Submitted on May 24, 2005
Accepted on December 13, 2005
Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes
K. W. Choy1, C. C. Wang2, A. Ogura3, T. K. Lau4, M. S. Rogers4, K. Ikeo3, T. Gojobori3, D. S. C Lam5, and C. P. Pang5*
1 Department of Ophthalmology & Visual Sciences, Chinese University of Hong Kong, Shatin, SAR, Hong Kong; Department of Obstetrics and Gynaecology, Chinese University of Hong Kong, Shatin, SAR, Hong Kong
2 Department of Obstetrics and Gynaecology, Chinese University of Hong Kong, Shatin, SAR, Hong Kong; Center for Information Biology & DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka, Japan
3 Center for Information Biology & DNA Data Bank of Japan, National Institute of Genetics, Mishima, Shizuoka, Japan
4 Department of Obstetrics and Gynaecology, Chinese University of Hong Kong, Shatin, SAR, Hong Kong
5 Department of Ophthalmology & Visual Sciences, Chinese University of Hong Kong, Shatin, SAR, Hong Kong
* To whom correspondence should be addressed. E-mail: cppang{at}cuhk.edu.hk.
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 to 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 un-normalized library. We screened 11,246 good quality ESTs, leading to the identification of 5,534 non-redundant 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: C. briggsae (26%), C. elegans (27%), A. gambiae (37%), D. melanogaster (32%), D. rerio (42%), F. rubripes (49%), R. norvegicusvalitus (51%), and M. musculus (59%). Nevertheless, 48% (2,680/5,534) of the genes expressed in the early developing eye are not shared with current NEIBank human eye cDNA data. In addition, eight known retinal disease genes exist 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.
