Single-cell sequencing reveals the evolution of immune molecules across multiple vertebrate species

Graphical abstract

Highlights

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  Macrophages develop evolutionary versatility in expressed genes.

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  B cell immunity is relatively conserved among vertebrate species.

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  Compensatory TCR cascade components are utilized by different species.

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  Mouse species shows the highest similarity in immune transcriptomes to human among multiple vertebrates.

Abstract

Introduction

Both innate and adaptive immune system undergo evolution from low to high vertebrates. Due to the limitation of conventional approaches in identifying broader spectrum of immune cells and molecules from various vertebrates, it remains unclear how immune molecules evolve among vertebrates.

Objectives

Here, we utilized carry out comparative transcriptome analysis in various immune cells across seven vertebrate species.

Methods

Single-cell RNA sequencing (scRNA-seq).

Results

We uncovered both conserved and species-specific profiling of gene expression in innate and adaptive immunity. Macrophages exhibited highly-diversified genes and developed sophisticated molecular signaling networks along with evolution, indicating effective and versatile functions in higher species. In contrast, B cells conservatively evolved with less differentially-expressed genes in analyzed species. Interestingly, T cells represented a dominant immune cell populations in all species and unique T cell populations were identified in zebrafish and pig. We also revealed compensatory TCR cascade components utilized by different species. Inter-species comparison of core gene programs demonstrated mouse species has the highest similarity in immune transcriptomes to human.

Conclusions

Therefore, our comparative study reveals gene transcription characteristics across multiple vertebrate species during the evolution of immune system, providing insights for species-specific immunity as well as the translation of animal studies to human physiology and disease.