We study genome architecture, genetic diversity, and the evolutionary forces that fashion genes and chromosomes. We’re interested in how nonadaptive processes shape genomes, including their nucleotide composition, compactness, conformation, chromosome number and telomeres. Much of our research employs protists (microbial eukaryotes). Protists have among the most diverse and eccentric genomes in the biological world, yet they are generally an untapped resource for studying genome evolution. We love weird genomes and trying to understand how they got that way.
Degrees and Institutions
B.Sc. (Biology) Acadia University
Ph.D. (Genetics and Evolution) Dalhousie University
Zhang X, Bauman N, Brown R, Richardson TH, Akella S, Hann E, Morey R, Smith DR. 2019. The mitochondrial and chloroplast genomes of the green alga Haematococcus are largely made up of nearly identical repetitive sequences. Current Biology. 25:R736-R737.
Szyszka-Mroz B, Cvetkovska M, Ivanov AG, Smith DR, Possmayer M, Maxwell DP, Hüner NPA. The Antarctic psychrophile, Chlamydomonas sp. UWO241, exhibits cold adapted protein kinases and thylakoid remodelling that confer a distinctive thylakoid protein phosphorylation pattern associated with a novel photosystem I / II energy distribution. Plant Physiology. 180:1291-1309.
Cvetkovska M, Orgnero S, Hüner NPA, Smith DR (2019) The enigmatic loss of light-independent chlorophyll biosynthesis from an Antarctic green alga in a light-limited environment. New Phytologist. 222:651–656.
Smith DR (2018) Haematococcus lacustris: the makings of a giant-sized chloroplast genome. AoB Plants. 10:ply058.
Smith DR (2018) Is it time to put a humidifier in the dry domain of writing scientific papers. EMBO reports. e46909.
Gaouda H, Hamaji T, Yamamoto K, Kawai-Toyooka H, Suzuki M, Noguchi H,Minakuchi Y, Toyoda A, Fujiyama A, Nozaki H, Smith DR (2018) Exploring the limits and causes of plastid genome expansion in volvocine green algae. Genome Biology and Evolution. 10:2248-2254.
Smith DR (2018) Bringing bioinformatics to the scientific masses. EMBO reports. 19:e46262.
Cvetkovska M, Szyszka-Mroz B, Possmayer M, Pittock P, Lajoie G, Smith DR, Hüner NPA (2018) Characterization of photosynthetic ferredoxin from the Antarctic algal Chlamydomonas sp. UWO241 reveals novel features of cold adaptation. New Phytologist. 219: 588-604.
Smith DR (2018) Plastid genomes hit the big time. New Phytologist. 219: 491-495.
Su Y, Willis L, Rehmann L, Smith DR, Jeffries T (2018) Spathaspora passalidarum selected for resistance to AFEX hydrolysate shows decreased cell yield. FEMS Yeast Research. 18:foy011.
Smith DR (2018) Attention, attention: your most valuable scientific assets are under attack. EMBO reports. 19:e45684.
Smith DR (2018) The Frankenthesis: this stitched-together monster is alive and coming to a campus near you. EMBO reports. 19:10-12.
Smith DR (2018) Lost in the light: genome evolution in colourless plastids. Advances in Botanical Research. 85:29-53.
Smith DR (2017) Evolution: In chloroplast genomes, anything goes. Current Biology. 27:R1305–07.
Smith DR (2017) Does cell size impact chloroplast genome size? Frontiers in Plant Science. 8:2116.
Sanitá Lima M, Smith DR (2017) Pervasive transcription of mitochondrial, plastid, and nucleomorph genomes across diverse plastid-bearing species. Genome Biology and Evolution. 9:2650-57.
Sanitá Lima M, Smith DR (2017) Don’t just dump your data and run. EMBO reports. 18:2087-89.
Sanitá Lima M, Smith DR (2017) Pervasive, genome-wide transcription in the organelle genomes of diverse plastid-bearing protists. G3: Genes | Genomes | Genetics. 7:3789-96.
Smith DR (2017) Let there be light: a contemporary primer on primary plastid endosymbiosis. Advances in Botanical Research. 84:31-56.
Hamaji T, Kawai-Toyooka H, Toyoda A, Minakuchi Y, Suzuki M, Fujiyama A, Nozaki H, Smith DR (2017) Multiple independent changes in mitochondrial genome conformation in chlamydomonadalean algae. Genome Biology and Evolution. 9:993-99.
Figueroa-Martinez F, Nedelcu A, Reyes-Prieto A, Smith DR (2017) The plastid genomes of nonphotosynthetic algae are not so small after all. Communicative & Integrative Biology. 10:e1283080.
Smith DR (2017) The plant Lophophytum pilfers mitochondrial genes from the species it parasitizes. The Scientist. 27:2.
Smith DR (2017) Confessions of a science blogaholic: highs, lows, and increasing liabilities. Frontiers in Communication. 1:15.
Figueroa-Martinez F, Nedelcu AM, Smith DR, Reyes-Prieto A (2017) The plastid genome of Polytoma uvella is the largest known among colorless algae and plants and reflects contrasting evolutionary paths to nonphotosynthetic lifestyles. Plant Physiology. 173:932-43.
Smith DR (2017) More than ever, scientists need to engage with the public: the stakes are high and they may be for keeps. EMBO reports. 18:185-6.
Cvetkovska M, Hüner NPA, Smith DR (2017) Chilling out: the evolution and diversification of psychrophilic algae, with a focus on Chlamydomonadales. Polar Biology. 40:1169-84.
Smith DR, Sanitá Lima M (2017) Unraveling chloroplast transcriptomes with ChloroSeq, an organelle RNA-Seq bioinformatics pipeline. Briefings in Bioinformatics. 18:1012-16.
Smith DR (2017) Goodbye genome paper, hello genome report: the increasing popularity of “genome announcements” and their impact on science. Briefings in Functional Genomics. 16:156-62.
Smith DR (2016) A walk in the park: Is Pokémon Go foreshadowing the future of biodiversity research and scientific outreach? EMBO reports. 17:1506–9.
Smith DR (2016) One scientist’s struggle to be a better writer, and a plea for undergraduate science-writing engagement. Science Communication. 38:666–74.
Sanita Lima M, Woods LC,Cartwright MW, Smith DR (2016) The (in)complete organelle genome: exploring the use and non-use of available technologies for characterizing mitochondrial and plastid chromosomes. Molecular Ecology Resources. 16:1279–86.
Smith DR (2016) The mutational hazard hypothesis of organelle genome evolution: ten years on. Molecular Ecology. 25:3769–3775.
Featherston F, Arakaki Y, Nozaki H, Durand PM, Smith DR (2016) Inflated organelle genomes and a circular-mapping mtDNA likely existed at the origin of coloniality in volvocine green algae. European Journal of Phycology. 51:369–77.
Smith DR, Keeling PJ (2016) Protists and the wild, wild west of gene expression: new frontiers, lawlessness, and misfits. Annual Review of Microbiology. 70:161–78.
Hanschen, et al. (2016) The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity. Nature Communications. 7:11370.
Smith DR (2016) Will publons popularize the scientific peer-review process? BioScience. 66:265–6.
Tian Y, Smith DR (2016) Recovering complete mitochondrial genome sequences from RNA-Seq: a case study of Polytomella non-photosynthetic green algae. Molecular Phylogenetics and Evolution. 98:57–62.
Possmayer M, Gupta RK, Szyska-Mroz B, Maxwell DP, Lachance MA, Hüner NPA, Smith DR (2016) Resolving the phylogenetic position of Chlamydomonas sp. UWO 241 (Chlorophyceae) with nuclear and organelle DNA sequences. Journal of Phycology. 52:305–10.
Smith DR (2016) Are you failing at scientific social media? EMBO reports. 17:123–4.
Smith DR (2016) The past, present, and future of mitochondrial genomics: have we sequenced enough mtDNAs? Briefings in Functional Genomics. 15:47–54.
Asmail SR, Smith DR (2016) Retention, erosion, and loss of the carotenoid biosynthetic pathway in the nonphotosynthetic green algal genus Polytomella. New Phytologist. 209:899–903.
Yan D, et al. (2015) Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae. Scientific Reports. 5:14465.
Smith DR (2015) Broadening the definition of a bioinformatician. Frontiers in Genetics. 6:258.
Smith DR (2015) Mutation rates in plastid genomes: they are lower than you might think. Genome Biology and Evolution. 7:1227–34.
Smith DR, Keeling PJ (2015) Mitochondrial and plastid genome architecture: reoccurring themes, but significant differences at the extremes. Proceedings of the National Academy of Sciences USA. 112:10177–84.
Del Vasto M, Figueroa-Martinez F, Featherston J, Gonzalez MA, Reyes-Prieto A, Durrand PM, Smith DR (2015) Massive and widespread organelle genomic expansion in the green algal genus Dunaliella. Genome Biology and Evolution. 7:656–63.
Figueroa-Martinez F, Nedelcu AM, Smith DR, Reyes-Prieto A (2015) When the lights go out: the evolutionary fate of free-living colourless green algae. New Phytologist. 206:972–82.
Ajoge HO, Olonitola SO, Smith DR (2015) Soil-transmitted helminths are a serious but understudied health concern in South Africa, requiring immediate attention from the scientific community. F1000Research. 3:209.
Smith DR (2015) Buying in to bioinformatics: an introduction to commercial sequence analysis software. Briefings in Bioinformatics. 16:700–9.
Smith DR (2015) The outsourcing and commercialization of science. EMBO Reports. 16:14–6.
Smith DR, Jackson CJ, Reyes-Prieto A (2014) Nucleotide substitution analyses of the glaucophyte Cyanophora suggest an ancestrally lower mutation rate in plastid vs mitochondrial DNA for the Archaeplastida. Molecular Phylogenetics and Evolution. 79:380–384.
Smith DR, Asmail SR (2014) Next-generation sequencing data suggest that certain nonphotosynthetic green plants have lost their plastid genomes. New Phytologist. 204:7–11.
Keeling PJ, (75 other authors, including Smith DR), Worden AZ (2014) The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biology. 12:e1001889.
Smith DR (2014) Last-gen nostalgia: a lighthearted rant and reflection on genome sequencing culture. Frontiers in Genetics. 5:146.
Smith DR, Vinogradov SN, Hoogewijs D (2014) Hemoglobins in the genome of the cryptomonad Guillardia theta. Biology Direct. 9:7.
Smith DR, Lee RW (2014) A plastid without a genome: evidence from the nonphotosynthetic green alga Polytomella. Plant Physiology. 164:1812–9.
Smith DR (2014) Mitochondrion-to-plastid DNA transfer: it happens. New Phytologist. 202:736–8.
Smith DR, Arrigo KR, Alderkamp AC, Allen AE (2014) Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae. Molecular Phylogenetics and Evolution. 71:36–40.
Smith DR (2014) Volvox, rolling out from under the shadow of Chlamydomonas. Journal of Heredity. 105:143–144.
Smith DR (2013) Are we divorced from the species we study? F1000Research. 2:254. This article was a front-page featured paper on the F1000Research website for the week of 10–14 Dec 2013, and included a comment from the journal’s editor.
Smith DR (2013) The battle for user-friendly bioinformatics. Frontiers in Genetics. 4:187.
Smith DR, Hua J, Archibald JM, Lee RW (2013) Palindromic genes in the linear mitochondrial genome of the nonphotosynthetic green alga Polytomella magna. Genome Biology and Evolution. 5:1661–7.
Smith DR, James ER (2013) What’s in a name? A lot if you’re a little known microbe. BioScience. 63:791–2.
Vinogradov SN, Bailly X, Smith DR, Tinajero-Trejo M, Poole RK, Hoogewijs D (2013) Microbial eukaryote globins. Advances in Microbial Physiology. 63:391–446.
Smith DR (2013) Death of the genome paper. Frontiers in Genetics. 4:72.
Smith DR, Keeling PJ (2013) Gene conversion shapes linear mitochondrial genome architecture. Genome Biology and Evolution. 5:905–12.
Smith DR (2013) Steal my sunshine. The Scientist. 27:34–40.
Hamaji T, Smith DR, Noguchi H, Toyoda A, Suzuki M, Kawai-Toyooka H, Fujiyama A, Nishi A, Marriage T, Olson BJSC, Nozaki H (2013) Mitochondrial and plastid genomes of the colonial green alga Gonium pectorale give insights into the origins of organelle DNA architecture within the Volvocales. PLoS ONE. 8:e57177.
Smith DR, Hamaji T, Olson BJSC, Durand PM, Ferris P, Michod RE, Nozaki H, Featherston J, Keeling PJ (2013) Organelle genome complexity scales positively with organism size in volvocine green algae. Molecular Biology and Evolution. 30:793–7.
Pombert JF, Xu J, Smith DR, Heiman D, Young S, Cuomo C, Weiss LM, Keeling PJ (2013) Complete genome sequences from three genetically distinct strains reveal a high intra-species genetic diversity in the microsporidian Encephalitozoon cuniculi. Eukaryotic Cell. 12:503–11.
Smith DR (2013) RNA-Seq data: a goldmine for organelle research. Briefings in Functional Genomics. 12:454–6.
Crosby K, Smith DR (2012) Does the mode of plastid inheritance influence plastid genome architecture? PLoS ONE. 7:e46260.
Smith DR (2012) Updating our view of organelle genome nucleotide landscape. Frontiers in Genetics. 3:175.
Smith DR (2012) Making your GenBank entry count. Frontiers in Genetics. 3:123.
Smith DR, Hua J, Lee RW, Keeling PJ (2012) 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. Molecular Phylogenetics and Evolution. 65:339–44.
Smith DR (2012) Not seeing the genomes for the DNA. Briefings in Functional Genomics. 11:289–90.
Smith DR, Keeling PJ (2012) Twenty-fold difference in evolutionary rates between the mitochondrial and plastid genomes of species with secondary red plastids. Journal of Eukaryotic Microbiology. 59:181–4.
Smith DR, Kayal E, Yanagihara AA, Collins AG, Pirro S, Keeling PJ (2012) First complete mitochondrial genome sequence from a box jellyfish reveals a highly fragmented, linear architecture and insights into telomere evolution. Genome Biology and Evolution. 4:52–8.
Leliaert F, Smith DR, Moreau H, Herron M, Verbruggen H, Delwiche CF, De Clerk O (2012) Phylogeny and molecular evolution of the green algae. Critical Reviews in Plant Sciences. 31:1–46.
Hua J, Smith DR, Borza T, Lee RW (2012) Similar relative mutation rates in the three genetic compartments of Mesostigma and Chlamydomonas. Protist. 163:105–15.
Smith DR, Burki F, Yamada T, Grimwood J, Grigoriev IV, Van Etten JL, Keeling PJ (2011) The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape. PLoS ONE. 6:e23624.
Smith DR (2011) Extending the limited transfer window hypothesis to inter-organelle DNA migration. Genome Biology and Evolution. 3:743–8.
Smith DR, Lee RW (2011) Nucleotide diversity in the colorless green alga Polytomella parva (Chlorophyceae, Chlorophyta): high for the mitochondrial telomeres, surprisingly low everywhere else. Journal of Eukaryotic Microbiology. 58:471–3.
Smith DR, Crosby K, Lee RW (2011) Correlation between nuclear plastid DNA abundance and plastid number supports the limited transfer window hypothesis. Genome Biology and Evolution. 3:365–71.
Smith DR, Hua J, Lee RW (2010) Evolution of linear mitochondrial DNA in three known lineages of Polytomella. Current Genetics. 56:427–38.
Smith DR, Lee RW, Cushman JC, Magnuson JK, Tran D, Polle JEW (2010) The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA. BMC Plant Biology. 10:83.
Smith DR, Lee RW (2010) Low nucleotide diversity in the organelle and nuclear genomes of Volvox carteri provides support for the mutational-hazard hypothesis. Molecular Biology and Evolution. 27:2244–56.
Smith DR (2009) Unparalleled GC content in the plastid DNA of Selaginella. Plant Molecular Biology. 71:627–39.
Smith DR, Lee RW (2009) Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis. BMC Evolutionary Biology. 9:120.
Smith DR, Lee RW (2009) The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA. BMC Genomics. 10:132.
Smith DR, Lee RW (2008) Nucleotide diversity in the mitochondrial and nuclear compartments of Chlamydomonas reinhardtii: investigating the origins of genome architecture. BMC Evolutionary Biology. 8:156.
Smith DR, Lee RW (2008) Mitochondrial genome of the colorless green alga Polytomella capuana: a linear molecule with an unprecedented GC content. Molecular Biology and Evolution. 25:487–96.
Smith DR, Snyder M (2007) Complete mitochondrial DNA sequence of the scallop Placopecten magellanicus: evidence of transposition leading to an uncharacteristically large mitochondrial genome. Journal of Molecular Evolution. 65:380–91.