Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes

Abstract

BackgroundMeiosis is a critical process in the reproduction and life cycle of flowering plants in which homologous chromosomes pair, synapse, recombine and segregate. Understanding meiosis will not only advance our knowledge of the mechanisms of genetic recombination, but also has substantial applications in crop improvement. Despite the tremendous progress in the past decade in other model organisms (e.g., Saccharomyces cerevisiae and Drosophila melanogaster), the global identification of meiotic genes in flowering plants has remained a challenge due to the lack of efficient methods to collect pure meiocytes for analyzing the temporal and spatial gene expression patterns during meiosis, and for the sensitive identification and quantitation of novel genes.ResultsA high-throughput approach to identify meiosis-specific genes by combining isolated meiocytes, RNA-Seq, bioinformatic and statistical analysis pipelines was developed. By analyzing the studied genes that have a meiosis function, a pipeline for identifying meiosis-specific genes has been defined. More than 1,000 genes that are specifically or preferentially expressed in meiocytes have been identified as candidate meiosis-specific genes. A group of 55 genes that have mitochondrial genome origins and a significant number of transposable element (TE) genes (1,036) were also found to have up-regulated expression levels in meiocytes.ConclusionThese findings advance our understanding of meiotic genes, gene expression and regulation, especially the transcript profiles of MGI genes and TE genes, and provide a framework for functional analysis of genes in meiosis.

Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks

“…Transcriptomic studies have been conducted in pollen, sperm, and anthers in diverse plant species, including Arabidopsis, rice, B. rapa, maize, and cotton (Gossypium hirsutum; Honys and Twell, 2004;Ma et al, 2007Ma et al, , 2008Ma et al, , 2012Chen et al, 2010;Fujita et al, 2010;Deveshwar et al, 2011;Yang et al, 2011;Dong et al, 2013;Wuest et al, 2013). While some studies were focused on tapetum and male gametophytes, others compared anthers of male sterile mutants with anthers of the wild type.…”

The Recombinases DMC1 and RAD51 Are Functionally and Spatially Separated during Meiosis in Arabidopsis

“…In brief, anthers were dissected from several inflorescences and kept in artificial pond water (Miller and Gow, 1989) until further use. PMCs were released from anthers and collected in a small volume of artificial pond water (Chen et al, 2010 (Albini et al, 1984), and meiocytes were incubated for 5 min at room temperature. A total of 8 mL of the enzyme mixture, containing extracted meiocytes, was transferred to a clean glass slide, and spreading was achieved by addition of 20 mL of 1% Lipsol (pH 9.0, borate buffer).…”

Chromosome Organization and Dynamics during Interphase, Mitosis, and Meiosis in Plants

“…Meiosis-specific patterns of chromatin remodeling have been also implicated in preconditioning specific chromosome regions to become sites of meiotic recombination events in mouse (Mus musculus) and budding yeast (Saccharomyces cerevisiae) studies (Borde et al, 2009;Baudat et al, 2010). Transcriptome analyses of Arabidopsis meiocytes showed that a staggering number of genes are expressed during meiotic prophase I (Chen et al, 2010). These gene expression patterns are also presumably results of chromatin remodeling in early meiosis.…”