Virginia Bioinformatics Institute workshop series focused on microbial gene sequence annotation
The Virginia Bioinformatics Institute (VBI) recently hosted a series of bioinformatics workshops centered on the theme of microbial gene sequence annotation.
The VBI Genome Annotation Workshop Series included workshops on Plant-Associated Microbe Gene Ontology (PAMGO) training, Oomycete Bioinformatics Resources training, and the Hyaloperonspora parastitica Genome Sequence Annotation Jamboree.
The PAMGO and Oomycete Bioinformatics workshops, which were held concurrently on August 8-10, involved presentations on structural and functional genomics and included in-depth discussions of the Gene Ontology and use of PAMGO terms in the annotation and analysis of gene products from microbes that associate with plant and animal hosts. Other sessions were devoted to hands-on exercises in association with literature and sequence/structural similarity-based PAMGO annotations. The Oomycete Bioinformatics workshop, supported by the NSF-funded oomycete molecular genetics research collaboration network, provided overviews of resources and tools used for annotation and analysis of oomycete genomic sequences, as well as hands-on training in their use. The workshops were attended by 26 participants including nine graduate students.
The Hyaloperonspora parasitica Genome Annotation Jamboree was a four-day workshop focused on analyzing the newly available draft genome sequence of the oomycete, which is a pathogen that causes downy mildew disease of the model plant Arabidopsis. The jamboree included presentations of the biology of H. parasitica, genomic resources currently available and tools for sequence annotation and analysis. Attendees divided into groups to participate in several days of manual annotation, which focused on specific topic areas such as pathogenicity, metabolism and genome organization. The jamboree was attended by 31 participants from six countries, including 13 graduate students.
About PAMGO
The PAMGO interest group was formed to develop new gene ontology (GO) terms describing the various processes, functions and cellular components related to microbe-host interactions. Plant-associated microbes have evolved similar mechanisms to evade, neutralize or suppress defense systems of their plant hosts and obtain nutrients. Such similarities can only be discovered if a controlled vocabulary is set in place to describe these processes amongst diverse microbe-host interactions. The PAMGO consortium is a collaboration between the Virginia Bioinformatics Institute, Cornell University, North Carolina State University, the University of Wisconsin-Madison, The Institute of Genomic Research (TIGR; a Division of the J.C. Venter Institute), and Wells College. The group works closely with the Gene Ontology Consortium. PAMGO is funded by the United States Department of Agriculture’s National Research Initiative-Cooperative State Research, Education and Extension Service and the National Science Foundation through the joint USDA-CSREES/NSF Microbial Genome Sequencing program. For more information, visit pamgo.vbi.vt.edu.
About the Hyaloperonospora parasitica Genome Sequencing Consortium
Downy mildew diseases cause billions of dollars of agricultural losses each year. H. parasitica infection of the model plant Arabidopsis thaliana is an important model for studying downy mildew diseases, and the defense responses of plants in general. The draft genome sequence of H. parasitica has been developed by an international consortium consisting of the Virginia Bioinformatics Institute and the Department of Plant Pathology, Physiology and Weed Science at Virginia Tech, the Washington University Genome Sequencing Center, Warwick University in the United Kingdom and The Wellcome Trust Sanger Institute in the United Kingdom. It is funded by grants from the United States Department of Agriculture’s National Research Initiative-Cooperative State Research, Education and Extension Service and the National Science Foundation through the joint USDA-CSREES/NSF Microbial Genome Sequencing program, and the British Biotechnology and Biological Sciences Research Council (BBSRC).
About the Oomycete Molecular Genetics Research Collaboration Network (OMGN)
OMGN is an international collaborative of researchers interested in oomycete molecular genetics and genomics. The goals of the collaborative are to promote communication, cooperation and the sharing of resources within the community, promote the involvement of a broad diversity of community participants, and facilitate the entry of junior researchers into the field. The network provides travel fellowships, training internships and training workshops. It is supported by grants from the National Science Foundation’s Research Collaboration Networks in Biology program. For more information, visit pmgn.vbi.vt.edu.
