Department of Biochemistry and Molecular Biology

Dalhousie University
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Sackler Symposium 2015

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Norway 2017

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Germany 2016

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Royal Society of Canada 2017

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Lab Group 2016

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John M. Archibald

Professor

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Department of Biochemistry and Molecular Biology , Department of Microbiology & Immunology

Email: john.archibald@dal.ca
Phone: 902-494-2536
Mailing Address: 
5850 College Street, Room 8-H1
Sir Charles Tupper Medical Building
PO Box 15000
Halifax, Nova Scotia, Canada B3H 4R2
 

Education

  • PhD, Dalhousie University

Academic Positions

Research Topics

Genome Evolution, gene transfer, endosymbiosis, molecular phylogeny

Research

Our laboratory uses molecular biological and computational methods to study the genes and genomes of prokaryotic and eukaryotic (nucleus-containing) microorganisms. Using a comparative genomics approach, we are interested in (1) the pivotal molecular and biochemical events that have shaped the evolution of eukaryotes; (2) understanding the evolutionary relationships amongst eukaryotic microbes; (3) how endosymbionts become organelles; and (4) understanding how eukaryotic genes, genomes and proteins change over time. We currently study the spread of photosynthetic organelles (chloroplasts) in eukaryotes and the extent to which lateral (horizontal) gene transfer has impacted the gene content of nuclear genomes.

Current Lab Members

Cedric Blais Grad Student (PhD)
Dudley Chung Postdoctoral Fellow (Dalhousie University)
Morgan Colp Grad Student (PhD)
Marlena Dlutek Lab Manager
Lucie Gallot-Lavellee Postdoctoral Fellow (Aix-Marseille University, France)
Jessica Latimer Grad Student (MSc)
Sari Matar Honours Student (2024)
Shannon Sibbald
 Grad Student (PhD)
Dmytro Tymoshenko Grad Student (PhD)

 

Publications

  1. Feng X, Zheng J, Irisarri I, Yu H, Zheng B, Ali Z, de Vries S, Keller J, Fürst-Jansen JMR, Dadras A, Zegers JMS, Rieseberg TP, Ashok AD, Darienko T, Bierenbroodspot MJ, Gramzow L, Petroll R, Haas FB, Fernandez-Pozo N, Nousias O, Li T, Fitzek E, Grayburn WS, Rittmeier N, Permann C, Rümpler F, Archibald JM, Theißen G, Mower JP, Lorenz M, Buschmann H, von Schwartzenberg K, Boston L, Hayes RD, Daum C, Barry K, Grigoriev IV, Wang X, Li FW, Rensing SA, Ari JB, Keren N, Mosquna A, Holzinger A, Delaux PM, Zhang C, Huang J, Mutwil M, de Vries J, Yin Y. (2023). Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution. bioRxiv preprint. 1:2023.01.31.526407. [Article]
  2. Rius, M., Rest, J. S., Filloramo, G., Vanclova, A., Archibald, J. M., & Collier, J.L. (2023). Horizontal gene transfer and fusion spread carotenogenesis among diverse heterotrophic protists. Genome. Biol. Evol. [Article]
  3. Zhang, X., Hu, Y., Cheng, Z. & Archibald, J. M. (2023). HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes. STAR Protocols. 4, 102014. [Article]
  4. Zhang, X., Hu, Y., Eme, L., Maruyama, S., Eveleigh, R.J.M., Curtis, B. A., Sibbald, S. J., Hopkins, J. F., Filloramo, G. V., van Wijk, K., & Archibald, J. M. (2022). Protocol for TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets. STAR Protocols. 3, 101175. [Article]
  5. Kim, J. I., Jo, B. Y., Park, M. G., Yoo, Y. D., Shin, W., & Archibald, J.M.(2022). Evolutionary dynamics and lateral gene transfer in raphidophycean plastid genomes. Frontiers Plant Sci. 13 [Article]
  6. Matthey-Doret*, C., Colp*., M.J., Escoll Guerrero, P., Thierry, A., Curtis, B. A., Sarrain, M., Gray, M.W., Lang B.F., Archibald, J.M., Buchrieser, C., & Koszul, R. (2022). Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin re-organization. Genome Res. 32, 1698-1710. [Article]
  7. Hess, S., Williams, S, Busch, A., Irisarri, I., Delwiche, C.F., de Vries, S., Darienko, T., Roger, A.J., Archibald, J. M., Buschmann, H., von Schwartzenberg, K., & de Vries, J. (2022). A phylogenomically informed five-order system for the closest relatives of land plants. Curr. Biol. 32, 1-10. [Article]
  8. Kim, J.I., Tanifuji, G., Minseok, J., Shin, W., & Archibald, J.M. (2022). Gene loss, pseudogenization and genome reduction in non-photosynthetic species of Cryptomonas (Cryptophyceae) revealed by comparative nucleomorph genomics. BMC Biol. 20:227. [Article]
  9. Lawniczak, M. K. N., Durbin, R., Flicek, P., Lindblad-Toh, K., Wei, X., Archibald, J. M., Baker, W. J., Belov, K., Blaxter, M. L., Marques Bonet, T., Childers, A. K., Coddington, J. A., Crandall, K. A., Crawford, A. J., Davey, R. P., Di Palma, F., Fang, Q., Haerty, W., Hall, N., Hoff, K. J., Howe, K., Jarvis, E. D., Johnson W. E., Johnson, R. N., Kersey, P. J., Liu, X., Lopez, J. V., Myers, E. W., Pettersson, O. V., Phillippy, A. M., Poelchau, M. F., Pruitt, K. D., Rhie, A., Castilla-Rubio, J. C., Sahu, S. K., Salmon, N. A., Soltis, P. S., Swarbreck, D., Thibaud-Nissen, F., Wang, S., Wegrzyn, J. L., Zhang, G., Zhang, H., Lewin, H. A., Richards, S. (2022). Standards recommendations for the Earth BioGenome Project. Proc. Natl. Acad. Sci. USA. 119, 4 [Article]
  10. Blaxter, M., Archibald, J. M., Childers, A. K., Coddington, J. A., Crandall, K. A., Di Palma, F., Durbin, R., Edwards, S. V., Graves, J. A. M., Hackett, K. J., Hall, N., Jarvis, E. D., Johnson, R. N., Karlsson, E. K., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Lindblad-Toh, K., Lopez, J. V., Moran, N.A., Robinson, G. E., Ryder, O. A., Shapiro, B., Soltis, P. S., Warnow, T., Zhang, G., & Lewin, H. A. (2022). Why sequence all eukaryotes? Proc. Natl. Acad. Sci. USA. 119, 4 [Article]
  11. Lewin, H. A., Richards, S., Lieberman Aiden, E., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, M.L., Cai, J., Caperello, N. D., Carlson, K., Castilla-Rubio, J. C., Chaw, S. M., Chen, L., Childers, A. K., Coddington, J. A., Conde, D. A., Corominas, M., Crandall, K. A., Crawford, A. J., DiPalma, F., Durbin, R., Ebenezer, T. E., Edwards, S. V., Fedrigo, O., Flicek, P., Formenti, G., Gibbs, R. A., Gilbert, M. T. P., Goldstein, M. M., Graves, J. M., Greely, H. T., Grigoriev, I. V., Hackett, K. J., Hall, N., Haussler, D., Helgen, K. M., Hogg, C. J., Isobe, S., Jakobsen, K. S., Janke, A., Jarvis, E. D., Johnson, W. E., Jones, S. J. M., Karlsson, E. K., Kersey, P. J., Kim, J. H., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Leebens-Mack, J. H., Li, X., Lindblad-Toh, K., Liu, X., Lopez, J. V., Marques-Bonet, T., Mazard, S., Mazet, J. A. K., Mazzoni, C. J., Myers, E. W., O'Neill, R. J., Paez, S., Park, H., Robinson, G. E., Roquet, C., Ryder, O. A., Sabir, J. S. M., Shaffer, H. B., Shank, T. M., Sherkow, J. S., Soltis, P. S., Tang, B., Tedersoo, L., Uliano-Silva, M., Wang, K., Wei, X., Wetzer, R., Wilson, J. L., Xu, X., Yang, H., Yoder, A. D., Zhang, G. (2022). The Earth BioGenome Project 2020: starting the clock. Proc. Natl. Acad. Sci. USA. 119, 4 [Article]
  12. Wright, V., Archibald, J. M., Beinart, R., Dawson, M.N., Hentschel, U., Keeling, P.J., Lopez, J.V., Martín-Durán, J.M., Petersen, J.M., Sigwart, J.D., Simakov, O., Sutherland, K.R., Sweet, M., Talbot, N., Thompson, A.W., Bender, S., Harrison, P.W., Rajan, J., Cochrane, G., Berriman, M., Lawniczak, M. & Blaxter, M. (2021). The Aquatic Symbiosis Genomics Project: probing the evolution of symbiosis across the tree of life. Wellcome Open Res. 6:254. Role: Co-author. [Article]
  13. Fürst-Jansen, J. M. R., de Vries, S. von Schwartzenberg, K. Archibald, J. M., & de Vries, J. (2021). Submergence of the filamentous Zygnematophyceae Mougeotia induces differential gene expression patterns associated with photosynthesis. Protoplasma. [Article]
  14. Salas-Leiva, D. E., Tromer, E. C., Curtis, B. A., Jerlstrom-Hultqvist, J., Kolisko, M., Yi, Z., Salas-Leiva, J. S., Gallot-Lavallée, L., Kops, J. J. P. L., Archibald, J. M., Simpson, A. G. B., & Roger, A. J. (2021). Genomic analysis finds no evidence of canonical eukaryotic DNA processing systems in a free-living protist. Nat. Comm. 12:6003.
  15. Rowarth, N. M., Curtis, B. A., Einfeldt, A. L., Archibald, J. M., Lacroix, C. R., & Gunawardena, A. H. L. A. N. (2021). RNA-Seq analysis reveals potential regulators involved in program cell death and remodeling of lace plant leaves (Aponogeton madagascariensis). BMC Plant Biol. 21:375.
  16. Filloramo, G. V., Blanche, E., Curtis, B. A., & Archibald, J. M. (2021). Re-examination of two diatom reference genomes using long-read sequencing. BMC Genomics. 22:379.
  17. Blais, C. & Archibald, J. M. (2021). The past, present and future of the Tree of Life. Curr Biol. 31, R311-329. IR
  18. Sibbald, S. J., Lawton, M. & Archibald, J. M. (2021) Mitochondrial genome evolution in pelagophyte algae. Genome Biol. Evol. 13(3) https://doi.org/10.1093/gbe/evab018 
  19. Gallot-Lavallée, L. & Archibald, J. M. (2020). Evolution: viral rhodopsins illuminate algal evolution. Curr. Biol. 30, R1469-1471. IC
  20. Archibald, J. M. (2020) Quick Guide: Cryptomonads. Curr. Biol. 30, R1116-R1115. IC
  21. Kim, J. I., Minseok, J., Archibald, J. M. & Shin, W. (2020). Comparative plastid genomics of non-photosynthetic chrysophytes: genome reduction and compaction. Frontiers in Plant Science. [Article]
  22. de Vries, S., de Vries, J., Archibald, J. M., & Slamovits, C. S. (2020). Comparative analyses of saprotrophy in Salisapilia sapeloensis and diverse plant pathogenic oomycetes reveal lifestyle-specific gene expression. FEMS Microbiol. Ecol. 96,0000. [Article]
  23. Sibbald, S. J., Eme, L., Archibald, J. M. & Roger, A. J. (2020) Lateral gene transfer mechanisms and pan-genomes in eukaryotes. Trends Parasitol. [Article]
  24. de Vries, J., de Vries, S., Curtis, B.A., Zhou, H., Penny, S., Feussner, K., Pinto, D.M., Steinert, M., Cohen, A., von Schwartzenberg, K., & Archibald, J. M. (2020) Heat stress response in the closest algal relatives of land plants reveals conserved stress signalling circuits. Plant J. 103, 1025-1048. [Article]
  25. Sibbald, S. J. & Archibald, J. M. (2020) Genomic insights into plastid evolution. Genome Biol. Evol. 12(7), 978-990. [Article]
  26. Colp, M. & Archibald, J. M. (2020) The language of symbiosis: insights from protist biology. In: Cellular dialogs in the holobiont. Bosch, T. and Hadfield, M. (eds.). CRC Press.
  27. Gallot-Lavallée, L. & Archibald, J. M. (2020) Spotlight: Phagocytosis in a shape-shifting bacterium. Trends Trends Microbiol. 28:429-430
  28. Tanifuji, G., Kamikawa, R., Moore, C. E., Mills, T., Onodera, N. T., Kashiyama, Y., Archibald, J. M., Inagaki, Y, & Hahimoto, T. (2020) Comparative plastid genomics of photosynthetic and non-photosynthetic Cryptomonas species reveals loss of photosynthesis. Genome Biol. Evol. [Article]
  29. Colp, M. J. & Archibald, J. M. (2019) Evolution: New protist predators under the sun. Curr. Biol. 29, R936-R-938.
  30. Archibald, J. M. , (2019) Genomics reveals alga-associated cyanobacteria hiding in plain sight. Proc. Natl. Acad. Sci. USA. 116, 15757-15759
  31. 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
  32. Kim, J. I., Shin, H., Škaloud, 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
  33. Grisdale, C. J., Smith, D. R., and Archibald, J. M. , (2019) Relative mutation rates in nucleomorph-bearing algae. Genome Biol. Evol. 11:1045-1053
  34. Åsman, A., Curtis, B. A. & Archibald, J. M. , (2019) Nucleomorph small RNAs in cryptophyte and chlorarachniophyte algae. Genome Biol. Evol. 11:1117-1134
  35. 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 [Online]
  36. de Vries, J. & Archibald, J. M., (2018) Plastid evolution: autonomy versus nuclear control. Advances in Botanical Research 85 (Plastid Genome Evolution):Chaw, S.-M. & Jansen, R. (eds.)
  37. 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.:
  38. Archibald, J. M. , (2018) Genomics: a very short introduction. (VSI Series) Oxford University Press:ISBN: 978-0-19-878620-7
  39. 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, X., Xu, X. and Wong, G.K. (, (2018) 10KP: A phylodiverse genome sequencing plan. Gigascience 7:1-9
  40. de Vries, J. and Archibald, J.M., (2018) Quick guide: plastid genomes. Curr. Biol. 28:R336-R337
  41. 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
  42. Kim, J.I., Yoon, H.S., Yi, G., Shin, W. and Archibald, J.M., (2018) Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements. BMC Genomics 19:275
  43. Lukeš, J., Jirsová, D., David, V., Wheeler, R. & Archibald, J. M., (2018) Massive mitochondrial DNA content in diplonemid and kinetoplastid protists. IUBMB Life 70:1267-1274
  44. 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
  45. Nowak, B. & Archibald, J. M. , (2018) Opportunistic but lethal: the mystery of paramoebae. Trends Parasitol. 34: 404-419
  46. de Vries S, de Vries J, von Dahlen JK, Gould SB, Archibald JM, Rose LE, Slamovits CH, (2018) On plant defense signaling networks and early land plant evolution Commun. Integr. Biol. 11:e1486168
  47. 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., & Archibald, J. M. , (2018) Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids BMC Biology 16:137
  48. Archibald, J. M. , (2018) Evolution: scaling life’s tree. Nature 560:26-27
  49. 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]
  50. 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:
  51. de Vries, J. & Archibald J. M., (2017) Endosymbiosis: did plastids evolve from a freshwater cyanobacterium? Curr. Biol. 27:R103-105
  52. Sibbald, S. J. & Archibald J. M., (2017) More protist genomes needed. Nature Ecol. Evol. :In Press.
  53. 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:
  54. 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
  55. 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.
  56. 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.
  57. 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
  58. Archibald J. M. , (2017) Evolution: Protein import into a nascent photosynthetic organelle. Curr. Biol. 27:R1004-1006
  59. Grisdale, C., & Archibald, J. M. , (2017) Secondary and tertiary endosymbiosis. Reference Module in Life Sciences. Elsevier Publishing. :ISBN: 978-0-12-809633-8.
  60. 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
  61. 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
  62. Kim, J. I., Moore, C. E., Archibald, J. M., Bhattacharya, D., Gangman, Y., Yoon, H. S., & Shin, W. , (2017) Evolutionary dynamics of cryptophyte plastid genomes. Genome Biol. Evol. 9:1859-1872
  63. 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. Ev 34:2355-2366
  64. de Vries, J., de Vries, S., Slamovits, C. H., Rose, L. E., and Archibald, J. M. , (2017) How embryophytic is the biosynthesis of phenylpropanoids and their derivatives in streptophyte algae? Plant and Cell Physiol 58:934-935. doi: 10.1093/pcp/pcx037
  65. 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)
  66. 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:
  67. 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.
  68. 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
  69. David, V. & Archibald J. M., (2016) Evolution: plumbing the depths of diplonemid diversity. Curr. Biol. :R1290-1292
  70. 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
  71. Archibald, J. M., (2016) One plus one equals one: symbiosis and the evolution of complex life. 224 pp. ISBN: 978-0-19-966059-9. (Paperback with new Afterward) Oxford University Press.:
  72. 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]
  73. Archibald, J. M. , (2015) Genomic perspectives on the birth and spread of plastids. Proc. Natl. Acad. Sci. USA. 112:10147-10153
  74. Archibald, J. M. , (2015) Endosymbiosis and eukaryotic cell evolution. Curr. Biol. 25:R911-R921
  75. 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):
  76. 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
  77. Archibald, J. M. , (2015) Evolution: Gene transfer in complex cells. Nature 524:423-424
  78. 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]
  79. 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]
  80. 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]
  81. 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]
  82. 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 [PubMed] [Article]
  83. 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 [PubMed] [Article]
  84. Tanifuji, G. & Archibald, J. M., (2014) Nucleomorph comparative genomics Endosymbiosis, Löffelhardt, W. Springer Wein New York:197-213
  85. Archibald, J. M., (2014) One plus one equals one: symbiosis and the evolution of complex life. Oxford University Press.:
  86. 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 [PubMed] [Article]
  87. 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 [PubMed] [Article]
  88. Maruyama, S., Eveleigh, R. J. M. & Archibald, J. M. , (2013) TreeTrimmer: a method for phylogenetic dataset size reduction BMC Research Notes 6:145 [PubMed] [Article]
  89. Kim E, Archibald JM, (2013) Ultrastructure and molecular phylogeny of the cryptomonad Goniomonas avonlea sp. nov. Protist 164(2):160-82 [PubMed] [Article]
  90. Eveleigh, R. J. M., Meehan, C.J., Archibald, J. M. & Beiko, R. G. , (2013) Being Aquifex aeolicus: untangling a hyperthermophile’s checkered past Genome Biol. Evol 5:2478-2497 [PubMed] [Article]
  91. Archibald, J. M., (2012) Obituary: Lynn Margulis (1938-2011) Curr. Biol. :R4-6
  92. Archibald, J. M., (2012) Plastid origins. Organelle genetics: evolution of organelle genomes and gene expression, Bullerwell, C. Editor. Springer-Verlag, New York.:19-38
  93. Gray, M.W. and Archibald, J.M., (2012) Origins of mitochondria and plastids. Genomics of Chloroplasts and Mitochondria, R. Bock and V. Knoop (eds.) Springer, Dordrecht:1-30
  94. 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 [PubMed]
  95. 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. [PubMed]
  96. 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., [56 AUTHORS], 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 [PubMed]
  97. 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 [PubMed]
  98. 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 [PubMed] [Article]
  99. Nakayama, T. & Archibald, J. M, (2012) Evolving a photosynthetic organelle. BMC. Biol 10:35 [PubMed]
  100. Archibald, J. M., (2012) The evolution of algae by secondary and tertiary endosymbiosis. Genomic insights into the biology of algae. Piganeau, G. (ed.) Elsevier Ltd: Academic Press:87-118
  101. Maruyama, S. & Archibald, J. M. , (2012) Endosymbiosis, gene transfer, and algal cell evolution. Advances in algal cell biology,Heimann, K. & Katsaros, C. (eds.) Walter de Gruyter:In Press
  102. Archibald, J. M., (2011) Origin of eukaryotic cells: 40 years on Symbiosis 54:69-86
  103. Lukes, J., Archibald, J.M., Keeling, P.J., Doolittle, W.F. and Gray, M.W., (2011) How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 63:528-537
  104. Hoef-Emden, K. & Archibald, J. M., (2011) Phylum Cryptophyta (Cryptomonads) In Handbook of Protoctista, Second Edition, L. Margulis (ed.) Jones and Bartlett:In Press
  105. Tanifuji, G., Onodera, N. T.,Wheeler, T. J., Dlutek, M., Donaher, N. & Archibald, J. M., (2011) Complete nucleomorph genome sequence of the non-photosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set. Genome Biol. Evol. 3:44-54 [PubMed]
  106. Kim, E., Harrison, J., Sudek, S., Jones, M. D. M., Wilcox, H. M., Richards, T. A., Worden, A. Z., & Archibald, J. M., (2011) Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life. Proc. Natl. Acad. Sci. U.S.A. 108:1496-1500 [PubMed]
  107. Richards, T. A. & Archibald J. M., (2011) Cell evolution: gene transfer agents and the origin of mitochondria Curr. Biol. 21:112-114 [PubMed]
  108. Doolittle, W.F., Lukeš, J., Archibald, J.M.. Keeling, P.J. and Gray, M.W., (2011) Comment on “Does constructive neutral evolution play an important role in the origin of cellular complexity?” Bioessays 33:427-429 [PubMed]
  109. McInerney, J. O., Martin, W. F., Koonin, E. V., Allen, J. F., Galerin, M. Y., Lane, N., Archibald, J. M. & Embley, T. M., (2011) Planctomycetes and eukaryotes: A case of analogy not homology. BioEssays 33:810-817 [PubMed]
  110. Tanifuji, G., Onodera, N. T., Gibeault, R., Dlutek, M., Cawthorn, R. J., Fiala, I., Lukes, J., Greenwood, S. J. & Archibald, J. M., (2011) Genomic characterization of Neoparamoeba pemaquidensis (Amoebozoa) and its kinetoplastid endosymbiont. Eukaryot. Cell 10:1143-1146 [PubMed]
  111. Maruyama, S., Suzaki, T., Weber, A. P., Archibald, J. M., & Nozaki, H., (2011) Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids. BMC Evol. Biol. 11:105 [PubMed]
  112. Kim, E. and Archibald, J. M., (2010) Plastid evolution: gene transfer and the maintenance of 'stolen' organelles BMC Biology 8:73 [PubMed]
  113. Curtis, B. A. and Archibald, J. M., (2010) Problems and progress in understanding the origins of mitochondria and plastids. Symbioses and stress, J. Seckbach and M. Grube (eds.) Springer-Verlag, Germany:41-62
  114. Hopkins, J. & Archibald, J. M., (2010) Plastid evolution and the nuclear genomic 'footprint' of red and green algal endosymbionts In: Red algae in the genomics age, Seckbach, J. & Chapman, D. J. (eds.) Springer-Verlag:191-204
  115. Silver, T. D., Moore, C. E. and Archibald, J. M., (2010) Nucleomorph ribosomal DNA and telomere dynamics in chlorarachniophyte algae J. Euk. Microbiol. 57:453-459 [PubMed]
  116. Kim, E., Park, J. S., Simpson, A. G. B., Matsunaga, S. Watanabe, M., Murakami, A., Sommerfeld, K., Onodera, N. T. and Archibald, J. M., (2010) Complex array of endobionts in Petalomonas sphagnophila, a large heterotrophic euglenid protist from Sphagnum-dominated peatlands. ISME Journal 4:1108-1120 [PubMed]
  117. Tanifuji, G. & Archibald, J. M., (2010) Actin gene family dynamics in cryptomonads and red algae J. Mol. Evol. 71:169-179 [PubMed]
  118. Curtis, B. A. & Archibald, J. M., (2010) A spliceosomal intron of mitochondrial DNA origin. Curr. Biol. 20:R919-920 [PubMed]
  119. Gray, M. W., Lukes, J., Archibald, J. M., Keeling, P. J., & Doolittle, W. F. , (2010) Cell biology. Irremediable complexity? Science 330:920-921 [PubMed]
  120. Archibald, J. M. & Richards, T. A., (2010) Gene transfer: anything goes in plant mitochondria BMC Biology 8:147 [PubMed]
  121. Archibald, J. M., and Lane, C. E., (2009) Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction. J. Heredity 100:582-590 [PubMed]
  122. Archibald, J. M., (2009) The origin and spread of eukaryotic photosynthesis-evolving views in light of genomics. Bot. Marina 52:95-103
  123. Archibald, J. M., (2009) Secondary endosymbiosis. Encyclopedia of Microbiology, Third Edition, Schaechter, M. (ed.) Oxford: Elsevier:438-446
  124. Archibald, J. M., (2009) The puzzle of plastid evolution. Curr. Biol. 19:R81-R88. [PubMed]
  125. Lane, C. E. & Archibald, J. M., (2009) Reply to Bodyl, Stiller and Mackiewicz: "Chromalveolate plastids: direct descent or multiple endosymbioses?" Trends Ecol. Evol. 24:121-122 [PubMed]
  126. Ota, S., Silver, T. D., Archibald, J. M. & Ishida, K.-I., (2009) Lotharella oceanica sp. nov.-a new planktonic chlorarachniophyte studied by light and electron microscopy. Phycologia 48:317-325.
  127. Archibald, J. M., (2009) Genomics: Green evolution, green revolution. Science 324:191-192 [PubMed]
  128. Moore, C. & Archibald, J. M., (2009) Nucleomorph genomes. Annu. Rev. Genet. 43:251-264
  129. Elias, M. & Archibald, J. M., (2009) The RJL family of small GTPases is an ancient eukaryotic invention probably functionally associated with the flagellar apparatus. Gene. 442:63-72 [PubMed]
  130. Burki, F., Inagaki, Y., Brate, J., Archibald, J. M., Keeling, P. J., Cavalier-Smith, T., Sakaguchi, M., Hashimoto, T., Horak, A., Kumar, S., Klaveness, D., Jakobsen, K. S., Pawkowski, J., & Shalchian-Tabrizi, K., (2009) Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol. Evol. 2009, 231-238 doi:10.1093/gbe/evp022:
  131. Donaher, N., Tanifuji, G., Onodera, N. T., Malfatti, S. A., Chain, P. S. G., Hara, Y., & Archibald, J. M., (2009) The complete plastid genome sequence of the secondarily non-photosynthetic alga Cryptomonas paramecium: reduction, compaction, and accellerated evolutionary rate. Genome Biol. Evol. 2009, 439-448: [PubMed]
  132. Elias, M. and Archibald, J. M., (2009) Sizing up the genomic footprint of endosymbiosis BioEssays 31:1273-1279 [PubMed]
  133. Fong, A., & Archibald, J. M., (2008) Evolutionary dynamics of light-independent protochlorophyllide oxidoreductase (LIPOR) genes in the secondary plastids of cryptophyte algae. Euk. Cell. 7:550-553 [PubMed]
  134. Khan, H., & Archibald, J. M., (2008) Lateral transfer of introns in the cryptophyte plastid genome. Nucleic Acids Res. doi:10.1093/nar/gkn095: [PubMed]
  135. Lane, C. E., & Archibald, J. M., (2008) The eukaryotic Tree of Life: endosymbiosis takes its TOL Trends Ecol. Evol. 23:268-275 [PubMed]
  136. Kim, E., Lane, C. E., Curtis, B. A., Kozera, C., Bowman, S., & Archibald, J. M., (2008) Complete sequence and analysis of the mitochondrial genome of Hemiselmis andersenii CCMP644 (Cryptophyceae). BMC Genomics 9:215 [PubMed]
  137. Lane, C. E. & Archibald, J. M., (2008) New members of the genus Hemiselmis (Cryptomonadales, Cryptophyceae) J. Phycol. 44:339-350
  138. Phipps, K., Donaher, N., Lane, C. E., & Archibald, J. M., (2008) Nucleomorph karyotype diversity in the freshwater cryptophyte genus Cryptomonas J. Phycol. 44:11-14
  139. Cuvelier, M. L., Ortiz, A., Kim, Eunsoo, Moehlig, H., Richardson, D. E., Heidelberg, J. F., Archibald, John M. & Worden, A. Z., (2008) Widespread distribution of a unique protistan lineage Env. Microbiol. doi: 10.1111/j.1462-2920.2008.01580.x: [PubMed]
  140. Kim, E. and Archibald, J. M., (2008) Diversity and evolution of plastids and their genomes The chloroplast-interactions with the environment, Aronsson, H. &, Sandelius, A. S. (eds.) Springer-Verlag, Berlin:1-40
  141. Keeling, P. J. and Archibald, J. M., (2008) Organelle evolution: what's in a name? Curr. Biol. 18:345-347 [PubMed]
  142. Archibald, J. M., (2008) Plastid evolution: remant algal genes in ciliates. Curr. Biol. 18:663-665
  143. Archibald, J. M., (2008) The eocyte hypothesis and the origin of eukaryotic cells. Proc. Natl. Acad. Sci. USA 51:20049-20050 [PubMed]
  144. Adl, S. M., Leander, B. S., Simpson, A. G. B., Archibald, J. M., Anderson, O. R., Bass, D., Bowser, S. S., Brugerolle, G., Farmer, M. A., Karpov, S., Kolisko, M., Lane, C. E., Lodge, D. J., Mann, D. G., Meisterfeld, R., Mendoza, L., Moestrup, O., Mozley-Standridge, S. E., Smirnov, A. V., & Spiegel, F. , (2007) Diversity, nomenclature, and taxonomy of protists. Syst. Biol. 56:684-689 [PubMed]
  145. Khan, H., Kozera, C., Curtis, B. A., Tarrant Bussey, J., Theophilou, S., Bowman, S., & Archibald, J. M. , (2007) Retrotransposons and tandem repeat sequences in the nuclear genomes of cryptomonad algae. J. Mol. Evol. 64:223-236 [PubMed]
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  147. Khan, H., Parks, N. Kozera, C., Curtis, B. A., Parsons, B., Bowman, S., & Archibald, J. M., (2007) Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny. Mol. Biol. Evol. 24:1832-1842 [PubMed]
  148. Silver, T. D., Koike, S., Yabuki, A., Kofuji, R., Archibald, J. M., & Ishida, K.-I., (2007) Phylogeny and nucleomorph karyotype diversity of chlorarachniophyte algae. J. Ekaryot. Microbiol. 54:403-410 [PubMed]
  149. Bhattacharya, D., Archibald, J. M., Weber, A. P. M. & Reyes-Prieto, A., (2007) How do endosymbionts become organelles? Understanding early events in plastid evolution. BioEssays 29:1239-1246 [PubMed]
  150. Archibald, J. M., (2007) Review of Genomics and Evolution of Microbial Eukaryotes Q. Rev. Biol. 82:275-276
  151. Lane, C. E., van den Heuvel, K., Kozera, C., Curtis, B. A., Parsons, B., Bowman, S., & Archibald, J. M., (2007) Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function. Proc. Natl. Acad. Sci. U.S.A. 104:19908-19913 [PubMed]
  152. Lane, C.E., Khan, H., MacKinnon, M., Fong, A., Theophilou, S., and Archibald, J.M., (2006) Insight into the diversity and evolution of the cryptomonad nucleomorph genome Mol. Biol. Evol. 23:856-865 [PubMed]
  153. Ruiz-Trillo, I., Lane, C. E., Archibald, J. M. and Roger, A. J., (2006) Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica. J. Euk. Microbiol. 53:379-384. [PubMed]
  154. Archibald, J. M., (2006) Endosymbiosis: double-take on plastid origins. Curr. Biol. 16:R690-R692 [PubMed]
  155. Archibald, J. M., (2006) Genome complexity in a lean, mean photosynthetic machine. Proc. Natl. Acad. Sci. USA 103:11433-11434 [PubMed]
  156. Lane, C. E. & Archibald, J. M., (2006) Novel nucleomorph genome architecture in the cryptomonad genus Hemiselmis. J. Euk. Microbiol. 53:515-521 [PubMed]
  157. Archibald, J. M., (2006) Algal genomics: exploring the imprint of endosymbiosis. Curr. Biol. 16:R1033-1035 [PubMed]
  158. Bhattacharya, D. & Archibald, J. M., (2006) Response to: "The difference between endosybmionts and organelles". Curr. Biol. 16:R1017-1018
  159. Archibald, J. M. & Keeling, P. J., (2005) On the origin and evolution of plastids. Microbial phylogeny and evolution, J. Saap (ed.) Oxford University Press, New York:238-260
  160. Patron, N. J., Waller, R. F., Archibald, J. M. & Keeling, P. J., (2005) Complex protein targeting to dinoflagellate plastids. J. Mol. Biol. 348:1015-1024 [PubMed]
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  163. Archibald, J. M. and Keeling, P. J., (2004) Ubiquitin and actin protein sequences support a cercozoan/foraminiferan ancestry for the plasmodiophorid plant pathogens. J. Euk. Microbiol. 51:1-6 [PubMed]
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  166. Rogers, M.B., Archibald, J.M., Field, M.A., Li, C., Striepen, B. and Keeling, P. J., (2004) Plastid-targeting peptides from the chlorarachniophyte Bigelowiella natans. J. Eukaryot. Microbiol. 51:529-535 [PubMed]
  167. Archibald, J. M., Rogers, M., Toop, M. Ishida, K., and Keeling, P. J., (2003) Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans. Proc. Natl. Acad. Sci. U.S.A. 100:7678-7683 [PubMed]
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  170. Archibald, J.M. and Keeling, P.J., (2003) Plant genomes: cyanobacterial genes revealed. Heredity 90:2-3 [PubMed]
  171. Longet, D., Archibald, J.M., Keeling, P.J., and Pawlowski, J., (2003) Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies. Int. J. Syst. Evol. Microbiol. 53:1735-1739 [PubMed]
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  173. Archibald, J. M. and Roger, A. J., (2002) Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signal. J. Mol. Evol. 55:232-245 [PubMed]
  174. Archibald, J. M. and Roger, A. J., (2002) Gene duplication and gene conversion shape the evolution of archaeal chaperonins. J. Mol. Biol. 316:1041-1050 [PubMed]
  175. Archibald, J. M., Cavalier-Smith, T., Maier, U-G. and Douglas, S., (2001) Molecular chaperones encoded by a reduced eukaryotic nucleus: the cryptomonad nucleomorph. J. Mol. Evol. 52:490-501 [PubMed]
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