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John M. Archibald

PhD (Dalhousie)


Professor

Senior Fellow, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity
University Research Professor (July 2016-June 2021)
Department member since 2003

Tupper 8-H1
902-494-2536
john.archibald@dal.ca
Lab Homepage

Research:

Genome Evolution, Endosymbiosis, Molecular Phylogeny


Research Areas

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.

Graduate Students

Vojtech David PhD
Shannon Sibbald MSc

Postdoctoral Fellows

Bruce Curtis Dalhousie University
Cameron Grisdale University of British Columbia
Daniel Moog Philipps University of Marburg, Germany

Honours Students

Morgan Colp Biochemistry Co-op (2017)

Lab Personnel

Marlena Dlutek Lab Manager

Publications

  1. 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
  2. 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:
  3. 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
  4. 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. :
  5. de Vries, J., Stanton, A., Archibald, J. M., & Gould, S. B. , (2016) Streptophyte terrestrialization in light of plastid evolution. Trends Plant Sci. Online-early. (Invited Opinion Article):
  6. 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]
  7. Archibald, J. M. , (2015) Genomic perspectives on the birth and spread of plastids. Proc. Natl. Acad. Sci. USA. 112:10147-10153
  8. Archibald, J. M. , (2015) Endosymbiosis and eukaryotic cell evolution. Curr. Biol. 25:R911-R921
  9. 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):
  10. 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
  11. Archibald, J. M. , (2015) Evolution: Gene transfer in complex cells. Nature 524:423-424
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. Tanifuji, G. & Archibald, J. M., (2014) Nucleomorph comparative genomics Endosymbiosis, Löffelhardt, W. Springer Wein New York:197-213
  19. Archibald, J. M., (2014) One plus one equals one: symbiosis and the evolution of complex life. Oxford University Press.:
  20. 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]
  21. 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]
  22. 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]
  23. Kim E, Archibald JM, (2013) Ultrastructure and molecular phylogeny of the cryptomonad Goniomonas avonlea sp. nov. Protist 164(2):160-82 [PubMed] [Article]
  24. 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]
  25. Archibald, J. M., (2012) Obituary: Lynn Margulis (1938-2011) Curr. Biol. :R4-6
  26. Archibald, J. M., (2012) Plastid origins. Organelle genetics: evolution of organelle genomes and gene expression, Bullerwell, C. Editor. Springer-Verlag, New York.:19-38
  27. 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
  28. 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]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. Nakayama, T. & Archibald, J. M, (2012) Evolving a photosynthetic organelle. BMC. Biol 10:35 [PubMed]
  34. 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
  35. 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
  36. Archibald, J. M., (2011) Origin of eukaryotic cells: 40 years on Symbiosis 54:69-86
  37. 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
  38. Hoef-Emden, K. & Archibald, J. M., (2011) Phylum Cryptophyta (Cryptomonads) In Handbook of Protoctista, Second Edition, L. Margulis (ed.) Jones and Bartlett:In Press
  39. 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]
  40. 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]
  41. Richards, T. A. & Archibald J. M., (2011) Cell evolution: gene transfer agents and the origin of mitochondria Curr. Biol. 21:112-114 [PubMed]
  42. 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]
  43. 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]
  44. 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]
  45. 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]
  46. Kim, E. and Archibald, J. M., (2010) Plastid evolution: gene transfer and the maintenance of 'stolen' organelles BMC Biology 8:73 [PubMed]
  47. 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
  48. 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
  49. 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]
  50. 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]
  51. Tanifuji, G. & Archibald, J. M., (2010) Actin gene family dynamics in cryptomonads and red algae J. Mol. Evol. 71:169-179 [PubMed]
  52. Curtis, B. A. & Archibald, J. M., (2010) A spliceosomal intron of mitochondrial DNA origin. Curr. Biol. 20:R919-920 [PubMed]
  53. Gray, M. W., Lukes, J., Archibald, J. M., Keeling, P. J., & Doolittle, W. F. , (2010) Cell biology. Irremediable complexity? Science 330:920-921 [PubMed]
  54. Archibald, J. M. & Richards, T. A., (2010) Gene transfer: anything goes in plant mitochondria BMC Biology 8:147 [PubMed]
  55. 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]
  56. Archibald, J. M., (2009) The origin and spread of eukaryotic photosynthesis-evolving views in light of genomics. Bot. Marina 52:95-103
  57. Archibald, J. M., (2009) Secondary endosymbiosis. Encyclopedia of Microbiology, Third Edition, Schaechter, M. (ed.) Oxford: Elsevier:438-446
  58. Archibald, J. M., (2009) The puzzle of plastid evolution. Curr. Biol. 19:R81-R88. [PubMed]
  59. 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]
  60. 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.
  61. Archibald, J. M., (2009) Genomics: Green evolution, green revolution. Science 324:191-192 [PubMed]
  62. Moore, C. & Archibald, J. M., (2009) Nucleomorph genomes. Annu. Rev. Genet. 43:251-264
  63. 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]
  64. 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:
  65. 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]
  66. Elias, M. and Archibald, J. M., (2009) Sizing up the genomic footprint of endosymbiosis BioEssays 31:1273-1279 [PubMed]
  67. 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]
  68. Khan, H., & Archibald, J. M., (2008) Lateral transfer of introns in the cryptophyte plastid genome. Nucleic Acids Res. doi:10.1093/nar/gkn095: [PubMed]
  69. Lane, C. E., & Archibald, J. M., (2008) The eukaryotic Tree of Life: endosymbiosis takes its TOL Trends Ecol. Evol. 23:268-275 [PubMed]
  70. 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]
  71. Lane, C. E. & Archibald, J. M., (2008) New members of the genus Hemiselmis (Cryptomonadales, Cryptophyceae) J. Phycol. 44:339-350
  72. 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
  73. 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]
  74. 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
  75. Keeling, P. J. and Archibald, J. M., (2008) Organelle evolution: what's in a name? Curr. Biol. 18:345-347 [PubMed]
  76. Archibald, J. M., (2008) Plastid evolution: remant algal genes in ciliates. Curr. Biol. 18:663-665
  77. Archibald, J. M., (2008) The eocyte hypothesis and the origin of eukaryotic cells. Proc. Natl. Acad. Sci. USA 51:20049-20050 [PubMed]
  78. 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]
  79. 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]
  80. Archibald, J. M., (2007) Nucleomorph genomes: structure, function, origin and evolution. BioEssays. 4:392-402 [PubMed]
  81. 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]
  82. 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]
  83. 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]
  84. Archibald, J. M., (2007) Review of Genomics and Evolution of Microbial Eukaryotes Q. Rev. Biol. 82:275-276
  85. 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]
  86. 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]
  87. 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]
  88. Archibald, J. M., (2006) Endosymbiosis: double-take on plastid origins. Curr. Biol. 16:R690-R692 [PubMed]
  89. Archibald, J. M., (2006) Genome complexity in a lean, mean photosynthetic machine. Proc. Natl. Acad. Sci. USA 103:11433-11434 [PubMed]
  90. Lane, C. E. & Archibald, J. M., (2006) Novel nucleomorph genome architecture in the cryptomonad genus Hemiselmis. J. Euk. Microbiol. 53:515-521 [PubMed]
  91. Archibald, J. M., (2006) Algal genomics: exploring the imprint of endosymbiosis. Curr. Biol. 16:R1033-1035 [PubMed]
  92. Bhattacharya, D. & Archibald, J. M., (2006) Response to: "The difference between endosybmionts and organelles". Curr. Biol. 16:R1017-1018
  93. 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
  94. 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]
  95. Kim, J. C., Ou, Y. Y., Badano, J., Esmail, M. A., Leitch, C. C., Fiedrich, E., Beales, P. L., Archibald, J. M., Katsanis, N., Rattner, J. B., Leroux, M. R. , (2005) MKKS/BBS6, a divergent chaperonin-like protein linked to the obesity disorder Bardet-Biedl syndrome, is a novel centrosomal component required for cytokinesis. J. Cell Sci. 118:1007-1020 [PubMed]
  96. Archibald, J. M., (2005) Jumping genes and shrinking genomes-probing the evolution of eukaryotic photosynthesis using genomics IUBMB Life 57:539-547 [PubMed]
  97. 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]
  98. Archibald, J. M. & Keeling, P. J., (2004) The evolutionary history of plastids: a molecular phylogenetic perspective. Organelles, genomes and eukaryote phylogeny: an evolutionary synthesis in the age of genomics, R. P. Hirt and D. S. Horner (eds.) Taylor and Francis Books, London:55-74
  99. Keeling, P. J., Archibald, J. M., Fast, N. M., Palmer, J. D. , (2004) Comment on "The evolution of modern eukaryotic phytoplankton". Science 306:2191b [PubMed]
  100. 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]
  101. 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]
  102. Archibald, J. M., Teh, E. M. and Keeling, P. J., (2003) Novel ubiquitin fusion proteins: ribosomal protein P1 and actin. J. Mol. Biol. 328:771-778 [PubMed]
  103. Archibald, J. M., Longet, D., Pawlowski, J. and Keeling, P. J., (2003) A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol. Biol. Evol. 20:62-66 [PubMed]
  104. Archibald, J.M. and Keeling, P.J., (2003) Plant genomes: cyanobacterial genes revealed. Heredity 90:2-3 [PubMed]
  105. 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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