High-throughput single-cell transcriptomics reveals the female germline differentiation trajectory in Arabidopsis thaliana

Zhimin Hou,Liping Liu,Yanhui Liu,Hanyang Cai,Xingyue Jin,Man Zhang,Lihua Zhao,Zhenxia Su,Yuan Qin

doi:10.1038/s42003-021-02676-z

Zhimin Hou, Liping Liu + Show 7 more

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https://doi.org/10.1038/s42003-021-02676-z

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Abstract

Female germline cells in flowering plants differentiate from somatic cells to produce specialized reproductive organs, called ovules, embedded deep inside the flowers. We investigated the molecular basis of this distinctive developmental program by performing single-cell RNA sequencing (scRNA-seq) of 16,872 single cells of Arabidopsis thaliana ovule primordia at three developmental time points during female germline differentiation. This allowed us to identify the characteristic expression patterns of the main cell types, including the female germline and its surrounding nucellus. We then reconstructed the continuous trajectory of female germline differentiation and observed dynamic waves of gene expression along the developmental trajectory. A focused analysis revealed transcriptional cascades and identified key transcriptional factors that showed distinct expression patterns along the germline differentiation trajectory. Our study provides a valuable reference dataset of the transcriptional process during female germline differentiation at single-cell resolution, shedding light on the mechanisms underlying germline cell fate determination.

Highlights

Female germline cells in flowering plants differentiate from somatic cells to produce specialized reproductive organs, called ovules, embedded deep inside the flowers
In Arabidopsis thaliana, the female germline cell is initiated from a single sub-epidermal cell in the distal nucellus to form the archesporial cell (AC), which is morphologically distinguishable from the neighboring somatic cells by its larger size and conspicuous nucleus
Our study provides an unsupervised classification of cell populations and describes the extent of heterogeneity at the molecular level among populations of different cell types in ovule primordia undergoing germline differentiation, revealing continuous, dynamic patterns of change in gene expression during female germline initiation and specification

Summary

Introduction

Female germline cells in flowering plants differentiate from somatic cells to produce specialized reproductive organs, called ovules, embedded deep inside the flowers. Previous gene profiling studies using bulk RNA sequencing (RNA-seq) analysis of ovule tissue or single-cell-type RNA-seq in combination with laserassisted microdissection or fluorescence-assisted cell-sorting techniques to isolate MMC have helped reveal the transcriptional network underlying MMC specification and differentiation[3,4,5]. Informative, these studies could not provide a comprehensive characterization of the continuous process of female germline cell differentiation. Our study provides an unsupervised classification of cell populations and describes the extent of heterogeneity at the molecular level among populations of different cell types in ovule primordia undergoing germline differentiation, revealing continuous, dynamic patterns of change in gene expression during female germline initiation and specification

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