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

Changbin Chen,Ernest F Retzel,John A Crow,Joann Mudge,Alan G Smith,James Huntley,Andrew D Farmer,Raymond J Langley,Gregory D May

doi:10.1186/1471-2229-10-280

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.

Highlights

Meiosis is a critical process in the reproduction and life cycle of flowering plants in which homologous chromosomes pair, synapse, recombine and segregate
Through the comparative analysis of sequencing datasets against the TAIR 9 reference data, at the cutoff point of five reads per million reads, a total of 13,723 genes were expressed in meiocytes, with 15,368 and 16,174 genes detected in seedling and anther controls, respectively (Figure 2A)
When genes expressed in meiocytes were partitioned by biological process, a smaller number of genes function in DNA or RNA metabolism, and a larger number of signal transduction genes were observed, which suggested a lower level of DNA or RNA metabolic activity and a higher level of signal transduction occurs in meiosis (Figure 2B)

Summary

Introduction

Meiosis is a critical process in the reproduction and life cycle of flowering plants in which homologous chromosomes pair, synapse, recombine and segregate. Other researchers have collected anthers that are undergoing meiosis in several species, such as Arabidopsis [16], rice [17,18], maize [19] and wheat [20] for transcriptomic studies, since anthers are much easier to obtain compared to meiocytes. As mentioned above, this approach is inefficient for the exploration of meiosis, as only a small portion of cells in anthers are meiocytes (Figure 1B). Genes identified through this approach included genes that are specific for anther wall development (Figure 1B) [16]

Methods

Results

Discussion

Conclusion