGK1)在其他生物的基因组中是保守的，这表明我们的注释EST集不仅为基因发现和功能基因组分析提供了宝贵的资源，而且还为系统发育分析提供了有价值的资源。我们最早的妊娠早期人眼cDNA文库可以提供跨物种的详细比较，以确定基因的生理功能，并阐明进化机制。
To complement cDNA libraries from the human eye at early gestation and to discover candidate genes associated with early ocular development, we used freshly dissected human eyeballs from week 9 - 14 of gestation to construct the early human fetal eye cDNA library. A total of 15,809 clones were isolated and sequenced from the unamplified and unnormalized library. We screened 11,246 good-quality ESTs, leading to the identification of 5,534 nonredundant clusters. Among them, 4,010 (72%) genes matched in the human protein database (Ensembl). The remaining 28% ( 1,524) corresponded to potentially novel or previously unidentified ESTs. We used BLASTX to compare our EST data with eight organisms and found common expression of a high portion of genes: Caenorhabditis briggsae (26%), Caenorhabditis elegans (27%), Anopheles gambiae (37%), Drosophila melanogaster (32%), Danio rerio (42%), Fugu rubripes (49%), Rattus norvegicusvalitus (52%), and Mus musculus (59%). Nevertheless, 48% (2,680 of 5,534) of the genes expressed in the early developing eye were not shared with current NEIBank human eye cDNA data. In addition, eight known retinal disease genes existed in our ESTs. Among them, six (COL11A1, BBS5, PDE6B, OAT, VMD2, and PGK1) were conserved among the genomes of other organisms, indicating that our annotated EST set provides not only a valuable resource for gene discovery and functional genomic analysis but also for phylogenetic analysis. Our foremost early gestation human eye cDNA library could provide detailed comparisons across species to identify physiological functions of genes and to elucidate evolutionary mechanisms.