title: Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes.
abstract: BACKGROUND
  Meiosis 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.
  
  
  RESULTS
  A 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.
  
  
  CONCLUSIONS
  These 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.
authors.affiliation: Department of Horticultural Science, University of Minnesota, 1970 Folwell Avenue, St. Paul, MN 55108, USA. chenx481@umn.edu
authors.forename: Changbin
authors.initials: C
authors.lastname: Chen
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Farmer
authors.forename: Raymond J
authors.initials: RJ
authors.lastname: Langley
authors.forename: Joann
authors.initials: J
authors.lastname: Mudge
authors.forename: John A
authors.initials: JA
authors.lastname: Crow
authors.forename: Gregory D
authors.initials: GD
authors.lastname: May
authors.forename: James
authors.initials: J
authors.lastname: Huntley
authors.forename: Alan G
authors.initials: AG
authors.lastname: Smith
authors.forename: Ernest F
authors.initials: EF
authors.lastname: Retzel
mesh_terms: D000704:Analysis of Variance; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D004251:DNA Transposable Elements / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D008540:Meiosis / Q000235:genetics*; D011058:Pollen / Q000166:cytology / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D029681:Arabidopsis Proteins; D004251:DNA Transposable Elements