Performing Department
(N/A)
Non Technical Summary
A wide diversity of microbes live on or in the tissues of plants, including bacteria, fungi, nematodes and oomycetes. All of these microbes, whether beneficial or pathogenic (disease-causing), have developed mechanisms to neutralize the defense systems used by plants to protect themselves against infection. Understanding the similarities in the ways these diverse microbes attack plants will help us understand the vulnerabilities of plants to infection, which will in turn help design new and effective methods for controlling plant disease. Currently, genome projects focused on a variety of plant pathogenic microbes are uncovering large numbers of genes that the microbes may use to attack plants. However, because these genome projects are going on in different research communities, the terminology that is used to describe the functions of the genes varies so much that it is very difficult to compare the functions of genes in the different microbes. This project will
establish a standardized set of terms, called a Gene Ontology, for describing the functions of genes used by microbes that live in or on plants, including pathogenic microbes. The work of establishing the terms will be carried out in collaboration with the Gene Ontology Consortium, which is a group of institutions involved in creating standardized terms for describing all the functions of genes in living organisms. Members of many different research communities will be trained in the use of the standardized terms, through training workshops, internships, presentations at meetings, and on-line training documents.
Animal Health Component
(N/A)
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Goals / Objectives
Plant-associated microbes span diverse kingdoms of life, including bacteria, fungi, oomycetes, nematodes and viruses. These microbes have all evolved mechanisms to solve the same problem, namely how to evade, suppress or neutralize the defense systems of their plant hosts. However, our ability to identify these mechanistic similarities among diverse organisms is greatly impeded by the lack of a set of standard terms to describe how these microbes interact with plants. The overall goal of this project is to extend the Gene Ontology with terms describing molecular functions, biological processes and cellular structures used by bacteria, fungi, oomycetes and nematodes for establishing associations with plants. This work will greatly facilitate the exchange of information about plant-associated microbes from diverse kingdoms of life, across diverse database systems holding that information. This exchange of information will advance our knowledge of how microbes establish
associations with plants, and hence facilitate the improvement of technologies for protecting plants from pathogens and promoting the role of beneficial microbes. The specific aims of the project are: 1. As participants in the Gene Ontology (GO) Consortium and in collaboration with relevant research communities, develop new GO terms and relationships for products of genes implicated in plant-interactions in the bacterial pathogens, Erwinia chrysanthemi, Pseudomonas syringae pv tomato, Agrobacterium tumefaciens, Agrobacterium radiobacter and Agrobacterium vitis, the fungus Magnaporthe grisea, the oomycetes Phytophthora sojae and Phytophthora ramorum, and the nematode Meloidogyne hapla. 2. Use the terms to annotate genes implicated directly in plant association by experimental evidence and also genes implicated by bioinformatic approaches such as sequence similarity and divergence rates. Use evidence codes to indicate the basis for annotation. The annotation process will drive the
development of the lower level (i.e. more specific) terms. 3. Test and evaluate methods for automating the transfer of Plant-Associated Microbe (PAM) GO term annotations to genomes of other plant-associated microbes closely related to the lead species, namely Pseudomonas syringae pv. phaseolicola, Erwinia amylovora, Sinorhizobium meliloti, Fusarium graminearum, Hyaloperonospora parasitica and Heterodera glycines ESTs. 4. Create reference gene sets for the wider community to use in generating automated GO annotations that have improved quality and relevance for plant-associated microbes. 5. Carry out training and outreach activities to engage the wider microbial genomics community in the use of PAM GO terms for annotation, functional genomics, and education, including three annual training workshops.
Project Methods
The development of new Gene Ontology terms for plant-microbe associations (PAM GO terms) will be carried out within the infrastructure of the GO Consortium. To facilitate interaction with the wider user community a formal interest group within the Consortium entitled Plant-associated Microbes has been created. Coordination among annotators at the five participating institutions will be managed by: (a) a senior-level Project Coordinator; (b) regular planning and coordination meetings, including an annual planning workshop; (c) an archived mailing list through which all discussion of new terms will pass; (d) a web site through which interested community members can access the archived mailing list and contribute to the discussion of new terms; (e) rapid posting of proposed terms in the GO discussion forums. The project will focus on pathogenesis- and virulence-related genes because there is a paucity of GO terms addressing infection processes, and much ongoing functional
genomics research is focused on these processes. Term assignments will be manually curated for around 400-800 genes in each of the bacteria and 1000-3000 genes in the eukaryotes. Factors most directly involved in infection will be addressed first and then factors associated with the in planta lifestyle, for example, nutritional adaptations. Annotation will include stringently reviewing existing term assignments produced by electronic annotation, as well as efforts concentrated on genes for which no appropriate terms yet exist. Annotation of the genomes will be carried out using the community annotation software platforms already established at each participating institution. Manual annotation and assignment of GO terms will be based on the full range of information available to annotators in the literature and public databases, not just on sequence similarity. Standard GO evidence codes will be used. Community annotation will be used to review, correct and update the GO annotations
assigned by the PAMGO curators. Automated transfer of GO terms from manually annotated genomes to related genomes will begin with creation of a list of putative orthologous genes using a modified bi-directional best BLASTP hit procedure, in which a statistical procedure is used to flag gene pairs in which the percentage amino acid identity is marginal for the particular genome comparison. Marginal gene pairs will be manually curated to create a robust ortholog list. A sample of electronically transferred terms will be manually curated in order evaluate and refine the transfer procedure.