Large Scale Genome Sequencing Projects

Over the last few years, a growing number of large scale genome sequencing projects has been launched, either by individual PIs, or by Institutes, of by Funding Centers. A list of those that has come to our attention is below.

The "Genome 10K" project aims to understand the genetic basis of evolutionary processes, and the organizers have already compiled a virtual database of existing sample collections of more than 16,000 vertebrate species. Last week, they published an outline of the project in the Journal of Heredity.

Consortium leader David Haussler, a professor of biomolecular engineering at the University of California, Santa Cruz, said the project will cost an estimated $50 million to $100 million in total, including approximately $30 million in sequencing costs. More.

A genome project aiming to build a whole-genome sequence map for 10,000 microbes in 3 years took off on Aug. 1 in China's southern city Shenzhen.

The project covers several research areas including industrial microorganism, agricultural microorganism, medical microorganism, etc. Archaebacteria, germ, epiphyte, origin organism, algae and virus will all be studied.

As the microbe branch of BGI-Shenzhen's "The Tree of Life Project" (BGI, Beijing Genomics Institute), the plan is supported by several top genome institutes, universities and enterprises such as Biotechnology Research Institute of the Chinese Academy of Agricultural Sciences and the Tianjin Institute of Industrial Biotechnology of Chinese Academy of Sciences.

BGI

The 1001 Genomes Project has a simple goal: to discover the whole-genome sequence variation in 1001 strains (accessions) of the reference plant Arabidopsis thaliana. The resulting information will pave the way for a new era of genetics that combines large-scale association studies in wild strains with forward genetic analyses in experimental crosses, in order to identify alleles underpinning phenotypic diversity across the entire genome and the entire species. The analyses enabled by this project will have broad implications for areas as diverse as evolutionary sciences, plant breeding and human genetics.

Drawing on the expertise of multidisciplinary research teams, the 1000 Genomes Project will develop a new map of the human genome that will provide a view of biomedically relevant DNA variations at a resolution unmatched by current resources. As with other major human genome reference projects, data from the 1000 Genomes Project will be made swiftly available to the worldwide scientific community through freely accessible public databases.

1001 Genomes

An international research consortium has been formed to create the most detailed and medically useful picture to date of human genetic variation. The 1000 Genomes Project will involve sequencing the genomes of at least a thousand people from around the world. The project will receive major support from the Wellcome Trust Sanger Institute in Hinxton, England, the Beijing Genomics Institute Shenzhen in China and the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH).

Drawing on the expertise of multidisciplinary research teams, the 1000 Genomes Project will develop a new map of the human genome that will provide a view of biomedically relevant DNA variations at a resolution unmatched by current resources. As with other major human genome reference projects, data from the 1000 Genomes Project will be made swiftly available to the worldwide scientific community through freely accessible public databases.

1000 Genomes

Sanger

BGI

NHGRI

The most basic aspects of human development and genetic structures can be mapped back to the common single-celled ancestors that animals shared with fungi. How did multicellularity evolve? What are the genes and gene families associated with the advent of multicellularity? How does this compare between two different major clades that underwent this transition (animals and fungi)? The comparison of these organisms to protists will provide the most complete picture of basic developmental mechanisms.

Selected divergent fungal, animal, and protest genomes will be sequenced at high coverage for the purpose of comparative analysis. The organisms selected for sequencing will fill crucial gaps in the knowledge of animal and fungal evolution. A complete rationale for this initiative is available at Animals and Fungi: Common Origin, But Independent Approaches to Multicellularity

To see the current OMP projects that are reported on GOLD, go to GOLD's Search page, and select the term <Origins of Multicellularity Project (OMP)> at the Relevance search field.

OMP

NHGRI

To take advantage of recent technological advances and to develop new ones, the NIH Roadmap has initiated the Human Microbiome Project (HMP) with the mission of generating resources enabling comprehensive characterization of the human microbiota and analysis of its role in human health and disease." [http://nihroadmap.nih.gov/hmp/].

The Human Genome Sequencing Center at the Baylor College of Medicine has joined the Genome Sequencing Center at Washington University, the Broad Institute of MIT and Harvard as well as the J. Craig Venter Institute to address some early goals of this project. The HMP will rely on metagenomic sample sequencing as a key method for comparisons of microbial communities between individuals, sites, and states (e.g., disease, diet, age). Pilot projects will determine the appropriate sequencing platforms, quality controls, and annotation pipelines for (1) generating reference genomes and (2) sequencing metagenomic samples. (see white papers)

To see the current HMP projects that are reported on GOLD, go to GOLD's Search page, and select the term <Human Microbiome Project (HMP)> at the Relevance search field.

HMP

NHGRI

BCM-HGSC

WashU

Broad

JCVI

Wikipedia

The Genomic Encyclopedia of Bacteria and Archaea (GEBA), launched on May 2007 by the Department of Energy (DOE) - Joint Genome Institute (JGI) The GEBA project aims the systematic filling in the sequencing gaps along the bacterial and archaeal branches of the tree of life and represents the first systematic attempt to use the tree of life itself as a guide for sequencing target selection. To test the feasibility of such a large scale project, DOE-JGI has initiated a pilot project to sequence 100 bacterial and archaeal organisms based on their phylogenetic position in the tree of life. The GEBA pilot project is carried out in collaboration with the German Resource Centre for Biological Material (DSMZ), which provides the DNA for the selected organisms.

To see the current GEBA projects that are reported on GOLD, go to GOLD's Search page, and select the term <GEBA> at the Relevance search field.

GEBA

DOE-JGI

DSMZ

The Human Gut Microbiome Initiative (HGMI) is running at the Genome Sequencing Center of the Washington University in St. Louis. HGMI aims to provide deep draft genome sequences for 100 cultured representatives of the phylogenetic diversity documented by 16S rRNA surveys of the human gut microbiota.

To see the current HGMI projects that are reported on GOLD, go to GOLD's Search page, and select the term <Human Gut Microbiome Initiative (HGMI)> at the Relevance search field.

HGMI

Proposal

The Saccharomyces Genome Resequencing Project (SGRP), is a collaboration between the Sanger Institute and Prof. Ed Louis' group at the Institute of Genetics, University of Nottingham. Our goal is to advance understanding of genomic variation and evolution by analysing sequences from multiple strains of the two Saccharomyces species, S cerevisiae and S paradoxus.

To see the current SGRP projects that are reported on GOLD, go to GOLD's Search page, and select the term <Saccharomyces Genome Resequencing Project (SGRP)> at the Relevance search field.

SGRP

Sanger

Phase one of the project was initiated in Fall 2004 with a grant to the J. Craig Venter Institute (JCVI). Auto-annotated genome sequences are deposited in GenBank, the NIH genetic sequence database.  For further information, see the J.Craig Venter Institute's Marine Microbial Genome Sequencing Project.

To see the current MMI projects that are reported on GOLD, go to GOLD's Search page, and select the term <Marine Microbial Initiative (MMI)> at the Relevance search field.

MMI

Moore F.

JCVI

The Fungal Genome Initiative (FGI) is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes being governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers not only the value of data from each organism given their role in basic research, health, agriculture, and industry, but also their value in comparative genomics.

FGI produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. Over 25 fungi have been sequenced or are being sequenced, including human and plant pathogens as well as fungi that serve as basic models for molecular and cellular biology.

Broad