Grant: $217,159 - National Science Foundation - Jul. 29, 2009
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Award Description: This project will investigate a novel method for producing large amounts of high-quality DNA sequence data for phylogenomic applications. The project will extend a strategy called 'microarray-based genome selection' (MGS), which is capable of enriching a DNA sample for thousands of genes, to simultaneous enrichment across distantly related species. As a result, this study has the potential to address the remaining practical obstacles to microarray hybridization across species (cross-species hybridization) and result in hugely increased scaling of MGS technology. Such a scaling up will expedite the assembly of the Tree of Life and accelerate the adoption of next-geenration DNA sequencing technologies in many biological fields. Frogs, a diverse group broadly used in biology, will be the model group for this research. This new genomic enrichment strategy will broadly extend the use of new sequencing technologies by accomplishing two main goals: 1) construction of significantly larger, cheaper and time-efficient molecular datasets, and 2) increasing the number of genetic markers in common across taxonomic groups, which will allow different parts of the Tree of Life to be merged together. The new lab procedures and design strategies will be published via a website and in peer-reviewed journals, further disseminating the MGS enrichment strategy to related disciplines, such as biomedical engineering.
Project Description: The purpose of this award is to develop phylogenetic applications of Microarray-based Genome Selection (MGS) technology. The expected outcomes are the development of across-genome MGS applications in phylogenetics, dissemination of the technology to other phylogenomics projects, and application of the technology to a study of amphibian genomes. The majority of our progress to date has been in the design, ordering and organization of the MGS microarrays and associated consumables, equipment and expertise. A sequence capture microarray design been finalized and manufactured by Roche NimbleGen, Inc. Currently, we have received delivery of eight sequence capture microarrays. Each array follows the same design, comprising 385,000 probes covering 128 nuclear loci, totaling 143,795 nucleotide pairs. These loci include single-copy loci from other vertebrate phylogenomic studies that we identified as having single-copy orthologs in the Xenopus tropicalis genome. In addition, the design includes 17 of 20 proposed control loci. During the design process, three of the original twenty control loci could not be covered by unique probes and were not laid on the array. These loci will be used as negative controls for the MGS experiments. The first MGS experiments have been completed. These MGS experiments captured genomic sequence information from four frog species. At the time of reporting, the success of these initial experiments is under assessment through quantitative PCR and Roche 454 sequencing, in collaboration with Rachael O?Neil of the University of Connecticut. Another proposed aim is to utilize bioinformatics to identify further candidate loci from the X. tropicalis genome for screening on microarrays. Currently, our modified scripts have been able to recover sequences of all exonic regions for over 20,000 genes from the X. tropicalis genome project. We are now evaluating the phylogenetic usefulness of these markers.
Jobs Summary: A POSTDOCTORAL FELLOW was appointed (0.95 FTE). Calculations for Number of Jobs were made using OMB guidance. (Total jobs reported: 1)
Project Status: Less Than 50% Completed
This award's data was last updated on Jul. 29, 2009. Help expand these official descriptions using the wiki below.