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Sequencing-Related NSF Grants Awarded June 19 — July 16, 2007

ATOL: Phylogenomics: A Genome Level Approach to Assembling the Bacterial Branches of the Tree of Life
Start date: May 1, 2006
Expires: September 30, 2007
Awarded amount to date: $388,722
Principal investigator: Jonathan Eisen
Sponsor: University of California-Davis
The aim of the project is to determine the evolutionary relationships between and within the major phyla of bacteria. This will be achieved by obtaining and interpreting complete genome sequences from members of seven or eight diverse bacterial groups that are not represented in current genome sequencing efforts. To sequence each genome, DNA will be broken into fragments and the DNA sequence of the fragments determined randomly. The resulting individual sequences will be assembled into one piece using computer software that recognizes overlaps between the different sequences. Any gaps left in the sequence will be filled in to produce a completed genome. Comparisons will then be made with existing genome databases to identify the genes present. A later stage of the project will involve lab-based studies to confirm the function of the sequenced genes. Some of these genes will be identified as potential phylogenetic markers — genes that are “especially useful” for measuring the evolutionary relationships between organisms. The evolutionary relationships between the different bacterial groups will be determined using evolutionary trees inferred from both individual phylogenetic markers, and whole-genome analyses that consider the presence or absence of all the genes in the genome.

Microbial Genome Sequencing: Shotgun Sequencing of Tetrahymena thermophila
Start date: June 1, 2006
Expires: September 30, 2007
Awarded amount to date: $791,949
Principal investigator: Jonathan Eisen
Sponsor: University of California-Davis
The primary goal of the project, a collaborative effort of the Institute for Genomic Research and the Tetrahymena research community, is the whole-genome shotgun-sequencing, assembly, and annotation of the expressed (macronuclear) T. thermophila genome. The project has three aims: To whole-genome shotgun sequence and assemble the macronuclear genome to a depth of 3.5-fold sequence coverage; annotate and analyze the genome sequence, including identification of putative genes, prediction of gene function, and other features standard for genomic analysis; and facilitate user-friendly and free access to the T. thermophila genome sequence and annotation by creating interlinked genome databases. This is a Microbial Genome Sequencing Award funded through a collaborative activity between the National Science Foundation and the Department of Agriculture. Funding for an additional 3-fold coverage has been obtained from the NIH, so the combined result of NSF and NIH support will be 6- to 7-fold coverage.

Population Genomics of Cold Adaptation in Poplar
Start date: July 1, 2007
Expires: June 30, 2008
Awarded amount to date: $481,659
Principal investigator: Matthew Olson
Sponsor: University of Alaska Fairbanks Campus
The project will develop population genetic tools for Populus balsamifera, or poplar tree, and use them to identify the genetic basis for phenotypic variation in bud set, an “important determinant” of cold adaptation and growth rate. The research also will test whether the same genes are responsible for variation and adaptive evolution of bud set in North American P. balsamifera and European P. tremula. The research will form the basis for the development of laboratory exercises in DNA sequence analysis, population genomics, and association mapping for undergraduate courses.

Single Copy Nuclear Genes in Basal Angiosperms
Start date: July 1, 2007
Expires: June 30, 2009
Awarded amount to date: $11,880
Principal investigator: Claude dePamphilis
Sponsor: Pennsylvania State University
Study focuses on DNA sequences 10 protein-coding genes in the nucleus of representative ancient flowering plants, including Amborella and Nuphar (yellow water lily); the magnolia relatives Persea (avocado), Aristolochia, and Liriodendron (tulip poplar); and an ancient monocot, Acorus (sweet flag). It will also study the “utility” of these genes for understanding relationships in flowering plants; evolutionary dynamics of duplicated copies of these genes in flowering plants; and molecular evolution of these genes following duplication. The research will produce protocols for using the DNA of nuclear genes in plant systematics.

Community Structure and Function of 8,000+ Year Old Microbial Mats from Antarctica
Start date: July 1, 2007
Expires: June 30, 2008
Awarded amount to date: $50,000
Principal investigator: Jenny Baeseman
Sponsor: Kent State University
The research project will examine dehydrated cyanobacterial mats from the McMurdo Dry Valleys in Antarctica that are at least 8,000 years old. Isolates from rehydrated mats will be analyzed for maximum growth conditions and compared to species isolated from present day mats. DNA extracted from ancient mats will be used to determine the evolutionary history of cyanobacteria in the Dry Valleys and compared to present day species. The genetic information gathered from this project will provide insights into the extent of evolution that occurred in cyanobacterial mat communities in the Dry Valleys over a 20,000-year period, linking temporal and genetic distance in this ecosystem.

The Scan

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The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.