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Debarshi Mustafi, Brian Kevany, Krzysztof Palczewski; Comparative genomic analysis reveals a functional evolution of vision across mammals. Invest. Ophthalmol. Vis. Sci. 2016;57(12):6563.
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© ARVO (1962-2015); The Authors (2016-present)
Dysfunction of photoreceptor and adjacent supporting cell layers is the driving force for the majority of retinal degenerative diseases. Comparative analysis of species can reveal genetic changes in specific pathways that underlie functional evolution and phenotypic variation. The discovery of conserved and divergent networks across species can delineate the genetic drivers of both phenotypic diversity and retinal pathology.
Ocular tissues from rodent species with varying photoreceptor populations (Rattus norvegicus, Mus musculus, Arvicanthis niloticus, Ictidomys tridecemlineatus) as well as from primates (Macaca fasicularis and Homo sapiens) were prepared for RNA-Seq. Libraries were sequenced with the Illumina platform and processed and aligned to pre-existing genomes or aligned de novo. Co-expression networks were constructed from RNA-Seq data by calculating Pearson correlations across rodent species. The concordance of gene expression with the Pearson correlation was such that the gene expression pattern was weighted against the pigment composition in rodent species. Discreet modules were then compared against data obtained from primate tissues.
Genome assembly across species revealed 12,029 genes conserved across all mammals whereas 1,070 genes were unique to rodents and 1,018 genes were found only in primates. Gene ontology analysis revealed species-specific patterns, such as transcription factor enrichment in primate ocular tissue. Coherent expression profiles of 873 rodent genes that exhibited topographical overlap were assembled into discreet modules by using average linkage hierarchical clustering to reveal those modules that had a preference for rod versus cone photoreceptor populations. Modular analysis revealed novel genes that co-localized with known photoreceptor genes to specific retinal compartments and coordinated with retinal disease networks.
RNA-seq across different retinal and behavioral environments revealed the evolutionary dynamics of the ocular transcriptome. This approach highlighted the separation of conserved genetic elements essential for ocular function from those evolutionary divergent features that have shaped higher order primate vision. Furthermore, co-expression analysis has identified novel genetic features of the retina and their roles in health and disease.
This is an abstract that was submitted for the 2016 ARVO Annual Meeting, held in Seattle, Wash., May 1-5, 2016.
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