Norwegian Consortium Assembles, Annotates Cod Genome from 454 Data

November 03, 2009

The cod is among the first vertebrates to have its genome assembled entirely from next-generation shotgun sequencing data. In a second project phase, which may also involve short-read sequencing technologies, the researchers plan to fill in gaps in the genome, improve the annotation, and sequence the transcriptomes and genomes of additional cod samples from different geographic areas.

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Young Investigator Profile

Long Cai

Assistant Professor
California Institute of Technology

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Blog

Higher Fees, Faster Service

The US Food and Drug Administration and medical device companies reach a deal to speed up the review process.

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Papers of Note

Chromosome-Scale Selective Sweeps and Genomic Diversity in C. elegans
Andersen, Gerke et al., Nature Genetics
Researchers at Princeton University and elsewhere discuss the effects of chromosome-scale selective sweeps on genomic diversity in Caenorhabditis elegans. Taking a high-throughput selective sequencing approach on a collection of 200 wild C. elegans strains, the team found that the nematode's "genome variation is dominated by a set of commonly shared haplotypes on four of its six chromosomes, each spanning many megabases." Further, the team reports on its population genetic modeling experiments, which showed that "this pattern was generated by chromosome-scale selective sweeps that have reduced variation worldwide; at least one of these sweeps probably occurred in the last few hundred years," it writes.

Dissecting the Regulatory Architecture of Gene Expression Quantitative Trait Loci
Gaffney, Veyrieras et al., Genome Biology
A team led by investigators at the University of Chicago this week report their use of a "Bayesian hierarchical model to estimate the enrichment of eQTLs [expression quantitative trait loci] in a wide variety of regulatory annotations" derived from 1,000 Genomes Project data. "We find that [approximately] 40 percent of eQTLs occur in open chromatin, and that they are particularly enriched in transcription factor binding sites, suggesting that many directly impact protein-DNA interactions," the authors write.
People on the Move

Life Technologies this week named Alan Sachs as head of global research and development and Ronnie Andrews as president of medical sciences.

Sachs was previously the vice president of exploratory and translational sciences for Merck Research Laboratories, where he spent 10 years in various leadership roles, Life Tech said. Prior to that Sachs served an associate professor of biochemistry and molecular biology at the University of California, Berkeley, and as a Whitehead fellow at the Whitehead Institute for Biomedical Research.

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Stephen O'Brien has left the National Cancer Institute's Laboratory of Genomic Diversity after 25 years to help launch a genome bioinformatics program at St. Petersburg University in Russia. O'Brien received a $5 million grant from the Russian Ministry of Education and Science last year under a program that aims to lure big-name researchers to Russia. Over the coming three years, O'Brien will spend at least four months per year in Russia working at the center, which is scheduled to open in May.

Saladax Biomedical said today that President and CEO Edward Erickson has resigned due to personal and family reasons, and that he will be replaced by Kevin Harter on an interim basis. Erickson will remain a member of the company's board of directors. Harter is a co-founder and senior VP of the Life Sciences Greenhouse, and he has served as executive chairman at Saladax.
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Norwegian Consortium Assembles, Annotates Cod Genome from 454 Data

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