Research Summary

• Gene and genome evolution
• Secondary endosymbiosis and the evolution of photosynthetic organelles
• Molecular evolution and systematics of microbial eukaryotes

The central focus of research in the Archibald Lab is to gain insight into the origin and evolution of eukaryotic (nucleus-containing) cells and their organelles using comparative genomics and proteomics. We are particularly interested in (1) the impact of endosymbiosis and parasitism on genome structure and content, (2) how endosymbionts become organelles, and (3) the higher-order structure of the tree of eukaryotic life. Research Page, Lab Positions

Dalhousie University, Halifax, Nova Scotia, Canada

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Recent Publications

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. In press.

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. doi:10.1038/srep21016.

de Vries, J., Stanton, A., Archibald, J. M., & Gould, S. B. 2016. Streptophyte terrestrialization in light of plastid evolution.s. Trends Plant Sci. Online-early (Invited Opinion Article).

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. In press.

Hoef-Emden, K. & Archibald J. M. 2016. 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-Verlag. In Press.

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. 7, 2955-2969.

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.

Archibald, J. M. 2015. Endosymbiosis and eukaryotic cell evolution. Curr. Biol. 25, R911-R921.

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.

Archibald J. M. 2015. Genomic perspectives on the birth and spread of plastids. Proc. Natl. Acad. Sci. USA 112, 10147-10153.

Archibald J. M. 2014. The cellular evolution. The Scientist 12, 74.

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.

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.

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. Riboswitches are widespread in unicellular marine eukaryotes and suggest alternatives to vitamin B1 uptake. ISME Journal. 8, 2517-2529.

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.

Tanifuji, G., Onodera, N. T., Brown, M. W., Curtis, B. A., Roger, A. J., Wong, G. K.-S., Melkonian, M. & Archibald, J. M. 2014. Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica : convergent reductive evolution and frequent recombination in nucleomorph-bearing algae. BMC Genomics. 15:374.

Archibald, J. M. 2014. One plus one equals one: symbiosis and the evolution of complex life. Oxford University Press.

Keeling, P. J., (75 other authors, including Archibald, J. M.), & Worden, A. Z. 2014. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol.12, e1001889.

Tanifuji, G. & Archibald, J. M. 2014. Nucleomorph comparative genomics. Endosymbiosis. Löffelhardt, W. (ed.). Springer Wein New York. Pp. 197-213.

Tanifuji, G., Onodera, N. T., Moore, C. E. & Archibald, J. M. 2014. Reduced nuclear genomes maintain high levels of gene transcription. Mol. Biol. Evol. 31:625-635.

Eveleigh, R. J. M., Archibald, J. M. & Beiko, R. G. 2013. Being Aquifex aeolicus: untangling a hyperthermophile’s checkered past. Genome Biol. Evol 5:2478-2497.

Smith D .R., Hua J., Archibald J. M., Lee R. W. 2013. Palindromic Genes in the Linear Mitochondrial Genome of the Nonphotosynthetic Green Alga Polytomella magna. Genome Biol Evol. 5(9):1661-7.

Flegontov P., Votýpka J., Skalický T., Logacheva M. D., Penin A. A., Tanifuji G., Onodera N. T., Kondrashov A. S., Volf P., Archibald J. M., Lukeš J. 2013. Paratrypanosoma is a novel early-branching trypanosomatid. Curr Biol. 23(18):1787-93.

Maruyama, S., Eveleigh, R. J. M. & Archibald, J. M. 2013. TreeTrimmer: a method for phylogenetic dataset size reduction. BMC Research Notes 6:145.

Kim, E., Archibald, J. M. 2013. Ultrastructure and molecular phylogeny of the cryptomonad Goniomonas avonlea sp. nov. Protist 164(2):160-82.

Maruyama, S. & Archibald, J. M. 2012. Endosymbiosis, gene transfer, and algal cell evolution. In: Advances in algal cell biology. Heimann, K. & Katsaros, C. (eds.). Walter de Gruyter. Pp 21-41.

Archibald, J. M. 2012. The evolution of algae by secondary and tertiary endosymbiosis. In: Genomic insights into the biology of algae. Piganeau, G. (ed.). Elsevier Ltd: Academic Press. pp. 87-118.

Nakayama, T. & Archibald, J. M. 2012. Evolving a photosynthetic organelle. BMC. Biol. 10, 35.

Hopkins, J. F., Eveleigh, R. J. M., Spencer, D. F., Laboissiere, S., Neilson, J. A. D., Durnford, D. G., Gray, M. W. & Archibald J. M. 2012. Proteomics reveals plastid- and periplastid-targeted proteins in the chlorarachniophyte alga Bigelowiella natans. Genome Biol. Evol. 4, 1391-1406.

Nakayama, T., Ishida, K.-I., & Archibald J. M. 2012. Broad distribution of TPI-GAPDH fusion proteins among eukaryotes: evidence for glycolysis in the mitochondrion? PLoS One. 7, e52340.

Curtis, B. A., Tanifuji, G., Burki, F., Gruber, A., Irimia, M., Maruyama, S., Arias, M. C., Ball, S. G., Gile, G. H., Hirakawa, Y., Hopkins, J. F., Kuo, A., Rensing, S. A., Schmutz, J., Symeonidi, A., Elias, M., Eveleigh, R. J. M., Herman, E. K., Klute, M. J., Nakayama, T., Oborník, M., Reyes-Prieto, A., Armbrust, V. E., Aves, S. J., Beiko, R. G., Coutinho, P., Dacks, J. B., Durnford, D. G., Fast, N. M., Green, B. R., Grisdale, C., Hempel, F., Henrissat, B., Höppner, M. P., Ishida, K.-I., Kim, E., Koreny, L., Kroth, P. G., Liu, Y., Malik, S.-B., Maier, U. G., McRose, D., Mock, T., Neilson, J. A. D., Onodera, N. T., Poole, A. M., Pritham, E. J., Richards, T. A., Rocap, G., Roy, S. W., Sarai, C., Schaack, S., Shirato, S., Slamovits, C. H., Spencer, D. F., Suzuki, S., Worden, A. Z., Zauner, S., Barry, K., Bell, C., Bharti, A. K., Crow, J. A., Grimwood, J., Kramer, R., Lindquist, E., Lucas, S., Salamov, A., McFadden, G. I., Lane, C. E., Keeling, P. J., Gray, M. W., Grigoriev, I. V., Archibald, J. M. 2012. Algal nuclear genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature. 492, 59-65.

Moore, C., Curtis, B. A., Tanifuji, G. & Archibald J. M. 2012. Nucleomorph genome sequence of the cryptophyte alga Chroomonas mesostigmatica reveals lineage-specific gene loss and genome complexity. Genome Biol. Evol. 4, 1162-1175.

Onodera, N., Ryu, J., Durbic, T., Nislow, C., Archibald, J. M., & Rohde, J. R. 2012. Genome sequence of Shigella flexneri serotype 5a strain M90T Sm. J. Bacteriol. 194, 3022.

Gray, M. W. & Archibald, J. M. 2012. Origins of mitochondria and plastids. In: Advances in photosynthesis and respiration (Genomics of chloroplasts and mitochondria). Bock, R. and Knoop, V. (eds.). Springer. pp. 1-30.

Archibald, J. M. 2012. Obituary: Lynn Margulis (1938-2011). Curr. Biol., 22, R4-6.

Archibald, J. M. 2012. Plastid origins. In: Organelle genetics: evolution of organelle genomes and gene expression. Bullerwell, C. (ed.). Springer-Verlag. pp. 19-38.

Lab News

'One Plus One Equals One' reviewed in Nature

•Co-op Student Morgan Colp has joined the lab. WELCOME Morgan!

Tree of Life web resource for c">cryptophytes

• New Centre at Dalhousie: CGEB

• Archibald wins major CIHR and DMRF awards

• Dalhousie tops international list of The Scientist's "Best Places to Work in Academia"

Last updated: April 2016