Introduction to OMGN
Because of their economic impact as plant pathogens, molecular,
genetic and genomics studies are well advanced in many oomycete
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 oomycete molecular
genetics community has a strong culture of collaboration and
communication, and sharing of techniques and resources. With the
recent blossoming of genetic and genomic tools for oomycetes, many
new investigators, from a variety of backgrounds, have become
interested in oomycete molecular genetics and genomics. The goals of
the Oomycete 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 two grants from the NSF Research Collaboration Networks in Biology
program.
The proposed network is open to all researchers with an interest in
oomycete molecular genetics and genomics, either at an experimental
or a computational level. Investigators new to the field are always
welcome, especially those interested in saprophytes and animal
pathogens. Please email Brett Tyler with a brief description of your
research interests if you wish to become a member of the network.
2009 Asilomar Meeting attendees.
Headlines
-
Third Oomycete Bioinformatics Training workshop June 3-5, 2009
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 five oomycete genome sequences Phytophthora sojae, Phytophthora ramorum, Phytophthora infestans, Hyaloperonospora arabidopsidis and Pythium ultimum.
Registration deadline May 20.
Travel fellowships of up to $850 will be available to participants. Faculty from predominantly undergraduate institutions, and graduate students from all institutions, are especially encouraged to apply. Deadline March 31, 2009. Applications received after the deadline will be considered only if funds remain.
For further information including registration and fellowship applications visit:
oomycete2009.vbi.vt.edu/index.php
-
2010 Oomycete Molecular Genetics Meeting, June 6-8, Toulouse, France
The next Oomycete Molecular Genetics Meeting will be organized by Arnaud Bottin (arnaud.bottin@neuf.fr), Bernard Dumas and Elodie Gaulin of the Université Paul Sabatier, Toulouse, France.
The draft program is available here.
The program and abstracts for the 2009 Asilomar meeting can be found here.
-
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:
- This is only a provisional assembly and is expected to contain many errors. An improved assembly will likely be released in Jan 2007.
- No gene predictions have been made.
- 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
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.