NAGRP Aquaculture Genome Projects

From: "John Liu" [liuzhan@auburn.edu]
To: "aquaculturegenomics" [aquaculturegenomics@acesag.auburn.edu]
Cc: "Grant Burgess" [Grant.Burgess@newcastle.ac.uk]
Subject: [aquaculturegenomics] Aquaculture genomics Newsletter 24
Date: Mon, 28 Dec 2009 22:41:20 -0500

Program for PAG Aquaculture 2010: Program for PAG Aquaculture 2010 (January 9-10, 2010) has been set and may be found at http://www.intl-pag.org/18/18-aqua.html.

Invited Speakers for The PAG Aquaculture 2010 Workshop: The PAG Aquaculture Workshop will be held in San Diego 9-10 January 2010. Invited speakers will include Dr. Jerry Dodgson (Michigan State University), Dr. Scott LaPatra (Clear Springs Foods, Inc.), and Dr. Derek Stemple (The Sanger Institute). Dr. Jerry Dodgson's lecture is entitled "Comparative Genome Sequencing: Low Price, High Value"; Dr. Derek Stemple's lecture is entitled "RNAseq Annotation of the Expressed Zebrafish Protein-Coding Genome"; and Dr. Scott LaPatra's lecture is entitled "Selective Breeding of Food Size Rainbow Trout: Current and Future Prospects".

Ten graduate students/postfdoctoral Fellows win Aquaculture Genomics Travel Award: As in the past years, the aquaculture genome community spent a significant proportion of its funds to support graduate students/post doctoral fellows to come to the PAG meeting. Ten students win the Aquaculture Genomics Travel Award. They are: Jason Abernathy of Auburn University, Marije Booman of Memorial University, Berenice Bougas of University of Laval, Zhi-Qiang Du of Iowa State University, Paolo Franchini of Stellenbosch University, Jianguo Lu of Auburn University, Nicole Quinn of Simon Fraser University, Filipe Reyes of University of Santiago, Ruhan Slabbert of Stellenbosch University, Jose Yanez of University of Chile.

Annual report is due: NRSP-8 participants are required to provide an annual report. Please submit your progress report to your species coordinators (catfish: Sylvie Quiniou; salmonids: Yniv Palti; Tilapia: Thomas Kocher; Striped bass: Craig Sullivan; oysters: Pat Gaffney; and Shrimps: John Benzie) to include progress toward the three objectives:

Objective 1: Enhance and integrate genetic and physical maps of agriculturally important animals for cross species comparisons and sequence annotation;

Objective 2: Facilitate integration of genomic, transcriptional, proteomic and metabolomic approaches toward better understanding of biological mechanisms underlying economically important traits;

Objective 3: Facilitate and implement bioinformatic tools to extract, analyze, store and disseminate information.

In addition, please provide a list of publications and a list of funds obtained through various venues including competitive grants from USDA and other federal agencies, industry grants, and commodity grants. The directors of Agricultural Experiment Stations need to know what levels of leverage activities we have been engaged to justify their support for NRSP-8 funds

The Oyster Genome Consortium’s community sequencing project with the DoE Joint Genome Institute was completed, with the delivery of high quality, Sanger sequencing paired-end reads for 37.5k cDNA clones, nearly a million 454 sequences from larval cDNA, and finished sequences from 58 BAC clones from the Pacific oyster (Crassostrea gigas) and two BACs from the eastern oyster (C. virginica).

The EST sequences are in preparation for submission to GenBank by 1 March 2010. Sequences for the 60 BAC clones were submitted to GenBank in December, 2009, with a public release date of 1 March 2010.

The cDNA clones sequenced by the Sanger method were obtained from four larval and three mixed adult tissue libraries. The bulk of the sequences were obtained from the adult libraries, which comprised tagged and pooled cDNA from two inbred lines. The average length of cDNAs in the libraries is 2.5 kb. The objectives of the EST sequencing were gene discovery and SNP identification within and between the inbred lines. The sequences, which average 678 bp in length, have been clustered and aligned against a variety of databases, including the compilation of C. gigas ESTs managed by INRA, Toulouse, FR (http://publiccontigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html) and the genome of the limpet Lottia gigantea at JGI (http://genome.jgi-psf.org/Lotgi1/Lotgi1.home.html). Nearly 12,000 clones, representing unigenes with good BLAST hits, will be resequenced by Illumina Genome Analyzer in January 2010, to provide a full-length cDNA resource. SNP candidates are currently being generated from the EST for analysis by Illumina Golden Gate Assay in mapping families and a panel of divergent stocks and closely related species.

The BAC clones were selected on the basis of positive hybridization to EST-based probes representing eight genes of interest (metallothionein (both species), transforming growth factor beta, tissue-induced metalloproteinase, VAV guanine nucleotide exchange factor, inhibitor protein kB, beta proteasome subunit LMPX, coagulation factor, and adaptor protein MyD88). For each set of BACs, contigs have been assembled, representing one or two haplotypes. For gene identification in the contigs we have relied largely on the extensive EST database recently finished by JGI (see above), as well as the Gigasbase and EST NCBI databases. Alignment of allelic contigs has allowed us to identify numerous macroindels and polymorphisms, the former often representing putatively active transposable elements of various classes (LTR- and non-LTR retrotransposons and DNA transposons, including pearl and MITEs), the latter including microindels, micro- and minisatellites, and single nucleotide polymorphisms. The extensive polymorphism observed is comparable to that reported for the ascidian Ciona, and is undoubtedly causing the difficulties, reported by the Chinese whole genome sequencing project, in assembling nearly 100x genome coverage obtained by Illumina Genome Analyzer sequencing. For more information of the oyster EST and BAC sequencing project, please contact Drs. Dennis Hedgecock and Patrick Gaffney.