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(Investigative Ophthalmology and Visual Science. 2006;47:2632-2638.)
© 2006 by The Association for Research in Vision and Ophthalmology, Inc.
doi:10.1167/iovs.05-1463
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Development and Characterization of a Normalized Canine Retinal cDNA Library for Genomic and Expression Studies

Barbara Zangerl,1 Qi Sun,2 Jarek Pillardy,2 Jennifer L. Johnson,3 Peter A. Schweitzer,4 Alvaro G. Hernandez,5 Lei Liu,5 Gregory M. Acland,4 and Gustavo D. Aguirre1

1From the Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; the 2Computational Biology Service Unit, Cornell Theory Center, the 3J. A. Baker Institute, and the 4Biotechnology Center, Cornell University, Ithaca, New York; and the 5W. M. Keck Center for Comparative and Functional Genomics, University of Illinois, Urbana, Illinois.

PURPOSE. Identification of causative mutations for retinal blinding disorders is often limited by restricted understanding of gene expression and underlying molecular mechanisms that trigger degenerative processes. This study was conducted to develop a catalog of canine retina-expressed genes that would provide a unique tool to investigate normal and altered function in the adult retina. Because of the conserved syntenies between the dog and human, this approach would identify new potential disease candidate genes for both species.

METHODS. A canine normalized retinal cDNA library was produced and analyzed by using a modified PhredPhrap algorithm. Computerized annotation provided gene homology and chromosomal location for individual clones and contigs in a Web-accessible database.

RESULTS. From 6316 cDNA clones, 3980 retinal expressed sequence tags (ESTs) were derived. Homology to the canine genome draft sequence was found for more than 99% of all ESTs, but only for 32% when compared with annotated canine cDNAs. Functional analysis suggests an enrichment of this library for genes involved with eye function and development, chaperone, or ribosomal functions when compared with mouse and human National Center for Biotechnology Information (NCBI) RefSeq entries.

CONCLUSIONS. A combination of annotation approaches with ongoing mapping and expression studies provide functional data covering at least 27% to 30% of the currently proposed canine catalog of genes expressed in the retina. This is an essential first step toward establishing an integrated network for gene identification and expression patterns suitable for functional genetics, comparative genomics and evolutionary analysis of genes and gene families with respect to the developmental and degenerative processes of the retina.






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