Single cell RNA sequencing of the adult Drosophila eye reveals distinct clusters and novel marker genes for all major cell types

Yeung, K.W.K.; Raja, Komal Kumar Bollepogu; Shim, Yoon-Kyung; Li, Yumei; Chen, Rui; Mardon, Graeme

doi:10.1038/s42003-022-04337-1

Cited by 12 publications

(16 citation statements)

References 88 publications

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“…Analyses of our data reveal many putative markers for each cell type, several of which have been validated using T2A-Gal4 drivers in vivo. The data generated in this study will likely benefit research groups that use the larval eye disc as a model system and compliments our previously published late larval and adult eye scRNA-seq data (Yeung, Bollepogu Raja et al 2022, Bollepogu Raja, Yeung et al 2023.…”

Section: Discussionsupporting

confidence: 76%

A single cell RNA sequence atlas of the earlyDrosophilalarval eye

Raja,

Yeung,

et al. 2024

Preprint

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The Drosophila eye has been an important model to understand principles of differentiation, proliferation, apoptosis and tissue morphogenesis. However, a single cell RNA sequence resource that captures gene expression dynamics from the initiation of differentiation to the specification of different cell types in the larval eye disc is lacking. Here, we report transcriptomic data from 13,000 cells that cover six developmental stages of the larval eye. Our data show cell clusters that correspond to all major cell types present in the eye disc ranging from the initiation of the morphogenetic furrow to the differentiation of each photoreceptor cell type as well as early cone cells. We identify dozens of cell type-specific genes whose function in different aspects of eye development have not been reported. These single cell data will greatly aid research groups studying different aspects of early eye development and will facilitate a deeper understanding of the larval eye as a model system.

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Section: Discussionsupporting

confidence: 76%

A single cell RNA sequence atlas of the earlyDrosophilalarval eye

Raja,

Yeung,

et al. 2024

Preprint

Self Cite

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“…First, the application of single cell transcriptomics in Drosophila has verified many of the known regulators and cell types but also identified new genes and cell markers [100][101][102][103] as well as detailed new insights into the regulation and function of the Drosophila visual system more broadly [104,105] (Box 2). Furthermore, combining sc-RNA-seq with other "-omics" approaches, such as single cell ATAC-seq chromatin profiling, has provided major new knowledge about the GRNs for Drosophila eye and optic lobe development, and predictive power to model and test the regulatory logic underling gene expression.…”

Section: Discussionmentioning

confidence: 99%

Looking across the gap: Understanding the evolution of eyes and vision among insects

Kittelmann,

McGregor

2024

BioEssays

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The compound eyes of insects exhibit stunning variation in size, structure, and function, which has allowed these animals to use their vision to adapt to a huge range of different environments and lifestyles, and evolve complex behaviors. Much of our knowledge of eye development has been learned from Drosophila, while visual adaptations and behaviors are often more striking and better understood from studies of other insects. However, recent studies in Drosophila and other insects, including bees, beetles, and butterflies, have begun to address this gap by revealing the genetic and developmental bases of differences in eye morphology and key new aspects of compound eye structure and function. Furthermore, technical advances have facilitated the generation of high‐resolution connectomic data from different insect species that enhances our understanding of visual information processing, and the impact of changes in these processes on the evolution of vision and behavior. Here, we review these recent breakthroughs and propose that future integrated research from the development to function of visual systems within and among insect species represents a great opportunity to understand the remarkable diversification of insect eyes and vision.

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“…Despite these important discoveries, the Drosophila eye proteome remains poorly characterized. Several resources for gene expression in the adult eye are available, such as transcriptomes of whole eyes, isolated photoreceptor nuclei, or single cells [26,[32][33][34][35], but global transcript levels often poorly correlate with protein expression levels [36][37][38]. Yet, there are very few resources for the ocular proteome or the molar abundances of proteins that are expressed in the eye [11,39,40].…”

Section: Introductionmentioning

confidence: 99%

Eye proteome of Drosophila melanogaster

Kumar,

Has,

Lam‐Kamath

et al. 2023

Proteomics

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Drosophila melanogaster is a popular model organism to elucidate the molecular mechanisms that underlie the structure and function of the eye as well as the causes of retinopathies, aging, light‐induced damage, or dietary deficiencies. Large‐scale screens have isolated genes whose mutation causes morphological and functional ocular defects, which led to the discovery of key components of the phototransduction cascade. However, the proteome of the Drosophila eye is poorly characterized. Here, we used GeLC‐MS/MS to quantify 3516 proteins, including the absolute (molar) quantities of 43 proteins in the eye of adult male Drosophila reared on standard laboratory food. This work provides a generic and expandable resource for further genetic, pharmacological, and dietary studies.

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Single cell RNA sequencing of the adult Drosophila eye reveals distinct clusters and novel marker genes for all major cell types

Cited by 12 publications

References 88 publications

A single cell RNA sequence atlas of the earlyDrosophilalarval eye

A single cell RNA sequence atlas of the earlyDrosophilalarval eye

Looking across the gap: Understanding the evolution of eyes and vision among insects

Eye proteome of Drosophila melanogaster

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