Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated <it>Arabidopsis </it>male meiocytes
<p>Abstract</p> <p>Background</p> <p>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...
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doaj-5801fe0979704ebbb902e62a8c89f6f12020-11-25T00:35:18ZengBMCBMC Plant Biology1471-22292010-12-0110128010.1186/1471-2229-10-280Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated <it>Arabidopsis </it>male meiocytesMay Gregory DCrow John AMudge JoannLangley Raymond JFarmer Andrew DChen ChangbinHuntley JamesSmith Alan GRetzel Ernest F<p>Abstract</p> <p>Background</p> <p>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., <it>Saccharomyces cerevisiae </it>and <it>Drosophila melanogaster</it>), 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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> http://www.biomedcentral.com/1471-2229/10/280 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
May Gregory D Crow John A Mudge Joann Langley Raymond J Farmer Andrew D Chen Changbin Huntley James Smith Alan G Retzel Ernest F |
spellingShingle |
May Gregory D Crow John A Mudge Joann Langley Raymond J Farmer Andrew D Chen Changbin Huntley James Smith Alan G Retzel Ernest F Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated <it>Arabidopsis </it>male meiocytes BMC Plant Biology |
author_facet |
May Gregory D Crow John A Mudge Joann Langley Raymond J Farmer Andrew D Chen Changbin Huntley James Smith Alan G Retzel Ernest F |
author_sort |
May Gregory D |
title |
Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated <it>Arabidopsis </it>male meiocytes |
title_short |
Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated <it>Arabidopsis </it>male meiocytes |
title_full |
Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated <it>Arabidopsis </it>male meiocytes |
title_fullStr |
Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated <it>Arabidopsis </it>male meiocytes |
title_full_unstemmed |
Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated <it>Arabidopsis </it>male meiocytes |
title_sort |
meiosis-specific gene discovery in plants: rna-seq applied to isolated <it>arabidopsis </it>male meiocytes |
publisher |
BMC |
series |
BMC Plant Biology |
issn |
1471-2229 |
publishDate |
2010-12-01 |
description |
<p>Abstract</p> <p>Background</p> <p>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., <it>Saccharomyces cerevisiae </it>and <it>Drosophila melanogaster</it>), 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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> |
url |
http://www.biomedcentral.com/1471-2229/10/280 |
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