Genome Project Solutions
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This is a sample of the projects we have underway or have recently completed:
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 (see also below). 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 (PHRINGE site here) Phytophthora sojae, Phytophthora ramorum, Hyaloperonospora arabidopsidis, and Pythium ultimum, the crustacean Daphnia pulex, the platyfish Xiphophorus maculatus, the monarch butterfly Danaus Plexippus, 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.
GATOR ("Genome Analysis Tools and Online Resources"). Modern sequencing technology is now so rapid and inexpensive that it is practical for any whole genome project to have very deep cDNA sequencing, from which gene modeling can be much more accurate than in the past. This, coupled with highly accurate assigning of orthologous genes as can be done with our PHRINGE system (see above) makes the standard genome browser, whose primary purpose was to enable manual gene structure curation, less important. We are building a gene-centric genome presentation system that will facilitate biological discovery even for those without strong programming skills. See more details.
Oomycete Genomes Project. This is an evolutionary analysis using PHRINGE 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 original funding of this work. PHRINGE was originally created for the interpretation of the genomes of Phytophthora sojae and P. ramorum by placing all genes in evolutionary context by comparing to P. infestans and two diatoms (Thalassiosira pseudonana and Phaeodactylum tricornutum), then later we added the genomes of Hyaloperonospora arabidopsidis and Pythium ultimum as part of those whole genome sequencing projects.
Genome descriptions have been published for all of these: P. sojae and P. ramorum, P. infestans, H. arabidopsidis, P. ultimum, T. pseudonana, and P. tricornutum.
Oomycete Genomes Project Homepage.
Genomes of Phytophthora sojae and P. ramorum. Our scientists played a leadership role in the sequencing, analysis, and publication of the genome of Phytophthora sojae and P. ramorum. Using whole genome analysis, we 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.
Genome of Daphnia pulex. Our scientists played a leadership role in the sequencing, analysis, and publication of the genome of Daphnia pulex, the first crustacean to have a complete genome sequence, uncovering the largest gene repertoire discovered for any organism to date, and showing that this highly expanded gene set is largely composed of duplicated genes of unknown function that are highly responsive to enviironmental challenges. This project was in collaboration with DOE Joint Genome Institute, and the Daphnia Genome Consortium. View the JGI's Daphnia pulex genome portal or see the manuscript, published in Science, here.
Genome of Physcomitrella patens. Our scientists played a leadership role in the sequencing, 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, published in Science, here.
Genome of Danaus plexippus. Our scientists played a leadership role in the sequencing, analysis, and publication of the complete genome sequence of the monarch butterfly, Danaus plexippus, in collaboration with Steven Reppert of the University of Massachusetts Medical School.
Learn more at our News section and see the manuscript, published in Cell, here, or go to our whole-genome evolutionary analysis homepage for the monarch butterfly here.
Genome of the glaucophyte, Cyanophora paradoxa. Our scientists played a leadership role in the sequencing, analysis, and publication of the complete genome sequence of the glaucophyte, Cyanophora paradoxa, through collaboration with Debashish Bhattacharya of Rutgers University and others. See the manuscript, published in Science, here.
Genome of Xiphophorus maculatus. The sequencing of the platyfish, Xiphophorus maculatus , a model for understanding some processes of cancer, was done by Washington University Genome Sequencing Center. Scientists at Genome Project Solutions have performed the genome assembly, identified and annotated all genes, created evolutionary trees of this complete gene set in comparison to a dozen other organisms. All work is being done in collaboration with Wes Warren of the Washington University Genome Sequencing Center, Ron Walter of Texas State University, Manfred Schartl of the University of Wurzburg, and others.
Genome of a biofuels alga. Our scientists led the sequencing and interpretations for the whole genome sequence of a green alga in collaboration with a private company interested in biofuels production.
Genome of Nannochloropsis gaditana. Our scientists played a leadership role in the sequencing, analysis, and publication of the complete genome sequence of the stramenopile Nannochloropsis gaditana in collaboration with Randor Radakovits, Robert Jinkerson, and Matthew Posewitz of the Colorado School of Mines. and Hongseok Tae and Robert Settlage of the Virginia Bioinformatics Institute. See the manuscript, published at Nature Communications, here, and our portal to the genome here.
Genome of Chlorella. Our scientists are working on the interpretations of the genome of the green alga Chlorella collaboration with Michael Guarnieri of the National Renewable Energy Center.
Genome of Potamopyrgus antipodarum. We have just begun work on whole genome sequencing and interpretation and polymorphism detection for the New Zealand mud snail, Potamopyrgus antipodarum in collaboration with Maurine Neiman and John Logsdon of the University of Iowa.
BAC clones of the Iris fulva genome. We are performing quality assessment, assembly, gene annotation, repeat analysis, and many other interpretations of the sequence of numerous BAC clones from the wild iris, Iris fulva, in collaboration with Michael Arnold of the University of Georgia and BGI.
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.
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.
