Archibald, John M. - Dalhousie University - Department of Biochemistry & Molecular Biology

研究领域

Gene and Genome Evolution Our laboratory uses molecular biological and computational methods to study the genes and genomes of eukaryotic (nucleus-containing) microorganisms. Using a comparative genomics approach, we are interested in (1) elucidating some of the pivotal molecular and biochemical events that have shaped the evolution of eukaryotes, (2) understanding the evolutionary relationships amongst eukaryotic microbes and (3) understanding how eukaryotic genes, genomes and proteins change over time. The main projects in the lab are as follows: Secondary endosymbiosis and nucleomorph genome evolution. The plastids (chloroplasts) of photosynthetic eukaryotes evolved from free-living prokaryotes by endosymbiosis. While all plastids appear to be derived from a single, ancient primary endosymbiotic event, photosynthesis has also spread laterally amongst unrelated eukaryotic cells by secondary endosymbiosis. This occurs when a heterotrophic eukaryote engulfs a photosynthetic eukaryote and retains its plastid.The cryptomonads and chlorarachniophytes are two secondary plastid-containing algal groups that have retained the nucleus of the eukaryotic endosymbiont in a highly derived form called a nucleomorph. The nucleomorph genomes of chorarachniophytes and cryptomonads are very fast evolving and are the smallest eukaryotic genomes known, having transferred most of their genetic material to their respective host cell nuclei. By studying the size, structure and content of nucleomorph genomes in these organisms we are trying to elucidate the fundamentals of eukaryotic genome evolution, endosymbiosis, intracellular gene transfer and genome reduction. Multigene family evolution One of the hallmarks of eukaryotic nuclear genomes is the presence of multigene families that have evolved by gene duplication. Using chaperonin genes as a model system, we are studying patterns of gene duplication in eukaryotic genomes and examining the extent to which gene conversion influences the functional differentiation of proteins encoded by duplicate genes.

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Muñoz-Gómez, S.A., Mejía-Franco, F.G., Durnin, K., Colp, M., Grisdale, C.J., Archibald, J.M., and Slamovits, C.H., (2017) The New Red Algal Subphylum Proteorhodophytina Comprises the Largest and Most Divergent Plastid Genomes Known. Curr. Biol. 27(11):1677-1684 [Article] Hoef-Emden, K. & Archibald, J. M., (2017) Phylum Cryptophyta (Cryptomonads). Handbook of the Protists (2nd edition of the Handbook of Protoctista by Margulis et al.). Archibald, J.M., Simpson, A.G.B, & Slamovits, C. (eds.). Springer: de Vries, J. & Archibald J. M., (2017) Endosymbiosis: did plastids evolve from a freshwater cyanobacterium? Curr. Biol. 27:R103-105 Sibbald, S. J. & Archibald J. M., (2017) More protist genomes needed. Nature Ecol. Evol. :In Press. Simpson, A. G. B., Slamovits, C. H. & Archibald, J. M., (2017) Protist diversity and eukaryote phylogeny. In: Handbook of the Protists (2nd edition of the Handbook of Protoctista by Margulis et al.) Archibald, J.M., Simpson, A.G.B, & Slamovits, C. (eds.). Springer: Eme, L., Gentekaki, E., Curtis, B., Archibald, J. M., and Roger, A. J., (2017) Lateral gene transfer in adaptation of the anaerobic parasite Blastocystis to the gut. Curr. Biol. 27:807-820 de Vries, J., Archibald, J. M., and Gould, S. B, (2017) The carboxy terminus of YCF1 contains a motif conserved throughout >500 million years of streptophyte evolution. Genome Biol. Evol. Online-Early:doi: 10.1093/gbe/evx013. Sibbald, S., Cenci, U., Colp, M., Eglit, Y., O’Kelly, C.J., & Archibald, J. M., (2017) Diversity and evolution of Paramoeba sp. and their kinetoplastid endosymbionts. J. Eukaryot. Microbiol. Online-Early :doi: 10.1111/jeu.12394. Archibald, J.M., Simpson, A.G.B, & Slamovits, C. (Eds.)., (2017) Edited work: Handbook of the Protists (2nd edition of the Handbook of Protoctista by Margulis et al.) Springer:In Press Cenci, U., Moog, D., Curtis, B. A., Tanifuji, G., Eme, L., Lukeš, J., and Archibald, J.M., (2016) Heme pathway evolution in kinetoplastid protists. BMC Evolutionary Biology 16:109, (doi:10.1186/s12862-016-0664-6) Cenci, U., Moog, D, & Archibald, J. M. , (2016) Origin and spread of plastids endosymbiosis. Algae symbioses. Grube, M., Muggia, L. & Seckbach, J. (eds.). Springer-Verlag: Tanifuji, G., Archibald, J. M., and Hashimoto, T., (2016) Comparative genomics of mitochondria in chlorarachniophyte algae: endosymbiotic gene transfer and organellar genome dynamics. Scientific Rep. 6 :21016. doi:10.1038/srep21016. de Vries, J., Stanton, A., Archibald, J. M., & Gould, S. B. , (2016) Streptophyte terrestrialization in light of plastid evolution. Trends Plant Sci. 21:467-476 David, V. & Archibald J. M., (2016) Evolution: plumbing the depths of diplonemid diversity. Curr. Biol. :R1290-1292 Caron, D. A., Alexander, H., Allen, A. E., Archibald, J. M., Armbrust, E. V., Bachy, C., Bharti, A., Bell, C. J., Dyhrman, S. T., Guida, S., Heidelberg, K. B., Kaye, J. Z., Metzner, J., Smith, S. R., & Worden, A. Z. , (2016) Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nature Rev. Microbiol. 15:6-20 Gile, G.H., Moog, D., Maier, U.-G., Slamovits, C., and Archibald, J. M., (2015) Dual organellar targeting of aminoacyl-tRNA synthetases in diatoms and cryptophytes. Genome Biol. Evol. 7(6):1728-42 [PubMed] Archibald, J. M. , (2015) Genomic perspectives on the birth and spread of plastids. Proc. Natl. Acad. Sci. USA. 112:10147-10153 Archibald, J. M. , (2015) Endosymbiosis and eukaryotic cell evolution. Curr. Biol. 25:R911-R921 Moog, D., Rensing, S. A., Archibald, J. M., Maier, U.-G., and Ullrich, K. K. , (2015) Localization and evolution of putative triose phosphate translocators in the diatom Phaeodactylum tricornutum. Genome Biol. Evol. On-line early (doi:10.1093/gbe/evv190): David, V., Flegontov, P., Gerasimov, E., Tanifuji, G., Hashimi, H., Logacheva, M.D., Maruyama, S., Onodera, N. T., Gray, M. W., Archibald, J. M., and Lukeš, J., (2015) Gene loss and error-prone RNA editing in the mitochondrion of Perkinsela, an endosymbiotic kinetoplastid. mBio. :6, e01498-15 Archibald, J. M. , (2015) Evolution: Gene transfer in complex cells. Nature 524:423-424 Tanifuji, G., Onodera, N. T., Moore, C. E. & Archibald, J. M. , (2014) Reduced Nuclear Genomes Maintain High Gene Transcription Levels Mol. Biol. Evol 31 (3):625-635 [PubMed] [Article] Nakayama, T., Kamikawa, R., Tanifuji, G., Kashiyama, Y., Ohkouchi, N., Archibald J. M., and Inagaki, Y., (2014) Complete genome of a non-photosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle Proc. Natl. Acad. Sci. USA. 111:11407-11412 [PubMed] [Article] McRose, D., Guo, J., Monier, A., Sudek, S., Wilken, S., Yan, S., Mock, T., Archibald, J. M., Begley, T. P., Reyes-Prieto, A. & Worden A. Z. , (2014) Alternatives to vitamin B1 uptake revealed with discovery of riboswitches in multiple marine eukaryotic lineages. ISME Journal Dec;8(12):2517-29 [PubMed] [Article] Hirakawa, Y., Suzuki, S., Archibald, J. M., Keeling, P. J. & Ishida, K.-I. , (2014) Overexpression of molecular chaperone genes in nucleomorph genomes. Mol. Biol. Evol. 31:1437-1443 [PubMed] [Article]