Tracing cell-type evolution by cross-species comparison of cell atlases

Wang, Jingjing; Sun, Huiyu; Jiang, Mengmeng; Li, Jiaqi; Zhang, Peijing; Chen, Haide; Mei, Yuqing; Fei, Lijiang; Lai, Shih‐Wei; Han, Xiaoping; Song, Xinhui; Xu, Suhong; Ming, Chi; Ouyang, Hongwei; Zhang, Dan; Yuan, Guo‐Cheng; Guo, Guoji

doi:10.1016/j.celrep.2021.108803

Cited by 63 publications

(62 citation statements)

References 62 publications

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“…Single-cell transcriptomics offers an opportunity for comprehensive cross-species and cross-tissues analysis of cell types. A recent study reported that the cell-type could be proposed as "evolutionary units" in comparative cell biology (Wang et al, 2021). In the current study, we propose that the different epithelial cells in mammal lung may evolve from different organs in zebrafish including swim bladder and gill.…”

Section: Discussionmentioning

confidence: 62%

“…Whether the lung evolves from the gill or the swim bladder is still a controversy based on morphological evidences (Perry and Sander, 2004;Zheng et al, 2011). A recent study reported that the cell types could be proposed as "evolutionary units" in comparative cell biology (Wang et al, 2021). To infer the evolutionary relationship of respiratory system at the single-cell level, we extracted orthologous genes and performed cross-species clustering analysis of zebrafish gill (Z_G), swim bladder (Z_SB) and mouse adult lung (M_AL), fetal lung (M_FL) (Han et al, 2018) (Figures 3A,B and Supplementary Table 3).…”

Section: Cross-species Analysis Of Cell-type Similaritymentioning

confidence: 99%

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Characterization of the Zebrafish Cell Landscape at Single-Cell Resolution

Jiang

Xiao

Weigao

et al. 2021

Front. Cell Dev. Biol.

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Zebrafish have been found to be a premier model organism in biological and regeneration research. However, the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here, we utilized Microwell-seq to analyze more than 250,000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single-cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single-cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall, our single-cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research.

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Section: Discussionmentioning

confidence: 62%

Section: Cross-species Analysis Of Cell-type Similaritymentioning

confidence: 99%

Characterization of the Zebrafish Cell Landscape at Single-Cell Resolution

Jiang

Xiao

Weigao

et al. 2021

Front. Cell Dev. Biol.

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“…It not only deepens our knowledge of cells but also provides novel insights into evolutionary and developmental biology [3]. Cross-species integration and comparison of scRNA-seq datasets allow us to explore, at single-cell resolution, the origins of cellular diversity and the evolutionary mechanisms that shape cellular form and function [3-11].…”

Section: Introductionmentioning

confidence: 99%

“…Lastly, evolutionary divergences are thought to be caused by transcriptional changes of groups of genes that evolve in a modular fashion and are controlled by transcription factors [21]. Extraction and comparison of gene modules between species will provide deep insights into evolutionary conservation and divergences [11, 22, 23].…”

Section: Introductionmentioning

confidence: 99%

Cross-species cell-type assignment of single-cell RNA-seq by a heterogeneous graph neural network

Liu

Shen

Zhang

2021

Preprint

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Cross-species comparative analyses of single-cell RNA sequencing (scRNA-seq) data allow us to explore, at single-cell resolution, the origins of cellular diversity and the evolutionary mechanisms that shape cellular form and function. Here, we aimed to utilize a heterogeneous graph neural network to learn aligned and interpretable cell and gene embeddings for cross-species cell type assignment and gene module extraction (CAME) from scRNA-seq data. A systematic evaluation study on 649 pairs of cross-species datasets showed that CAME outperformed six benchmarking methods in terms of cell-type assignment and model robustness to insufficiency and inconsistency of sequencing depths. Comparative analyses of the major types of human and mouse brains by CAME revealed shared cell type-specific functions in homologous gene modules. Alignment of the trajectories of human and macaque spermatogenesis by CAME revealed conservative gene expression dynamics during spermatogenesis between humans and macaques. Owing to the utilization of non-one-to-one homologous gene mappings, CAME made a significant improvement on cell-type characterization cross zebrafish and other species. Overall, CAME can not only make an effective cross-species assignment of cell types on scRNA-seq data but also reveal evolutionary conservative and divergent features between species.

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“…Single-cell data in evolutionary contexts have generally been applied to distantly related taxa (Tosches et al 2018; Hodge et al 2019; Liang et al 2018), typically focusing on cell type diversity (Sebé-Pedrós et al 2018; La Manno et al 2016; Colquitt et al 2021; Feregrino and Tschopp 2021; J. Wang et al 2021). Evolutionary analysis of different cell types across species, particularly on short time scales, has received less attention (Liang et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Single-nucleus transcriptomes reveal functional and evolutionary properties of cell types in the Drosophila accessory gland

2021

Preprint

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Many traits responsible for male reproduction evolve quickly, including gene expression phenotypes in germline and somatic male reproductive tissues. Rapid male evolution in polyandrous species is thought to be driven by competition among males for fertilizations and conflicts between male and female fitness interests that manifest in post-copulatory phenotypes. In Drosophila, seminal fluid proteins secreted by three major cell types of the male accessory gland and ejaculatory duct are required for female sperm storage and use, and influence female post-copulatory traits. Recent work has shown that these cell types have overlapping but distinct effects on female post-copulatory biology, yet relatively little is known about their evolutionary properties. Here we use single-nucleus RNA-Seq of the accessory gland and ejaculatory duct from Drosophila melanogaster and two closely related species to comprehensively describe the cell diversity of these tissues and their transcriptome evolution for the first time. We find that seminal fluid transcripts are strongly partitioned across the major cell types, and expression of many other genes additionally define each cell type. We also report previously undocumented diversity in main cells. Transcriptome divergence was found to be heterogeneous across cell types and lineages, revealing a complex evolutionary process. Furthermore, protein adaptation varied across cell types, with potential consequences for our understanding of selection on male post-copulatory traits.

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Tracing cell-type evolution by cross-species comparison of cell atlases

Abstract: Highlights d Single-cell transcriptional data systematically infers cell-type evolution d A roadmap for the origin and diversity of major cell categories d Muscle cells and neurons are conserved cell types d Conserved transcription factor repertoire specifies major cell categories

Cited by 63 publications

References 62 publications

Characterization of the Zebrafish Cell Landscape at Single-Cell Resolution

Characterization of the Zebrafish Cell Landscape at Single-Cell Resolution

Cross-species cell-type assignment of single-cell RNA-seq by a heterogeneous graph neural network

Single-nucleus transcriptomes reveal functional and evolutionary properties of cell types in the Drosophila accessory gland

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