Transcriptomes of isolated Oryza sativa gametes characterized by deep sequencing: evidence for distinct sex‐dependent chromatin and epigenetic states before fertilization

Abstract

SUMMARYThe formation of a zygote by the fusion of egg and sperm involves the two gametic transcriptomes. In flowering plants, the embryo sac embedded within the ovule contains the egg cell, whereas the pollen grain contains two sperm cells inside a supporting vegetative cell. The difficulties of collecting isolated gametes and consequent low recovery of RNA have restricted in-depth analysis of gametic transcriptomes in flowering plants. We isolated living egg cells, sperm cells and pollen vegetative cells from Oryza sativa (rice), and identified transcripts for approximately 36 000 genes by deep sequencing. The three transcriptomes are highly divergent, with about three-quarters of those genes differentially expressed in the different cell types. Distinctive expression profiles were observed for genes involved in chromatin conformation, including an unexpected expression in the sperm cell of genes associated with active chromatin. Furthermore, both the sperm cell and the pollen vegetative cell were deficient in expression of key RNAi components. Differences in gene expression were also observed for genes for hormonal signaling and cell cycle regulation. The egg cell and sperm cell transcriptomes reveal major differences in gene expression to be resolved in the zygote, including pathways affecting chromatin configuration, hormones and cell cycle. The sex-specific differences in the expression of RNAi components suggest that epigenetic silencing in the zygote might act predominantly through female-dependent pathways. More generally, this study provides a detailed gene expression landscape for flowering plant gametes, enabling the identification of specific gametic functions, and their contributions to zygote and seed development.

Zygotic Genome Activation Occurs Shortly after Fertilization in Maize

“…This finding might explain the strongly condensed, compact sperm cell chromatin (see also Figure 1A). Indeed, a similar observation was reported for rice sperm cells (Russell et al, 2012;Anderson et al, 2013). Notably, no chromatin gene is among the TOP80 genes in maize egg cells.…”

“…We used published RNA-seq data from rice sperm and egg cells (Anderson et al, 2013) and initially identified the rice homologs using public databases, i.e., EnsemblPlants and RiceAnnotationGenomeProject, which combine data from many species to identify putative orthologs. If the identity of the homologs/ orthologs was unclear or unknown due to a lack of sequence information, we did not include them in the comparison.…”

“…While OrthoMCL is based only on a comparison of protein sequences, Ensembl Compara also uses information from phylogenetic trees and therefore interprets sequence similarities based on the evolutionary development of a gene. Rice gene expression data (TPM) were obtained from Anderson et al (2013). Maize and rice TPMs were square root transformed, and plastid transcripts were removed.…”

Intercellular communication in Arabidopsis thaliana pollen discovered via AHG3 transcript movement from the vegetative cell to sperm

“…However, transcriptome studies of isolated sperm cells showed that sperm cells contain thousands of transcripts, consistent with transcriptional activity (13,30). This idea is supported by the identification of several sperm cell-specific genes, such as GEX1 and DUO1 (31,32).…”

Plant germline formation: common concepts and developmental flexibility in sexual and asexual reproduction

“…Nevertheless, recent methodological advances have allowed the transcriptional profiling of such rare cell types by combining laserassisted microdissection or micromanipulation with microarray and/ or RNA-Seq analyses. These studies have provided novel insights into the transcriptional basis of germline specification and development (Wüest et al, 2010;Schmidt et al, 2011Schmidt et al, , 2012Schmidt et al, , 2014Okada et al, 2013;Wüest et al, 2013;Abiko et al, 2013;Anderson et al, 2013;Chettoor et al, 2014).…”