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Series GSE237206 Query DataSets for GSE237206
Status Public on Oct 01, 2023
Title Evolution of neuronal cell classes and types in the vertebrate retina [Marmoset]
Organism Callithrix jacchus
Experiment type Expression profiling by high throughput sequencing
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.
 
Overall design Single cell RNA-seq was performed on cells isolated from fresh retina. Fluorescence-activated cell sorting was used to collect Calcein blue(CB)-positive live cells. For some collections, CB+ cells were further seprated using CD90/THY1 and/or CD73 expression as an strategy to enrich for RGCs and/or to deplete phototreceptors, respectively (Please note that he enrichment strategy was not effective for some species/samples). Approximately 8000 cells were recovered from each sample, and each cell was sequenced to a depth of ~40000 reads.
 
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
Submission date Jul 12, 2023
Last update date Dec 15, 2023
Contact name Joshua William Hahn
E-mail(s) joshhahn@berkeley.edu
Organization name UC Berkeley
Department Chemical and Biomolecular Engineering
Lab Karthik Shekhar
Street address Stanley Hall
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platforms (1)
GPL28240 Illumina NovaSeq 6000 (Callithrix jacchus)
Samples (8)
GSM7596872 Adultmarmoset_Fovea_1S1
GSM7596873 Adultmarmoset_Fovea_1S2
GSM7596874 Adultmarmoset_Fovea_1S3
This SubSeries is part of SuperSeries:
GSE237215 Evolution of neuronal cell classes and types in the vertebrate retina
Relations
BioProject PRJNA994171

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE237206_Marmoset_count_mat.csv.gz 131.6 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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