D. Smith

Publications115
h-index30
Citations4,080
Highly Influential Citations296
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The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing
TLDR
This Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.
Phylogeny and Molecular Evolution of the Green Algae
TLDR
Current understanding of organelle genome evolution in the green algae is summarized, genomic insights into the ecology of oceanic picoplanktonic prasinophytes, molecular mechanisms underlying the evolution of complexity in volvocine green algae, and the Evolution of genetic codes and the translational apparatus in green seaweeds are summarized.
Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes
TLDR
It is argued that organelle DNA repair processes, mutation rates, and population genetic landscapes are all important factors leading to the observed convergence and divergence in organelle genome architecture.
Unparalleled GC content in the plastid DNA of Selaginella
  • D. Smith
  • Biology
    Plant Molecular Biology
  • 23 September 2009
TLDR
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.
Correlation between Nuclear Plastid DNA Abundance and Plastid Number Supports the Limited Transfer Window Hypothesis
TLDR
Analysis of newly available genome sequences from diverse mono- and polyplastidic taxa shows that the limited transfer window hypothesis holds, and NUPT content was positively related to nuclear genome size, indicating that in addition to plastid number, NUPTs are influenced by the forces controlling the expansion and contraction of noncoding nuclear DNA.
Mutation Rates in Plastid Genomes: They Are Lower than You Might Think
  • D. Smith
  • Biology
    Genome biology and evolution
  • 13 April 2015
TLDR
It is argued that for many protists the plastid mutation rate is lower than that of the mitochondrion, including groups with primary or secondary plastids as well as nonphotosynthetic algae.
Complete Mitochondrial DNA Sequence of the Scallop Placopecten magellanicus: Evidence of Transposition Leading to an Uncharacteristically Large Mitochondrial Genome
TLDR
Transposition involving tRNAs or tRNA-like structures is occurring and is responsible for the large size and abundance of noncoding DNA in the molecule, suggesting a small, compact organization is an actively maintained feature of metazoan mtDNA.
The GC-Rich Mitochondrial and Plastid Genomes of the Green Alga Coccomyxa Give Insight into the Evolution of Organelle DNA Nucleotide Landscape
TLDR
This work presents the GC-rich mitochondrial and plastid DNAs from the trebouxiophyte green alga Coccomyxa sp.
Buying in to bioinformatics: an introduction to commercial sequence analysis software
  • D. Smith
  • Biology
    Briefings Bioinform.
  • 1 September 2014
TLDR
This review highlights some of the currently available and most popular commercial bioinformatics packages, discussing their prices, usability, features and suitability for teaching.
Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae.
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