Evolutionary cell type mapping with single-cell genomics

Tanay, Amos; Sebé-Pedrós, Arnau

doi:10.1016/j.tig.2021.04.008

Cited by 56 publications

(68 citation statements)

References 125 publications

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“…Accordingly, a repertoire of neuron types in the brain was also dramatically altered during evolution [ 145 , 146 , 147 , 148 ]. Like many neuron types, general cell types are evolutionary units that have diversified in structure and function since the beginning of multicellularity [ 149 , 150 , 151 , 152 ].…”

Section: Tabula Gallusmentioning

confidence: 99%

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Towards Tabula Gallus

Yamagata

2022

IJMS

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The Tabula Gallus is a proposed project that aims to create a map of every cell type in the chicken body and chick embryos. Chickens (Gallus gallus) are one of the most recognized model animals that recapitulate the development and physiology of mammals. The Tabula Gallus will generate a compendium of single-cell transcriptome data from Gallus gallus, characterize each cell type, and provide tools for the study of the biology of this species, similar to other ongoing cell atlas projects (Tabula Muris and Tabula Sapiens/Human Cell Atlas for mice and humans, respectively). The Tabula Gallus will potentially become an international collaboration between many researchers. This project will be useful for the basic scientific study of Gallus gallus and other birds (e.g., cell biology, molecular biology, developmental biology, neuroscience, physiology, oncology, virology, behavior, ecology, and evolution). It will eventually be beneficial for a better understanding of human health and diseases.

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Section: Tabula Gallusmentioning

confidence: 99%

“…Such cell-type phylogenetics over very long evolutionary spans and phyla (mammals vs. aves vs. fish) has generally been considered challenging. However, recent progress shows that such analysis leads to being able to envision the function of novel cell types even in human tissues [ 107 , 147 , 150 , 151 , 152 , 155 ].…”

Section: Tabula Gallusmentioning

confidence: 99%

Towards Tabula Gallus

Yamagata

2022

IJMS

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“…To gain deeper knowledge of these processes requires data on differential gene expression at cellular resolution during embryogenesis, to allow us to understand the distinct cell types that build animals. This can now be achieved by using single-cell analysis [2][3][4][5]. However, this approach has only been applied to a few models and there is therefore a great need to perform this work in additional key taxa [6][7][8][9][10][11][12][13].…”

Section: Introductionmentioning

confidence: 99%

An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis

Leite

Schoenauer

Blakeley

et al. 2022

Preprint

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Spiders are a diverse order of chelicerates that diverged from other arthropods over 500 million years ago. Research on spider embryogenesis has made important contributions to understanding the evolution of animal development. In particular, studies of the common house spider Parasteatoda tepidariorum using developmental candidate gene approaches have provided key insights into the regulation and evolution of many processes including axis formation, segmentation and patterning. However, there remains a paucity of knowledge about the cells that build spider embryos, their gene expression profiles and fate. Single-cell transcriptomic analyses have been revolutionary in describing these complex landscapes of cellular genetics in a range of animals. Therefore, we carried out single-cell RNA sequencing of P. tepidariorum embryos at stages 7, 8 and 9, which encompass the establishment and patterning of the body plan, and initial differentiation of many tissues and organs. We identified 23 cell clusters marked by many developmental toolkit genes, as well as a plethora of non-candidate genes not previously investigated. We found many Hox genes were markers of cell clusters, and Hox gene paralogs often were present in different clusters. This provided further evidence of sub- and/or neo-functionalisation of these important developmental genes after the whole genome duplication in the arachnopulmonate ancestor. We also examined the spatial expression of marker genes for each cluster to generate a comprehensive cell atlas of these embryonic stages. This revealed new insights into the cellular basis and genetic regulation of head patterning, hematopoiesis, limb development, gut development and posterior segmentation. This atlas will serve as a platform for future analysis of spider cell specification and fate, and the evolution of these processes among animals at cellular resolution.

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“…Likewise, the pigment cells are also proposed to have also arisen through a heterochronic co-option of an adult program for the formation of these cells (Perillo et al, 2020), although the possible evolution of this cell type is still poorly investigated. Single-cell RNA-sequencing (scRNA-seq) has revolutionized our understanding of cell-type diversity within an organism (Konstantinides et al, 2018;Marioni and Arendt, 2017;Morris, 2019;Shapiro et al, 2013;Tanay and Sebé-Pedrós, 2021). This technology profiles the transcriptome of individual cells within an organism, preserving the heterogeneity of cell states that are lost in traditional bulk sequencing.…”

Section: Introductionmentioning

confidence: 99%

New hypotheses of cell type diversity and novelty from comparative single cell and nuclei transcriptomics in echinoderms

Hatleberg

Telmer

Hinman

2022

Preprint

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Cell types are the fundamental building blocks of metazoan biodiversity and offer a powerful perspective for inferring evolutionary phenomena. With the development of single-cell transcriptomic techniques, new definitions of cell types are emerging. This allows a conceptual reassessment of traditional definitions of novel cell types and their evolution. Research in echinoderms, particularly sea star and sea urchin embryos have contributed significantly to understanding the evolution of novel cell types, in particular the primary mesenchyme cells (PMCs) and pigment cells that are found in sea urchin but not sea star embryos. This paper outlines the development of a gene expression atlas for the bat star, Patiria miniata, using single nuclear RNA sequencing (snRNA-seq) of embryonic stages. The atlas revealed 22 cell clusters covering all expected cell types from the endoderm, mesoderm and ectoderm germ layers. In particular, four distinct neural clusters, an immune cluster, and distinct right and left coelom clusters were revealed as distinct cell states. A comparison with Strongylocentrotus purpuratus embryo single cell transcriptomes was performed using 1:1 orthologs to anchor and then compare gene expression patterns. S. purpuratus primordial germ cell equivalents were not detected in P. minata, while the left coelom of P. miniata has no equivalent cell cluster in S. purpuratus. Pigment cells of S. purpuratus map to clusters containing immune mesenchyme and neural cells of P. miniata, while the PMCs of S. purpuratus are revealed as orthologous to the right coelom cluster of P. miniata. These results suggest a new interpretation of the evolution of these well-studied cell types and a reflection on the definition of novel cell types.

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Evolutionary cell type mapping with single-cell genomics

Cited by 56 publications

References 125 publications

Towards Tabula Gallus

Towards Tabula Gallus

An atlas of spider development at single-cell resolution provides new insights into arthropod embryogenesis

New hypotheses of cell type diversity and novelty from comparative single cell and nuclei transcriptomics in echinoderms

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