PMRD: a curated database for genes and mutants involved in plant male reproduction
© Cui et al.; licensee BioMed Central Ltd. 2012
Received: 1 April 2012
Accepted: 7 November 2012
Published: 15 November 2012
Male reproduction is an essential biological event in the plant life cycle separating the diploid sporophyte and haploid gametophyte generations, which involves expression of approximately 20,000 genes. The control of male reproduction is also of economic importance for plant breeding and hybrid seed production. With the advent of forward and reverse genetics and genomic technologies, a large number of male reproduction-related genes have been identified. Thus it is extremely challenging for individual researchers to systematically collect, and continually update, all the available information on genes and mutants related to plant male reproduction. The aim of this study is to manually curate such gene and mutant information and provide a web-accessible resource to facilitate the effective study of plant male reproduction.
Plant Male Reproduction Database (PMRD) is a comprehensive resource for browsing and retrieving knowledge on genes and mutants related to plant male reproduction. It is based upon literature and biological databases and includes 506 male sterile genes and 484 mutants with defects of male reproduction from a variety of plant species. Based on Gene Ontology (GO) annotations and literature, information relating to a further 3697 male reproduction related genes were systematically collected and included, and using in text curation, gene expression and phenotypic information were captured from the literature. PMRD provides a web interface which allows users to easily access the curated annotations and genomic information, including full names, symbols, locations, sequences, expression patterns, functions of genes, mutant phenotypes, male sterile categories, and corresponding publications. PMRD also provides mini tools to search and browse expression patterns of genes in microarray datasets, run BLAST searches, convert gene ID and generate gene networks. In addition, a Mediawiki engine and a forum have been integrated within the database, allowing users to share their knowledge, make comments and discuss topics.
PMRD provides an integrated link between genetic studies and the rapidly growing genomic information. As such this database provides a global view of plant male reproduction and thus aids advances in this important area.
KeywordsPlant male reproduction Database Gene Mutant Pollen Anther
Male reproduction is a complex and highly coordinated biological process that includes the development of the male reproductive organ, the stamen, that contain the microspores/pollen, as well as subsequent pollen release, pollination, pollen tube growth, guidance, reception, gamete migration and finally fertilization [1–6]. The stamen comprises an anther with multiple specialized cells/tissues for the production of viable pollen and a filament that supports the anther. Microspore/pollen development requires meiotic and subsequent mitotic divisions, and numerous cooperative functional interactions between the gametophytic and sporophytic tissues within the anther. Pollen development needs precise spatiotemporal expression of genes, orchestrated activity and localized control of enzymes, cell-to-cell communication, cell development and differentiation [2, 6]. Furthermore, disruption of gene expression by environmental effects, or genetic mutations, frequently results in reduced fertility, or complete male sterility, causing loss of agricultural yield. Control of plant fertility is also of economic importance with some male sterile lines used in agriculture for crop improvement, for example in breeding of super hybrid rice .
Due to the importance of male reproduction, much effort has been applied to understand the molecular regulation of plant male reproduction. Transcriptome analysis has indicated that more than 20,000 genes are expressed in rice (Oryza sativa) developing anthers and about 18,000 in Arabidopsis (Arabidopsis thaliana) pollen [8–10]; suggesting extensive gene expression changes during anther development and pollen formation . Furthermore, recent forward and reverse genetic studies have identified a large number of male sterile mutants and related genes [1, 12, 13]. However, it is time-consuming and inefficient for individual researchers to access accurate information on male reproduction in plants. This is particularly relevant in the context of comparative analysis between species.
To bridge the gap between genetic studies and genomic information in plant male reproduction, we systematically collected male sterile mutant and gene information by manual curation, and created the PMRD (Plant Male Reproduction Database) database. This database provides a bi-directional integration of the rapidly growing genomic data and knowledge from genetic studies, which will undoubtedly improve our understanding of the mechanisms of plant male reproduction. PMRD functions not only as a high quality curated database for browsing and retrieving knowledge on genes and mutants in plant male reproduction, but also as a dynamic website with build-in bioinformatics tools to access genomic information. Moreover, PMRD is designed with knowledge sharing features that include wiki and forum tools to facilitate community annotation, information sharing and education.
Construction and content
Collection of plant male reproduction related genes
PMRD current data status
Other (31) species
Data entry and curation
Curation of information from publications into a well-structured searchable repository of knowledge is a critical step in biological database construction. This included manual review of papers, identification of biological entities, definition of the experimental methods used, conversion of experimental results and phenotypic observations into a standard format, and summarizing gene function data. In the PMRD curation process, papers were initially examined and checked whether appropriate for inclusion as an MS/MR gene in PMRD. The criterion for inclusion as an MS gene was that mutation of the gene must cause defects in male reproduction. Once identified the full-name, gene symbol and a brief description of the gene were obtained. Information was collated associated with the gene product expression pattern, molecular and biological function. Genes in rice and Arabidopsis were then mapped onto RAP-DB and TAIR locus, and included in PMRD. For other species, gene names mentioned in the papers were used. Gene expression assays in both rice and Arabidopsis were curated in detail using controlled anatomy and stage vocabularies. If the papers included genetic or transgenic studies of mutants, the curators captured the following information: mutant names, mutated genes, mutagenesis methods, dominance, mutant phenotypes and male sterility categories. All curated information was checked and confirmed by senior experts in this field.
Database design implementation
Utility and discussion
Database web interface
Comparative functional genomics study is an emerging approach that relies upon the application of the vast accumulated knowledge available for model species to less characterized species. Recently, a number of comparative, or functional genomics websites for plants have been developed, such as PLAZA, Phytozome, the Floral Genome Project, MoccaDB, SolRgene and BRAD [19, 34–38]. As more plant genome sequences become available, it will be interesting to extend and apply the current knowledge in PMRD for comparative studies. Future versions of PMRD will provide cross-species tools for comparing and mining male reproduction related genes. Finally there is an urgent need for automatic literature curation, since manual text curation is a challenging job for annotators, which requires much expertise and devotion. A number of gateway databases for model species have adopted text-mining tools. The Mouse Genome Informatics has initiated a dictionary based text mining tool to help biocuration . Flybase has developed natural language processing and automatic experimental information categorization tools to aid curation [40, 41]. At the moment the data sources of PMRD are mostly literature from genetic and molecular studies. In such papers, information is often organized into discernable sections, such as initial characterization of a gene, gene expression assays, and morphological phenotype observations, etc. Two text-mining tools are currently available for the Arabidopsis [42, 43]; it is hoped that such text-processing software will be used in future updates and maintenance of the database.
Finally, plant male reproduction covers a wide range of biological processes and the improvement of PMRD requires continuous effort and community contributions. The first version of PMRD is based on data collected mainly from anther and pollen development. For future updates, we have opened online data collection tables to extend the detailed coverage of related topics.
Plant Male Reproduction Database (PMRD) is a comprehensive resource for browsing and retrieving knowledge about genes and mutants related to plant male reproduction. Currently, PMRD holds information for 4203 genes and 484 mutants associated with plant male reproduction across 33 plant species. The two major model plant species, rice and Arabidopsis, have the greatest number of entries and most detailed curation. The ultimate goal of the database is to extend this further to provide a dynamic and comprehensive information resource with associated data mining tools to aid research in plant male reproduction.
Availability and requirement
The PMRD database is freely accessible at .
Gene Expression Omnibus
Kyoto Encyclopedia of Genes and Genomes
- MR gene:
Male reproduction related gene
- MS gene:
Male sterile gene
The Rice Annotation Project Database
The Arabidopsis Information Resource.
We thank Prof. Hugh Dickinson, Prof. Weicai Yang, Prof. Chris Franklin, Dr. Bing Zhang, Prof. Lijia Qu, Prof. David Twell, Prof. Yaoguang Li, Prof. De Ye and Dr. Jie Xu for helpful discussions. We would also like to thank the BBSRC China Partnership Scheme for providing the opportunity to link together colleagues working in Plant Reproduction in the UK and China, and initiating the idea for a reproduction database.
This work was supported by Funds from the National Natural Science Foundation of China [31110103915 and 30830014 to DB.Z.]; from the National Basic Research Program of China [2013CB129602 to DB.Z.]; the Chinese Transgenic Project [2011ZX08012-002 to DB.Z]; the National 863 High-Tech Project [2011AA10A101 and 2012AA10A302 to DB.Z]; and a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions.
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