Genome Project Solutions
This is a sample of the projects we have underway or have recently completed:
Oomycete Genomes Project. This is an evolutionary analysis of all gene families of seven completely sequenced genomes (five oomycetes and two diatoms), the creation of colinearity maps for all homologous genes, and linking to information on gene structure and function. Our News section has more information on the funding of this work and on our reaching our latest milestone.
Oomycete Genomes Project Homepage.
GATOR ("Genome Analysis Tools and Online Resources"). With today's sequencing cost and capability, any eukaryotic genome project can easily have a very large number of EST sequences to get very accurate gene structural models. Our whole genome evolutionary analysis assigns orthology much more accurately than the error-prone distance-based methods in common usage. These factors combine to make the standard genome browser format an anachronism. We are building a genome presentation system that will facilitate biological discovery even for those without strong programming skills. Get more details.
PHRINGE ("Phylogenetic Resources for the Interpretation of Genomes"), is a set of methods for whole-genome evolutionary analysis and forms part of the GATOR system. PHRINGE determines the orthologous and paralogous relationships of all genes in sets of completely sequenced genomes, allowing the most accurate possible inference of gene functions and the reconstruction of patterns of gene duplications and losses. Users can see the multiple sequence alignments and phylogenetic trees of all genes, compare intron-exon structures, and see the relative arrangements of homologs across all genomes. We have used these methods for interpretations of several whole genome sequencing projects, including those of the oomycetes Phytophthora sojae and Phytophthora ramorum, the crustacean Daphnia pulex, and the frog Xenopus tropicalis. PHRINGE was developed from an earlier product called "PhIGs"; a published manuscript describes that work.
For more information, see the PHRINGE Overview Page, read about details of the PHRINGE Pipeline, or read about why it is important to use evolutionary analysis to identify orthologs.
Genome of Daphnia pulex. The first crustacean to have a complete genome sequence is Daphnia pulex, recently sequenced by the DOE Joint Genome Institute (JGI). Our scientists are playing a leadership role in interpreting this genome and coordinating the publications that will describe it.
Learn more about the Daphnia Genome Consortium or view the JGI's Daphnia pulex genome portal.
Genome of Physcomitrella patens. Our scientists recently led the analysis and publication of the complete genome sequence of the moss, Physcomitrella patens, revealing many aspects of the evolutionary conquest of land by plants. This project was in collaboration with DOE Joint Genome Institute, Ralph Quatrano of Washington University, Brent Mishler of the University of California Berkeley and over 40 other scientists from around the world. View the JGI's genome portal.
Learn more at our News section and see the manuscript, pulished in Science, here.
Other Whole Eukaryotic Genome Sequencing Projects Underway. We are providing scientific leadership for several other projects that are underway, including the:
1. Glaucophyte, Cyanophora paradoxa (learn more in our News section), through collaboration with Debashish Bhattacharya of Rutgers University.
2. Monarch butterfly, Danaus plexippus (learn more in our News section), in collaboration with Steven Reppert of the University of Massachusetts Medical School.
3. An alga in collaboration with a private company interested in biofuels production.
4. Spider mite, Tetranychus urticae, in collaboration with the DOE Joint Genome Institute, Miodrag Grbic of the University of Western Ontario, and others.
5. Polychaete, Capitella capitata, in collaboration with the DOE Joint Genome Institute and others. The high-depth draft sequencing of this genome is complete and analysis is underway. View the JGI's genome portal.
Plastid Genome Sequencing. Our scientists have sequenced, annotated, and analyzed nearly 100 plastid genomes, addressing questions of evolutionary relatedness as well as molecular biology and genome structure. See a list of our manuscripts on this subject.
Mitochondrial Genome Sequencing. Our scientists have sequenced, annotated, and analyzed more than 250 mitochondrial genomes to address questions of comparative genomics, molecular biology, lateral gene transfer, and phylogenetics. Although the overwhelming majority are from animals, this work has included fungi and protists as well. See a list of our manuscripts on this subject.
Organelle Databases and Tools. In collaboration with Robert Jansen of the University of Texas at Austin and Stacia Wyman, now at the Fred Hutchinson Cancer Research Center, we developed DOGMA ("Dual Organellar Genome Annotator"), a tool for the semi-automated annotation of plastid and mitochondrial genes. Read the DOGMA manuscript. We are working to build a database that will facilitate large-scale comparisons of the various features of these organellar genomes.
Use of Genome-Level Characters for Phylogeny. Our scientists have pioneered the use of genome-level features such as the relative arrangements of genes as a way of determining the evolutionary relationships of some groups of organisms. See a list of our manuscripts on this subject.
Evolutionary Transfer of Genes into the Nucleus. Using whole genome analysis, we have detected that the nuclear genomes of oomycetes (which do not have plastids) have hundreds of genes that were transferred from cyanobacteria (presumably the progenitor of plastids) and from red algae. It has long been thought that the chromalveolates had acquired their plastids secondarily by endosymbiosis of a red algae, an event here domonstrated to have occurred before the oomycetes branched from the chromalveolates. Read the manuscript that describes this work.
cDNA Sequencing. Our scientists have been involved in the sequencing and interpretations of many hundreds-of-thousands of cDNA sequences, including those of Daphnia under various stress conditions, stalk-eyed flies, and 20 different crop plants of the Compositae family.
Whole Genome Duplication. The conclusive evidence that two rounds of whole genome duplication created the vertebrates was found using whole genome evolutionary analysis. Read the full text of the publication or download the pdf. Read the journal's news article or download it as a pdf.
