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

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. In Press.

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. In Press

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.

Hoef-Emden, K. & Archibald, J. M., (2014) 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.). Jones & Bartlett Publishers. Under Revision. (Invited book chapter)

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 DR, Hua J, Archibald JM, Lee RW., (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 MD, Penin AA, Tanifuji G, Onodera NT, Kondrashov AS, Volf P, Archibald JM, 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. 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

• Dr. Daniel Moog has joined the lab. WELCOME Daniel!

• Dr. Ugo Cenci has joined the lab. WELCOME Ugo!

• Undergraduate students Shannon Sibbald and Louis Martin have joined the lab. WELCOME!


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: July 2014