NRSP-8: NAGRP Aquaculture Genome Program
From: John Liu [mailto:firstname.lastname@example.org] Sent: Mon, 10 Jul 2006 11:47:13 -0600 To: email@example.com Subject: [aquaculturegenomics] Aquaculture genomics Newsletter 9 Aquatic Genome Workshop in Hawaii cancelled: The originally planned Aquatic Genome Workshop in Hawaii in October has been cancelled due to schedule conflicts with other conferences. In consideration that the next International Marine Biotechnology Conference (IMBC) is to be held soon after that in February 2007 in Eilat, Israel, the subject matters of the original Workshop have been arranged in the agenda of IMBC in Eilat. User Agreement CSP 06-SE-20 for "Sequencing of EST and BAC libraries for the Pacific oyster" is signed with JGI: Supported by the Community Sequencing Program of the Joint Genome Institute, the project will sequence up to 133 BAC clones which are positive for known genes (Cunningham et al. 2006 Mar. Biotech. In press), and 150,000 cDNA clones, both directions, from 5 or 6 cDNA libraries, spanning two pre-feeding larval stages, two feeding larval stages, and adult tissues. The plan is to have all of this completed by the fall. The Aquaculture Genomics community appreciates the support of JGI for aquaculture species. Please also join me to send congratulations to Dr. Dennis Hedgecock and the OGC Steering Committee including Drs. Pat Gaffney, Philippe Goulletquer, Ximing Guo, Kim Reece, and Greg Warr for their leadership and hard work to bring this application to a success. Particular appreciation also goes to Greg Warr and the South Carolina group for their efforts in lining up the BAC clones for sequencing, and Andy Gracey for help in lining up the cDNA libraries. Efforts of all OGC members for this project are greatly appreciated. US-EU workshop on the future of livestock genomics to be held in Brussels: A Workshop on the future of livestock genomics will be held in Brussels, Belgium during July 17-18, 2006. A tentative agenda can be found at: http://ec.europa.eu/research/biotechnology/ec-us/docs/eu-us_animal_genomics_en.pdf Aquaculture Genomics community hopes for eligibility for Functional Genomics funding in the next round of competition: USDA CSREES FY 2006 National Research Initiative (competitive grant program) information can be found at http://www.csrees.usda.gov/fo/fundview.cfm?fonum=1112 There was a good discussion at the last PAG Conference concerning the way the Program 43.0, Animal Genome is currently set up: Applied Animal Genomics, Tools and Reagents, Bioinformatics, and Functional Genomics (Functional Genomics will appear on alternate years beginning in FY 2006). For 2006 round of competition, the Functional Genomics Program is offered only for species with a 5x genome sequencing coverage. As a result, no aquaculture species is eligible for Functional Genomics funding. The Aquaculture Genomics community requests and appreciates considerations for changing this policy. Planning for next year's PAG is moving along. Dr. Dennis Hedgecock of the University of Southern California will be the next organizer for the Aquaculture Genomics Workshop to be held in San Diego next January. If you have any suggestions or comments concerning the format, organization, and invited speakers for the Workshop, please contact Dr. Hedgecock (firstname.lastname@example.org). NOAA National Marine Aquaculture Initiative fund linkage mapping project in striped bass: NOAA National Marine Aquaculture Initiative has recently approved funding of a project to produce a linkage map of the striped bass using microsatellite markers. Drs. Craig Sullivan, Charlene R. Couch, and Caird E. Rexroad III are principal investigators of the project. Aqua-genomics community on-line directory: The NRSP-8 Bioinformatics Group has helped us to set up An Aqua-genomics community on-line directory http://www.animalgenome.org/cgi-bin/angenmap/aqua_dir.pl, which is now up running. For details, contact Dr. Zhiliang Hu (email@example.com). Aquaculture Genomics community publication collection database is now in place: The NRSP-8 Bioinformatics Group has helped us to set up an Aquaculture Genomics community publication collection database http://www.animalgenome.org/cgi-bin/angenmap/aqua_pub.pl. In order to upload your papers to the database, go to Aqua-genomics community on-line directory http://www.animalgenome.org/cgi-bin/angenmap/aqua_dir.pl, Click the "notebook" icon to the right of your entry; Choose "To edit the profile by the owner"; Select "Upload Your Publications" (in PDF or other common file types); Login; Fill in needed info for a paper and browse for the file to upload; Click "upload" button. Bioinformatics utility tool box: The NRSP-8 Bioinformatics Group has developed a Bioinformatics utility tool box, at the NAGRP Bioinformatics site. Currently there are 6 utility tools in the "box": 1. Expeditor: Design primers gene structure and EST information from different species. 2. Prim2: Design primers on the consensus of 2 similar sequences. 3. A sequence alignment diagram drawing tool. 4. Gene ontology (GO) terms classifications counter. 5. DNA Sequence Reverse Complement Converter 6. Query the Bovine SNP Database by blast. http://www.animalgenome.org/bioinfo/resources/util/. For details, please contact Dr. Jim Reecy (firstname.lastname@example.org). Animal Genomics Software Archive: NAGRP Bioinformatics group have set up an animal genomics software archive site for publicly shared software (http://db.genome.iastate.edu/ftp/share/). Those who wish to share their software with the community, please feel free to contact us for information on how to deposit your software to this archive. The livestock sequence Blast server: A NAGRP Blast Server is now in service ( http://www.animalgenome.org/blast/) through the effort of the NAGRP Bioinformatics group. This blast server uses a local copy of NCBI blast suite, which includes bl2seq, blastall, megablast, blastpgp, blastclust, netblast, etc. The local sequence data sets include all non-human, non-mouse EST sequences from the GenBank, Whole Genome Shotgun (WGS) sequence assemblies for different organisms from Genbank. These data sets are updated from Genbank every night. The local sequence data sets also include TIGR Gene Indices for Cattle, Chicken, Pig, Salmon, Catfish, and Rainbow Trout. The TIGR Indices are updated weekly (done every Saturday night). Currently users can use the web server for their blast. Links to the blast server are included on each of the species pages under resources. World Aquaculture geneticists met in France: The Ninth International Aquaculture Genetics Conference was held in Montpellier, France in June 25-30, 2006 with over 200 geneticists from all over the world. The topics covered can be found from http://www.mediaqua.fr/IAGA/web/program.htm The proceedings will be published in a special issue of Aquaculture. The Aquaculture Genomics community appreciates the effort of Dr. Béatrice Chatain and her organizing committees for their hard work and congratulates them for the success of the meeting. Postdoctoral Fellow position available for fish genomics: A postdoctoral fellow position is available at West Virginia University to work with Caird Rexroad. For details, please visit: http://aaas.sciencecareers.org/texis/jobsearch/details.html?id=448891f64a0420&q=molecular%20biology&pp=25&view=1&page=1 If you have any items to be shared among the members of the Aquaculture Genomics community, please drop a note to Dr. John Liu (email@example.com).