David Roy Smith

Summary

Affiliation: Dalhousie University
Country: Canada

Publications

  1. pmc Updating our view of organelle genome nucleotide landscape
    David Roy Smith
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia Vancouver, British Columbia, Canada
    Front Genet 3:175. 2012
  2. pmc Gene conversion shapes linear mitochondrial genome architecture
    David Roy Smith
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
    Genome Biol Evol 5:905-12. 2013
  3. ncbi request reprint RNA-Seq data: a goldmine for organelle research
    David Roy Smith
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
    Brief Funct Genomics 12:454-6. 2013
  4. doi request reprint Organelle genome complexity scales positively with organism size in volvocine green algae
    David Roy Smith
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    Mol Biol Evol 30:793-7. 2013
  5. doi request reprint Twenty-fold difference in evolutionary rates between the mitochondrial and plastid genomes of species with secondary red plastids
    David Roy Smith
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
    J Eukaryot Microbiol 59:181-4. 2012
  6. doi request reprint Relative rates of evolution among the three genetic compartments of the red alga Porphyra differ from those of green plants and do not correlate with genome architecture
    David R Smith
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    Mol Phylogenet Evol 65:339-44. 2012
  7. doi request reprint Not seeing the genomes for the DNA
    David Roy Smith
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
    Brief Funct Genomics 11:289-90. 2012
  8. pmc First complete mitochondrial genome sequence from a box jellyfish reveals a highly fragmented linear architecture and insights into telomere evolution
    David Roy Smith
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
    Genome Biol Evol 4:52-8. 2012
  9. pmc Nucleotide diversity in the mitochondrial and nuclear compartments of Chlamydomonas reinhardtii: investigating the origins of genome architecture
    David Roy Smith
    Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    BMC Evol Biol 8:156. 2008
  10. pmc The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape
    David Roy Smith
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 6:e23624. 2011

Detail Information

Publications24

  1. pmc Updating our view of organelle genome nucleotide landscape
    David Roy Smith
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia Vancouver, British Columbia, Canada
    Front Genet 3:175. 2012
    ....
  2. pmc Gene conversion shapes linear mitochondrial genome architecture
    David Roy Smith
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
    Genome Biol Evol 5:905-12. 2013
    ....
  3. ncbi request reprint RNA-Seq data: a goldmine for organelle research
    David Roy Smith
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
    Brief Funct Genomics 12:454-6. 2013
    ..Here, I argue that these data are an excellent and untapped resource for investigating many aspects of organelle function and evolution. ..
  4. doi request reprint Organelle genome complexity scales positively with organism size in volvocine green algae
    David Roy Smith
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    Mol Biol Evol 30:793-7. 2013
    ..Together, these findings support the view that nonadaptive processes, like random genetic drift, promote the expansion of noncoding regions in organelle genomes...
  5. doi request reprint Twenty-fold difference in evolutionary rates between the mitochondrial and plastid genomes of species with secondary red plastids
    David Roy Smith
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
    J Eukaryot Microbiol 59:181-4. 2012
    ..These findings have implications for understanding the origins and evolution of organelle genome architecture and the genes they encode...
  6. doi request reprint Relative rates of evolution among the three genetic compartments of the red alga Porphyra differ from those of green plants and do not correlate with genome architecture
    David R Smith
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    Mol Phylogenet Evol 65:339-44. 2012
    ..These findings are supported by within-species silent-site polymorphism data from P. purpurea...
  7. doi request reprint Not seeing the genomes for the DNA
    David Roy Smith
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
    Brief Funct Genomics 11:289-90. 2012
    ....
  8. pmc First complete mitochondrial genome sequence from a box jellyfish reveals a highly fragmented linear architecture and insights into telomere evolution
    David Roy Smith
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
    Genome Biol Evol 4:52-8. 2012
    ..The silent-site nucleotide variation within the A. moseri mtDNA is among the highest observed from a eukaryotic genome and may be associated with elevated rates of recombination...
  9. pmc Nucleotide diversity in the mitochondrial and nuclear compartments of Chlamydomonas reinhardtii: investigating the origins of genome architecture
    David Roy Smith
    Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    BMC Evol Biol 8:156. 2008
    ..For measuring pisilent we sequenced the complete mitochondrial genome and portions of 7 nuclear genes from 7 geographical isolates of C. reinhardtii...
  10. pmc The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape
    David Roy Smith
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 6:e23624. 2011
    ....
  11. pmc Extending the limited transfer window hypothesis to inter-organelle DNA migration
    David Roy Smith
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    Genome Biol Evol 3:743-8. 2011
    ..I also show that plastid genomes are depauperate in mtDNA-derived sequences (PTMTs), irrespective of the number of mitochondria per cell and plastid genome size, which may reflect the lack of a DNA uptake system in plastids...
  12. pmc The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA
    David Roy Smith
    Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    BMC Genomics 10:132. 2009
    ..carteri draft nuclear genome sequence...
  13. pmc Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis
    David Roy Smith
    Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    BMC Evol Biol 9:120. 2009
    ..reinhardtii mitochondrial and nuclear genomes, which are respectively compact and bloated, allow for a complete analysis of nucleotide diversity and genome compactness in all three genetic compartments of this model organism...
  14. pmc Correlation between nuclear plastid DNA abundance and plastid number supports the limited transfer window hypothesis
    David Roy Smith
    Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Genome Biol Evol 3:365-71. 2011
    ..These findings are consistent with data on nuclear DNAs of mitochondrial origin (NUMTs), suggesting that similar processes govern the abundance of both NUPTs and NUMTs...
  15. doi request reprint Evolution of linear mitochondrial DNA in three known lineages of Polytomella
    David Roy Smith
    Department of Biology, Dalhousie University, Halifax, NS, Canada
    Curr Genet 56:427-38. 2010
    ..These elevated rates could be the result of a greater number of vegetative cell divisions and/or small population sizes in Polytomella species as compared with other chlamydomonadalean algae...
  16. pmc The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA
    David Roy Smith
    Department of Biology, Dalhousie University, Halifax, Canada
    BMC Plant Biol 10:83. 2010
    ..This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri...
  17. doi request reprint Unparalleled GC content in the plastid DNA of Selaginella
    David Roy Smith
    Department of Biology, Dalhousie University, Halifax, NS, Canada
    Plant Mol Biol 71:627-39. 2009
    ..Ultimately, these findings provide convincing support for the earlier proposed theory that the GC content of land-plant organelle DNA is positively correlated and directly connected to levels of organelle RNA editing...
  18. doi request reprint Low nucleotide diversity for the expanded organelle and nuclear genomes of Volvox carteri supports the mutational-hazard hypothesis
    David Roy Smith
    Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 27:2244-56. 2010
    ..carteri contributed to a low V. carteri population size and thus a reduced 2N(g)μ. Complete mitochondrial and plastid genome maps for V. carteri are also presented and compared with those of C. reinhardtii...
  19. pmc Palindromic genes in the linear mitochondrial genome of the nonphotosynthetic green alga Polytomella magna
    David Roy Smith
    Department of Biology, University of Western Ontario, London, Ontario, Canada
    Genome Biol Evol 5:1661-7. 2013
    ..The possible origins and consequences of this bizarre genomic architecture are discussed. ..
  20. doi request reprint Similar relative mutation rates in the three genetic compartments of Mesostigma and Chlamydomonas
    Jimeng Hua
    Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
    Protist 163:105-15. 2012
    ..To guide future work, we describe evolutionary divergence data of all publically available Mesostigma viride strains and identify, for the first time, three distinct lineages of Mesostigma...
  21. pmc Does the mode of plastid inheritance influence plastid genome architecture?
    Kate Crosby
    Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    PLoS ONE 7:e46260. 2012
    ..000001) than those that are maternally, uniparentally (when isogamous), or biparentally inherited. Potential explanations for this observation are discussed...
  22. doi request reprint Nucleotide diversity of the colorless green alga Polytomella parva (Chlorophyceae, Chlorophyta): high for the mitochondrial telomeres, surprisingly low everywhere else
    David Roy Smith
    Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
    J Eukaryot Microbiol 58:471-3. 2011
    ..parva, and are used to understand the modes and tempos of genome evolution within green algae...