About this item:

668 Views | 0 Downloads

Author Notes:

Correspondence to: John M. Nickerson, Ph.D., Associate Professor, Department of Ophthalmology, Emory University, B5602, 1365B Clifton Road, N.E., Atlanta, GA 30322; Phone: 404-778-4411; FAX: 404-778-2231; litjn@emory.edu

We thank several major sequencing centers for making whole genome sequences available for these analyses. In accordance with the wishes of these centers, we quote each requested acknowledgment below.

"The zebrafish sequence data were produced by the Zebrafish Sequencing Group at the Sanger Institute and can be obtained from D_rerio. The zebrafish draft assemblies were provided by The Wellcome Trust Sanger Institute, Cambridge, UK."

"The Xenopus tropicalis EST sequence data were produced by the Xenopus tropicalis Sequencing Group at the Sanger Institute and can be obtained from X_tropicalis."

"The Tetraodon nigroviridis V7 assembly (February 2004) was provided by Genoscope, Evry, France in collaboration with The Broad Institute, Cambridge, MA."

We thank the Medaka Genome Sequencing Project: "The data has been provided freely by the National Institute of Genetics and the University of Tokyo for use in this publication/correspondence only."

"The opossum sequence was made freely available by The Broad Institute, Cambridge, MA."

"The February 2004 chicken draft sequence was produced by The Genome Sequencing Center at Washington University School of Medicine, St. Louis, MO."

The fugu IRBP gene locus sequence "has been provided freely by the Fugu Genome Consortium for use in this publication/correspondence only."

Stickleback and fathead minnow ESTs were obtained from GenBank and the sequences were kindly deposited by the Stanford Human Genome Center, the US EPA, and the DOE Joint Genome Institute Pimephales promelas EST project.

Subject:

Interphotoreceptor retinoid-binding protein gene structure in tetrapods and teleost fish

Tools:

Journal Title:

Molecular Vision

Volume:

Volume 12

Publisher:

, Pages 1565-1585

Type of Work:

Article | Post-print: After Peer Review

Abstract:

Purpose The interphotoreceptor retinoid-binding protein (IRBP) gene possesses an unusual structure, encoding multiple Repeats, each consisting of about 300 amino acids. Our goals were to gain insight into the function of IRBP, and to test the current model for the evolution of IRBP, in which Repeats were replicated from a simpler ancestral gene. Methods We employed a bioinformatics approach to analyze IRBP loci in recently completed or near-complete genome sequences of several vertebrates and nonvertebrate chordates. IRBP gene expression in zebrafish was evaluated by reverse transcriptase PCR (RT-PCR) and in situ mRNA hybridizations with gene-specific probes. Results Patterns of exons and introns in the IRBP genes of tetrapods were highly similar, as were predicted amino acid sequences and Repeat structures. IRBP gene structure in teleost fish was more variable, and we report a new gene structure for two species, the Japanese puffer fish (Takifugu rubripes) and the zebrafish (Danio rerio). These teleost genomes contain a two-gene IRBP locus arranged head-to-tail in which the first gene, Gene 1, is intronless and contains a single large exon encoding three complete Repeats. It is followed by a second gene, Gene 2, which corresponds to the previously reported gene consisting of two Repeats spread across four exons and three introns. Each of the two zebrafish genes is transcribed. Gene 2 is expressed in the photoreceptors and RPE, and Gene 1 is expressed in the inner nuclear layer and weakly in the ganglion cell layer. Conclusions The tetrapod IRBP gene structure is highly conserved while the teleost fish gene structure was a surprise: It appears to be a two-gene locus with distinct Repeat organization in each open reading frame. This gene structure and gene expression data are consistent with possible neofunctionalization or sub-function partitioning of Gene 1 and Gene 2 in the zebrafish. We suggest that the two-gene locus in teleost fish arose as a consequence of either the known whole genome duplication or single gene tandem duplication.

Copyright information:

©2006 Molecular Vision

Export to EndNote