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Introduction to PMGN

Because of their economic impact as plant pathogens, molecular, genetic and genomics studies are well advanced in Phytophthora species. These organisms have served as lead species for the entire Stramenopiles lineage, a major radiation of crown eukaryotes, distinct from plants, animals and fungi. The Phytophthora molecular genetics community has developed with a strong culture of collaboration and communication, and sharing of techniques and resources. With the recent blossoming of genetic and genomic tools for Phytophthora, many new investigators, from a variety of backgrounds, have become interested in Phytophthora molecular genetics. The goals of the Phytophthora Molecular Genetics Research Collaboration Network is to facilitate the integration of these investigators into the community and to further strengthen the cooperative culture of this community. A particular emphasis is placed on training and integrating junior faculty and faculty from institutions under-represented in the U.S. research infrastructure. The network's activities have been supported by a $497,467 grant (5/1/02 - 4/30/07 ) from the NSF Research Collaboration Networks in Biology program.

The proposed network is open to all researchers with an interest in Phytophthora molecular genetics, either at an experimental or a computational level. Investigators new to the field are especially welcome. Please contact Brett Tyler with a brief description of your research interests if you wish to become a member of the network.

Genome Annotation Workshop Series, Virginia Bioinformatics Insitute, August 2007.

Headlines

• Bioinformatics Workshop Series, Virginia Bioinformatics Institute, July 2008

July 14-16, 2008: Plant-Associated Microbe Gene Ontology (PAMGO) Training Workshop

The PAMGO Training Workshop will provide two days of lectures on genome annotation, including an introduction to the Gene Ontology and PAMGO and instruction on how to evaluate the reliability of gene models produced by gene prediction software, how to evaluate functional predictions produced by annotation software and how to use the Gene Ontology to accurately describe the functions of gene products. A third day will be devoted to hands-on exercises in annotation of genes involved in host-associated microbes. Examples for annotation will be chosen based on the interests of the participants. The workshop will be valuable to researchers working in animal-microbe interactions as well as plant-microbe interactions.

July 16-18, 2008: Oomycete Bioinformatics Training Workshop

The Oomycete Bioinformatics Workshop will provide a day of lectures introducing the wide variety of oomycete genomics and bioinformatics resources currently available followed by a two-day "mini-jamboree" in which participants will carry out in-depth comparisons of genes from the four oomycete genome sequences currently available: Phytophthora sojae, Phytophthora ramorum, Phytophthora infestans and Hyaloperonospora parasitica.

 

Travel Fellowships

Travel fellowships of up to $800 will be available to participants attending one of the workshops and of up to $1,000 for those attending both workshops. Faculty from predominantly undergraduate institutions, and graduate students from all institutions, are especially encouraged to apply. The deadline for fellowship applications is March 1, 2008.

Visit the Bioinformatics Workshop Series website for more details.

• Training Fellowships in Oomycete Genomics and Bioinformatics

We are pleased to announce a new program of training fellowships for the oomycete community.  These fellowships are funded by the new NSF Research Collaboration Networks grant to the community.  The new grant is focused on oomycete genomics, so the focus of the training program is on oomycete genomics and bioinformatics. Requests for molecular genetics training also will be considered if funds are available.

The deadline for applications is January 31, 2008.

Visit the Traineeships page for more details.

• Oomycete Molecular Genetics Workshop, UK 2008

The 2008 Oomycete Molecular Genetics Workshop will be held at the Birnam Institute from May 6-9, 2008. The Birnam House Hotel and the Atholl Arms are holding double/twin rooms for the nights of May 6, 7, and 8th.

Birnam is on the edge of the highlands and is a beautiful place. The River Tay flows through it (on its way to Dundee and SCRI), and there is a good chance you may see jumping salmon at that time of year. There's white water rafting, mountain biking and hill walking for the energetic and some very pleasant short walks for the others (The Hermitage, for example)!! There will be a half-day off into the program for you to enjoy the area.

Travel fellowships are available for students, postdocs and junior faculty from the US and developing countries. The deadline for travel fellowship applications is February 8, 2008.

Visit the Workshops page for registration and travel fellowship information.

• International Late Blight Conference Invitation, China 2008

GILB, CIP and the Chinese Academy of Agricultural Sciences (CAAS) are organizing a Third International Conference on Late Blight to be held in Beijing between April 3-6, 2008.  This conference builds on the earlier ones in Hamburg, Germany, in 2002 and Quito, Ecuador, in 1999. For more information and pre-registration visit: http://research.cip.cgiar.org/GILB/

• Release of the first full coverage assembly of the P. infestans genome

  The Broad Institute is pleased to announce public release of the first full coverage assembly (version 1.0) of the phytophthora infestans genome. The sequence can be found on our web site at www.broad.mit.edu/ annotation/genome/phytophthora_infestans. It will also be available in GenBank/EMBL/DDBJ under the accession AATU01000000 once the databases have uploaded the sequence and made it available.

  This assembly was generated from over 9x coverage of the genome. It includes 190 Mb of the estimated 242 Mb of the full genome. The remainder is believed to be mostly high copy repeat and tandem repeat sequences, as almost all of the unassembled sequences align at high identity to portions of the assembled genome. The N50, or weighted median, contig size is 44.4 kilobases (kb) and the N50 supercontig, or scaffold, is 1.57 megabases (Mb). The N50 represents the size of assembled sequence block for which 50% of the assembled bases are in a unit of that size or larger.

  Alignment of the available ESTs suggests that we are capturing ~95% of the unique protein coding sequence in the current assembly. Alignments of the ESTs are available on our web site. Full automated gene annotations will follow as they become available.

  We are very pleased to reach this important milestone in the phytophthora infestans project. We hope that this sequence will provide great value to the community in your research and looking forward to receiving feedback about the sequence.

• Hyaloperonopora parasitica draft genome sequence released

A provisional assembly of the Hyaloperonospora parasitica draft genome sequence has been released by the Washington university genome Sequence Center. The sequence may be downloaded from here. Blast searches of the sequence can be conducted with VBI Toolkit Blast Notes:

1. This is only a provisional assembly and is expected to contain many errors. An improved assembly will likely be released in Jan 2007.
2. No gene predictions have been made.
3. Use of the sequence is governed by WUGSCs data policy. In addition, the investigators responsible for creating the sequence (Brett Tyler, John McDowell, Jim Beynon and Sandra Clifton) reserve the right to publish the first genome wide analysis of the sequence. Please contact Brett Tyler if you have questions about this.

 

• Oomycete Gene Nomenclature Proposal

Download Gene Nomenclature

With the arrival of genome sequences of Phytophthora sojae, P. ramorum, P. infestans, P. capsici, and Hyaloperonospora parasitica as well as EST resources for several other oomycetes, a vast plethora of genes have suddenly become available to the community. This has generated a need to standardize the naming of oomycete genes in order to maximize the value of comparative genomics approaches. A proposal for standardized naming of oomycete genes has been developed by a committee representing the community with input from attendees at the 2006 meeting in Wageningen. The proposal can be downloaded here. Input is requested from community members. Please email your comments and suggestions to Howard Judelson by August 31, 2006. After that date, a final nomeclature recommendation will be created and forwarded to journals that publish papers on oomycete molecular genetics.