NAGRP Aquaculture Genome Projects

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From: "John Liu" []
To: "aquaculturegenomics" []
Cc: "Grant Burgess" []
Subject: [aquaculturegenomics] Aquaculture genomics Newsletter 34
Date: Tue, 02 Sep 2013 17:14:55 -0600

 Aquaculture Genomics Workshop Call for Abstract Submissions: The
International Plant & Animal Genome XXII meeting is January 11-15, 2014, in
San Diego, CA, USA ( The aquaculture genomics community
will gather for a 1.5 day workshop on the January 11th and 12th. In addition to 
invited plenary speakers, additional workshop speakers will be chosen by the 
committee from abstracts submitted directly via e-mail to the Aquaculture 
Genomics Workshop Chair, Dr. Steven Roberts ( In order to be
selected for an oral presentation, you must meet the abstract submission 
deadline of September 30, 2013. Please note that all abstracts (for both oral 
and poster presentations) must also be submitted directly to PAG. Abstracts 
being considered for an oral presentation will be reviewed by committee after 
the September 30, 2013 internal deadline, and those selected for oral 
presentations will be notified in October 2013. At this time, selected speakers 
will be instructed on how to properly register on the PAG website. Abstracts 
will be judged on both the scientific quality of the abstract, and interest to 
USDA National Animal Genome Project (National Research Support Project NRSP-8) 
aquaculture species stakeholders. For additional information please visit

 Aquaculture Genomics Workshop Travel Awards: The Aquaculture Genomics group 
of the NRSP-8 is pleased to announce the availability of a limited number of 
travel awards, of up to $1000, to support the attendance of graduate students
and postdoctoral fellows at PAG XXII in San Diego, CA. All full-time graduate
students and postdoctoral fellows who submit an abstract to the Aquaculture
Genomics Workshop are eligible for consideration with the following restrictions:
a graduate student can only receive a travel award once, and a maximum of two
travel awards will be granted to a single PI¡¦s group. Applicants should submit t
a completed application available at Deadline
for applications is October 15th, 2013 and applications should be sent via e-mail
to Steven Roberts ( Please note that travel award applicants
must also arrange for their supervisor to send an e-mail confirming their status 
as a current graduate student or postdoctoral fellow. For additional information
please visit

 Draft Rainbow Trout Genome Sequences: The new rainbow trout draft genome 
assembly headed by Mike Miller (UC Davis) is available on the NAGRP data 
repository. The assembly was from 13,824 out of the 14,900 MTP BAC clones in 
1,152 pools that represent approximately 50X sequence coverage per BAC. The 
assembly is estimated to cover ~70% of the rainbow trout genome.
The sequences are also available for blast on the NAGRP blast server.

 The NRSP8 Animal Genome Project has been renewed for 2013-2018 with
the following objectives:

Objective 1: Advance the status of reference genomes for all species, including
basic annotation of worldwide genetic variation, by broad sequencing among
different lines and breeds of animals.

Objective 2: Develop strategies to identify and exploit genes and allelic variation
that contribute to economically relevant phenotypes and traits, in part through
improving functional annotation of the genomes of our species.

Objective 3: Facilitate analysis, curation, storage, distribution and application 
of the enormous datasets now being generated by next-generation sequencing and 
related "omics" technologies with regard to animal species of agricultural 
interest.  Dr. John Liu of Auburn University and Dr. Caird Rexroad of the USDA 
National Center for Cool and Cold Water Aquaculture have been selected to serve 
as Coordinators for the Aquaculture portion of this project. Aquaculture 
represents many species, therefore we are seeking investigators to from US 
institutions to serve as Species Leaders for the following duties:

1) Identifying uses of Coordinator funds that benefit individual species groups;

2) Assisting Workshop Organizers with finding speakers, judging student
   abstracts for travel awards, etc;

3) Assembling the annual report for your species group;

4) Attending PAG at least every other year.

Dr. Yniv Palti, Dr. Sylvie Quiniou, and Dr. Craig Sullivan have agreed to continue
to serve as Species Leaders for Salmonids, Catfish, and Striped Bass, respectively. 
We are asking for those who are interested in serving as species leaders for Shrimp, 
and for Oysters to reply to Caird and John with Name, Affiliation, species that 
would be represented and a listing of the corresponding research community.

The NRSP8 Aquaculture Coordinators provided research support for four projects: Through open competition, four projects received funds from NRSP-8 Aquaculture Coordinators. These projects are entitled: 1) Improving the Rainbow Trout Genome Assembly using Moleculo Technology (P.I. Michael Miller, University of California Davis); 2) A flexible Platform for Querying Disparate Oyster Datasets (qDOD) (P.I. Steve Roberts, University of Washington); 3) NRSP-8 Research Support Funds for Moronid Reference Transcriptomes (P.I. Adam Fuller, USDA ARS); and 4) Assessing Demographic and Evolutionary Relationships between Shrimp Populations by Sequencing a Shrimp Diversity Panel (P.I. Zhiqiang Du and Max Rothschild, Iowa State University).

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