Genomics for Biodiversity
The ArkChip: multi-species genome sequencing for Conservation Genomics


Steven M. Carr (scarr@mun.ca)
Department of Biology    Memorial University of Newfoundland     St. John's NL A1B3X9
[http://www.mun.ca/biology/scarr/ArkChip_for_COSEWIC.html]

Abstract

    In the study of Species-at-Risk, the degree to which the loss or decline of local populations affects others and threatens species extinction depends critically on the spatial scale of population differentiation and gene flow. Phylogeographic analysis of mitochondrial DNA  sequences can provide extremely detailed information on the fine-scale population structure of species, which can inform decisions about the biological independence of "Designatable Units" in species that are considered Endangered, Threatened or of Special Concern  by COSEWIC under SARA.

    Single-locus studies may of mtDNA often lack sufficient detail, and analysis of complete mtDNA genomes by conventional methods remains laborious. The use of microarray "DNA chips" for "DNA re-sequencing" of new individuals with respect to a reference sequence allows generation of complete individual mtDNA sequences in a single experiment. Experiments with a first-generation 30Kbp human mtDNA microchip show that the method is efficient, accurate, and cost effective. We propose to develop DNA re-sequencing technology as a practical method for assessing the genetic structure of DFO fisheries species and SARA Species-at-Risk. As a "proof of principle" experiment, we will design a DNA microchip for the Atlantic cod mtDNA genome, and use it to extend our genomics study of the stock structure and phylogeography of Atlantic Cod.

    A second-generation, multi-species "ArkChip" will include up to 300,000bp on a single chip that accommodates up to 20 species' mtDNA genomes.  Use of the extensive database of reference mtDNA genomes (n > 400) allows experiments to be standardized; available nucDNA loci can be incorporated. Costs of each component project (e.g., Wolffish) are reduced proportionately. A breakthrough into high-throughput genomics would enable cost-effective, co-ordinated investigation of multiple species of interest to Species-at-Risk agencies, managers, and recovery teams.

The "ArkChip" Concept
    "Helix & Primer" genomics laboratory
      Bio4900 - Fundamentals of Genetic Biotechnology
            (three-week short course
offered 15 Aug - 02 Sept 2005)


Genomics: the study of complete gene sets in organisms
     "Genomic Thinking  ": high-throughput, massively-parallel approaches
       Biodiversity Genomics: intra- & inter-specific variation in DNA genomes
                     genomic approaches to fisheries, conservation & population biology
                     Ex.: Population & Stock Structure in Atlantic Cod

       High-throughput, massively parallel biotechnology: "DNA Chips"
           DNA Re-Sequencing Chips for biodiversity
          The Arkchip: multiplex, multi-species DNA sequence detection
 
       
Strategies for obtaining mtDNA genomes  of novel species:

                    Ex.: Long-Range PCR & "leap-frog" sequencing of Wolffish


All material ©2005 by Steven M. Carr