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| Status |
Public on Oct 01, 2023 |
| Title |
Evolution of neuronal cell classes and types in the vertebrate retina [Squirrel] |
| Organism |
Ictidomys tridecemlineatus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs (Baden et al., 2020). One might expect that retinal cell types evolved to accommodate these varied needs, but this has not been systematically studied. Here, we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a teleost fish, a bird, a reptile and a lamprey. Molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells [RGCs] and Müller glia) is striking, with transcriptomic differences across species correlated with evolutionary distance. Major subclasses are also conserved, whereas variation among types within classes or subclasses is more pronounced. However, an integrative analysis revealed that numerous types are shared across species based on conserved gene expression programs that likely trace back to the common ancestor of jawed vertebrates. The degree of variation among types increases from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified mammalian orthologs of midget RGCs, which comprise >80% of RGCs in the human retina, subserve high-acuity vision, and were believed to be primate-specific (Berson, 2008); in contrast, the mouse orthologs comprise <2% of mouse RGCs. Projections both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.
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| Overall design |
Single nucleus RNA-seq was performed on nuclei isolated from frozen retina. Fluorescence-activated cell sorting was used to collect DAPI-positive nuclei. For some collections, DAPI+ nculei were further seprated using NEUN/RBFOX3 and/or CHX10/VSX2 expression as an strategy to enrich for RGCs and/or bipolar cells, respectively (PLease note that he enrichment strategy was not effective for some species/samples). Approximately 8000 nuclei were recovered from each sample, and each nucleus was sequenced to a depth of ~40000 reads.
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| Contributor(s) |
Hahn J, Monavarfeshani A, Qiao M, Kao A, Kölsch Y, Kumar A, Rasys AM, Richardson R, Baier H, Lucas RJ, Li W, Meister M, Trachtenberg JT, Yan W, Peng Y, Sanes JR, Shekhar K |
| Citation(s) |
38092908 |
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| Submission date |
Jul 12, 2023 |
| Last update date |
Dec 15, 2023 |
| Contact name |
Joshua William Hahn |
| E-mail(s) |
[email protected]
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| Organization name |
UC Berkeley
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| Department |
Chemical and Biomolecular Engineering
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| Lab |
Karthik Shekhar
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| Street address |
Stanley Hall
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platforms (1) |
| GPL30340 |
Illumina NovaSeq 6000 (Ictidomys tridecemlineatus) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE237215 |
Evolution of neuronal cell classes and types in the vertebrate retina |
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| Relations |
| BioProject |
PRJNA994176 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE237212_Squirrel_count_mat.csv.gz |
49.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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