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

Contact John Archibald




Recent Publications

de Vries, S., de Vries, J., Archibald, J. M., & Slamovits, C. S. 2019. Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. PLoS Genetics. Under Review.

Tanifuji, G., Kamikawa, R., Moore, C. E., Mills, T., Onodera, N. T., Kashiyama, Y., Archibald, J. M., Inagaki, Y, & Hahimoto, T. 2019. Comparative plastid genomics of photosynthetic and non-photosynthetic Cryptomonas species reveals loss of photosynthesis. Genome Biol. Evol. Under review.

Archibald, J. M. 2019. Genomics reveals alga-associated cyanobacteria hiding in plain sight. Proc. Natl. Acad. Sci. USA. In Press.

Åsman, A., Curtis, B. A. & Archibald, J. M. 2019. Nucleomorph small RNAs in cryptophyte and chlorarachniophyte algae. Genome Biol. Evol. 11, 1117-1134.

Grisdale, C. J., Smith, D. R., and Archibald, J. M. 2019. Relative mutation rates in nucleomorph-bearing algae. Genome Biol. Evol. 11, 1045-1053.

Sibbald, S. J., Hopkins, J. F., Filloramo, G. V., & Archibald, J. M. 2019. Ubiquitin fusion proteins in complex algae: implications for the spread of eukaryotic photosynthesis. BMC Genomics 20: 38

Kim, J. I., Shin, H., Skaloud, P., Jung, J., Yoon, H.S., Archibald, J.M & Shin, W. 2019. Comparative plastid genomics of Synurophyceae: inverted repeat dynamics and gene content variation. BMC Evol. Biol. 19: 20

de Vries, S., de Vries, J., von Dahlen, J.K., Gould, S.B., Archibald, J.M., Rose, L.E., Slamovits, C.H. 2018. On plant defense signaling networks and early land plant evolution. Commun. Integr. Biol. 11: e1486168.

Cenci, U., Sibbald, S. J., Curtis, B. A., Eme, L., Moog, D., Henrissat, B., Maréchal, E., Chabi, M., Djemiel, C., Roger, A. J., Kim, E., and Archibald, J. M. 2018. Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea: phylogenomic and metabolic insights into the evolution of secondary plastids. BMC Biology 16: 137

Cheng, S., Melkonian, M., Smith, S. A., Brockington, S., Archibald, J. M., Delaux, P.-M., Li, F.-W., Melkonian, B., Mavrodiev, E. V., Sun, W., Fu, Y., Yang, H., Soltis, D. E., Graham, S. W., Soltis, P. S., Liu, Z., Xu, X., and Wong, G. K.-S. 2018. 10KP: a phylodiverse genome sequencing plan. GigaScience 7: 1-9.

Lukes, J., Jirsova, D., David, V., Wheeler, R. & Archibald, J. M. 2018. Massive mitochondrial DNA content in diplonemid and kinetoplastid protists. IUBMB Life 70(12):1267-1274.

Nowak, B. & Archibald, J. M. 2018. Opportunistic but lethal: the mystery of paramoebae. Trends Parasitol. 34, 404-419.

Archibald, J. M. 2018. Evolution: scaling lifes tree. Nature. 560, 26-27.

Archibald, J. M. 2018. Genomics: a very short introduction. Oxford University Press (VSI Series).

de Vries, J., Curtis, B.A., Gould, S.B. and Archibald, J.M. 2018. Embryophyte stress signalling evolved in the algal progenitors of land plants. Proc. Natl. Acad. Sci. USA 115: E3471-E3480.

Kim, J. I., Yoon, H. S., Gangman, Y., Shin, W., & Archibald, J. M. 2018.Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements. BMC Genomics 19: 275.

de Vries, J. & Archibald, J. M. 2018. Quick guide: plastid genomes. Curr. Biol. 28:R336-R337.

Raina, J.B., Eme, L., Pollock, F.J., Spang, A., Archibald, J.M. and Williams, T.A. 2018. Symbiosis in the microbial world: from ecology to genome evolution. Biol Open. 7(2): pii: bio032524.

de Vries, J. & Archibald, J. M. 2018. Plastid evolution: autonomy versus nuclear control. Advances in Botanical Research, Volume 85 (Plastid Genome Evolution). Chaw, S.-M. & Jansen, R. (eds.). In Press.

de Vries, J. & Archibald, J. M. 2018. Plant evolution: landmarks on the path to terrestrial life. New Phytol. Online early. doi: 10.1111/nph/14975.

Tanifuji, G., Cenci, U., Moog, D., Dean, S., Nakayama, T., David, V., Fiala, I., Curtis, B. A., Sibbald, S.J., Onodera, N.T., Colp, M., Flegontov, P., Johnson-MacKinnon, J., McPhee, M., Inagaki, Y., Hashimoto, T., Kelly, S., Gull, K., Lukeš, J., and Archibald, J. M. 2017. Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis. Scientific Rep. 7, 11688. doi:10.1038/s41598-017-11866-x.

Eleni Gentekaki, Bruce A. Curtis, Courtney Stairs, Vladimír Klimeš, Marek Eliáš, Dayana Salas, Emily K. Herman, Laura Eme, Maria C. Arias, Bernard Henrissat, Frédérique Hilliou, Mary Klute, Hiroshi Suga, Shehre-Banoo Malik, Arthur W. Pightling, Martin Kolisko, Richard A. Rachubinski, Alexander Schlacht, Darren M. Soanes, Anastasios D. Tsaousis, John M. Archibald, Steven G. Ball, Joel B. Dacks, C. Graham Clark, Mark van der Giezen, Andrew J. Roger. 2017. Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis. PLoS Biol. 15, e2003769.

Archibald, J. M. 2017. Evolution: Protein import into a nascent photosynthetic organelle. Curr. Biol. 27, R1004-1006.

Kim, J. I., Moore, C. E., Archibald, J. M., Bhattacharya, D., Gangman, Y., Yoon, H. S., & Shin, W. 2017. Evolutionary dynamics and lineage-specific gene loss in the plastid genomes of cryptophyte algae. Genome Biol. Evol. 9, 1859-1872.

Kamikawa, R., Moog, D., Zauner, S., Tanifuji, G., Ishida, K.-I., Miyashita, H., Mayama, S, Hashimoto, T, Maier, U.-G., Archibald, J. M., and Inagaki, Y. 2017. A non-photosynthetic diatom reveals early steps of reductive evolution in plastids. Mol. Biol. Evol. 34, 2355-2366.

Muñoz-Gómez, S. A., Mejía-Franco, F. G., Durnin, K., Colp, M., Grisdale, C. J., Archibald, J. M., Slamovits, C. H. 2017. The new red algal subphylum Proteorhodophytina is defined by the largest and most divergent plastid genomes known. Curr. Biol. 27, 1677-1684.

de Vries, J., de Vries, S., Slamovits, C. H., Rose, L. E., and Archibald, J. M. 2017. How embryophytic is penylpropanoid biosynthesis in streptophyte algae? Plant and Cell Physiol. 58, 934-935.

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. 4, 598-607.

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. 9, 473-479.

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.

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.

Simpson, A. G. B., Slamovits, C. H. & Archibald, J. M. 2017. Protist diversity and eukaryote phylogeny. 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.

Grisdale, C., & Archibald, J. M. 2017. Secondary and tertiary endosymbiosis. In: Reference Module in Life Sciences. Elsevier Publishing. ISBN: 978-0-12-809633-8.

Sibbald, S. J. & Archibald J. M. 2017. More protist genomes needed. Nature Ecol. Evol. 1, DOI: 10.1038/s41559-017-0145.

de Vries, J. & Archibald J. M. 2017. Endosymbiosis: did plastids evolve from a freshwater cyanobacterium? Curr. Biol. R1290-1292.

Edited work: Handbook of the Protists (2nd edition of the Handbook of Protoctista by Margulis et al.). 2017. Archibald, J.M., Simpson, A.G.B, & Slamovits, C. (Eds.). Springer.

Lab News

•Morgan Colp has won the Peter Dolphin Memorial Prize in Biochemistry as well as the University Medal in Biochemistry.

•John Archibald appointed Director of Dalhousie’s Centre for Comparative Genomics & Evolutionary Bioinformatics.

•Genomics: a very short introduction published Spring 2018.

• Archibald elected to the College of New Scholars, Artists and Scientists of the Royal Society of Canada (2016-2021).

Paperback of 'One Plus One Equals One' published in 2016.

Last updated: July 2019