NRSP-8: NAGRP Aquaculture Genome Program

Home Catfish Oysters Salmonids Shrimp Striped Bass


From: John Liu []
Sent: Mon, 10 Jul 2006 11:47:13 -0600
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

 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:

 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
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 (

 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 
which is now up running.  For details, contact Dr. Zhiliang Hu 

 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  In order to 
upload your papers to the database, go to Aqua-genomics community 
on-line directory, 
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.  For details, 
please contact Dr. Jim Reecy (

 Animal Genomics Software Archive:  NAGRP Bioinformatics group have set up 
an animal genomics software archive site for publicly shared software 
(  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 ( 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 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:

If you have any items to be shared among the members of the Aquaculture 
Genomics community, please drop a note to Dr. John Liu