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Debarshi Mustafi, Brian Kevany, Xiaodong Bai, Krzysztof Palczewski, ; Species specific genetic signatures in the mammalian eye revealed by RNA-Seq. Invest. Ophthalmol. Vis. Sci. 2014;55(13):4567.
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© ARVO (1962-2015); The Authors (2016-present)
Large scale genome sequencing projects have discovered genetic variants in humans that underlie functional variation. Understanding these variants in the face of evolution can reveal how genomes dynamically adapt that lead to functional and phenotypic variations in mammals. By carrying out transcriptomic studies from eye, retina, and macular tissue from a diverse set of mammals, we sought to identify the evolutionary genetic signatures that underlie higher order vision.
RNA-Seq of eye, retina, and macular tissue from mammals with varying retinal photoreceptor cellular compositions and distributions was carried out. Tissue from Rattus norvegicus (rat, nocturnal, ~1% cones), Mus musculus (mouse, nocturnal, ~3% cones), Arvicanthis niloticus (Nile rat, diurnal, ~33% cones), Ictidomys tridecemlineatus (ground squirrel, diurnal, ~97% cones), Macaca fasicularis (monkey, diurnal, ~5% cones, macula present), and Homo sapiens (human, diurnal, ~5% cones, macula present) were isolated and prepared for transcriptome analysis using the Illumina sequencing platform. Rhodopsin knockout mice (lacking a photoreceptor layer) and Nrl knockout mice (abundance of cone-like cells) were also used in the study.
Mapping the reads to known genomes of mouse, rat, human and monkey revealed 16, 933 uniquely mapped genes with an expression ≥ 1 RPKM among the 4 species. Of these unique genes, 91% of them had a homolog in mouse. Using these species as a scaffold, transcripts from Nile rat and ground squirrel were mapped to obtain relative abundances. Pathway analysis revealed over-represented networks unique to and shared among species. Metabolic and transcriptional network variances across species illustrated differential use of specific genetic elements, many with unannotated function, that drive visual function.
RNA-Seq of eye tissue across this diverse set of mammals that vary in circadian behavior and photoreceptor environment in this work provide an unprecedented insight into the genes that may drive rod versus cone aspects of vision. The genetic trends identified across species can enrich our understanding of causative genes in specific retinopathies and improve our therapeutic strategies for rod versus cone dystrophies and even geographic diseases of the eye that affect the macula versus the peripheral retina.
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