Roger, Andrew - Dalhousie University - Department of Biochemistry & Molecular Biology

研究领域

Determining the "super-kingdoms" of eukaryotic organisms by phylogenomics. Using genomic surveys and molecular genetic methods, we isolate genes coding for multiple highly conserved proteins (ribosomal proteins, cpn60, hsp70 and hsp90, elongation factors, tubulins, RNA polymerases etc.) from diverse aerobic and anaerobic, parasitic and free-living protists. We do computer-based phylogenetic analyses of these sequences to: reconstruct ancient relationships amongst the unicellular protistan eukaryotes and other major eukaryotic groups. In particular we are investigating a hypothetical eukaryote super-kingdom called the 'Excavata' that is proposed to contain organisms such as Giardia, Trichomonas, trypanosomes and a variety of aerobic and anaerobic flagellates and amoebae. Comparative genomics of unicellular eukaryotes Through EST surveys, we characterize the highly expressed genes from a wide variety of protistan genomes. We are specifically interested in the gene content of anaerobic protists, that have acquired genes by lateral gene transfer (LGT) from Eubacteria, Archaebacteria and Eukaryotes. By studying LGT in these organisms we are gaining an understanding of how both parasitic and free-living unicellular eukaryotic genomes change over time. The biology and evolution of mitochondria, hydrogenosomes and mitosomes Mitochondria are derived from an ancient endosymbiosis of a eubacterium in eukaryotic cells. Although all known eukaryotes appear to have diverged from each other since this event, many unicellular eukaryotes that live in oxygen-poor habitats (e.g. the human gut or anoxic fresh-water environments) lack aerobic mitochondrial functions and instead have transformed their mitochondria into hydrogen-producing 'hydrogenosomes or reduced mitosomes. We are interested in characterizing the functional biodiversity of these alternatives to mitochondria and understanding the mechanisms by which they have evolved. Modeling the evolution of genes and genomes We collaborate extensively with statisticians and computer scientists to develop stochastic models of gene, protein and genome evolution. We are particularly interested in creating models that capture the dynamic nature of molecular evolution over the 3.5 billion years of divergence in the tree of life.

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Muñoz-Gómez, S.A., Wideman, J.G., Roger, A.J., and Slamovits, C.H., (2017) The origin of mitochondrial cristae from alphaproteobacteria. Mol. Biol. Evol. 34(4):943-956: [PubMed] [Article] Muñoz-Gómez, S.A., and Roger, A.J., (2016) Leaving negative ancestors behind. eLife. 5:e20061 [Article] Gawryluk RM, Eme L, Roger AJ., (2015) Gene fusion, fission, lateral transfer, and loss: Not-so-rare events in the evolution of eukaryotic ATP citrate lyase. Mol Phylogenet Evol. 91:12-16 [PubMed] Leger MM, Petrů M, Žárský V, Eme L, Vlček Č, Harding T, Lang BF, Eliáš M, Doležal P, Roger AJ., (2015) An ancestral bacterial division system is widespread in eukaryotic mitochondria. Proc Natl Acad Sci U S A. pii: 201421392: [PubMed] Nývltová E, Stairs CW, Hrdý I, Rídl J, Mach J, Pačes J, Roger AJ, Tachezy J., (2015) Lateral gene transfer and gene duplication played a key role in the evolution of Mastigamoeba balamuthi hydrogenosomes. Mol Biol Evol. 2(4):1039-55 [PubMed] Sharpe, S.C., Eme, L., Brown, M.W. and Roger, A.J. , (2015) Timing the origins of multicellular eukaryotes through phylogenomics and relaxed molecular clock analyses. Evolutionary Transitions to Multicellular Life, Advances in Marine Genomics 2, I. Ruiz-Trillo and A.M. Nedelcu (Eds.) Springer Science:In Press Stairs CW, Eme L, Brown MW, Mutsaers C, Susko E, Dellaire G, Soanes DM, van der Giezen M, Roger AJ., (2014) A SUF Fe-S Cluster Biogenesis System in the Mitochondrion-Related Organelles of the Anaerobic Protist Pygsuia Curr. Biol 24(11):1176-1186 [PubMed] [Article] Eme L, Sharpe SC, Brown MW, Roger AJ., (2014) On the age of eukaryotes: evaluating evidence from fossils and molecular clocks. Cold Spring Harb Perspect Biol. 1;6(8): [PubMed] Klimeš V, Gentekaki E, Roger AJ, Eliáš M., (2014) A large number of nuclear genes in the human parasite blastocystis require mRNA polyadenylation to create functional termination codons. Genome Biol Evol. 6(8):1956-61 [PubMed] Tanifuji G, Onodera NT, Brown MW, Curtis BA, Roger AJ, Ka-Shu Wong G, Melkonian M, Archibald JM., (2014) Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae. BMC Genomics. 15(1):374 [PubMed] Kamikawa R, Kolisko M, Nishimura Y, Yabuki A, Brown MW, Ishikawa SA, Ishida K, Roger AJ, Hashimoto T, Inagaki Y., (2014) Gene content evolution in Discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa. Genome Biol Evol. 6(2):306-15 [PubMed] Wang HC, Susko E, Roger AJ., (2014) An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation. Mol Biol Evol. 31(4):779-92 [PubMed] Tsaousis AD, Gentekaki E, Eme L, Gaston D, Roger AJ., (2014) Evolution of the cytosolic iron-sulfur cluster assembly machinery in Blastocystis species and other microbial eukaryotes. Eukaryot Cell. 13(1):143-53 [PubMed] Gentekaki, E., Kolisko, M., Boscaro, V., Bright, K.J., Dini ,F., Di Giuseppe, G., Gong, Y., Miceli, C., Modeo, L., Molestina, R.E,. Petroni, G., Pucciarelli, S., Roger, A.J., Strom, S.L. and Lynn, DH. , (2014) Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages. Mol. Phylogenet. Evol. 78C:36-42 Leger MM, Gawryluk RM, Gray MW, Roger AJ., (2013) Evidence for a hydrogenosomal-type anaerobic ATP generation pathway in Acanthamoeba castellanii. PLoS One. 8(9):e69532 [PubMed] [Article] Brown MW, Sharpe SC, Silberman JD, Heiss AA, Lang BF, Simpson AG, Roger AJ., (2013) Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads. Proc Biol Sci. 280(1769):20131755 [PubMed] Suga H1, Chen Z, de Mendoza A, Sebé-Pedrós A, Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sánchez-Pons N, Torruella G, Derelle R, Manning G, Lang BF, Russ C, Haas BJ, Roger AJ, Nusbaum C, Ruiz-Trillo I., (2013) The Capsaspora genome reveals a complex unicellular prehistory of animals. Nat Commun. 4:2325 [PubMed] Gaston D, Roger AJ., (2013) Functional divergence and convergent evolution in the plastid-targeted glyceraldehyde-3-phosphate dehydrogenases of diverse eukaryotic algae. PLoS One. 8(7):70396 [PubMed] Kamikawa R, Brown MW, Nishimura Y, Sako Y, Heiss AA, Yubuki N, Gawryluk R, Simpson AG, Roger AJ, Hashimoto T, Inagaki Y., (2013) Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes. BMC Evol Biol. 13:131 [PubMed] Wang HC, Susko E, Roger AJ., (2013) The site-wise log-likelihood score is a good predictor of genes under positive selection. J Mol Evol. 6(5):280-94 [PubMed] Harding T, Brown MW, Plotnikov A, Selivanova E, Park JS, Gunderson JH, Baumgartner M, Silberman JD, Roger AJ, Simpson AG., (2013) Amoeba stages in the deepest branching heteroloboseans, including Pharyngomonas: evolutionary and systematic implications. Protist 164(2):272-86 [PubMed] Susko E, Roger AJ., (2013) Problems with estimation of ancestral frequencies under stationary models. Syst Biol. 62(2):330-8 [PubMed] Tsaousis, A.D, Leger, M. M., Stairs C.W., and Roger, A.J., (2012) The Biochemical Adaptations of Mitochondrion-Related Organelles of Parasitic and Free-Living Microbial Eukaryotes to Low Oxygen Environments Anoxia: Cellular Origin, Life in Extreme Habitats and Astrobiology 21(2):51-81 Tsaousis AD, Ollagnier de Choudens S, Gentekaki E, Long S, Gaston D, Stechmann A, Vinella D, Py B, Fontecave M, Barras F, Lukeš J, Roger AJ., (2012) Evolution of Fe/S cluster biogenesis in the anaerobic parasite Blastocystis. Proc Natl Acad Sci U S A. 109(26):10426-31 [PubMed] Brown MW, Kolisko M, Silberman JD, Roger AJ., (2012) Aggregative multicellularity evolved independently in the eukaryotic supergroup Rhizaria. Curr Biol. 22(12):1123-7 [PubMed]