Publications from John Archibald and the Archibald Lab

Tanifuji, G., Onodera, N. T., Moore, C. E. & Archibald, J. M., (2014) Reduced nuclear genomes maintain high levels of gene transcription. Mol. Biol. Evol In Press (Published online December 2013)

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

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. In Press.

Kim, E. & Archibald, J. M. 2012. Ultrastructure and molecular phylogeny of the cryptomonad Goniomonas avonlea sp. nov. Protist. e-pub ahead of print.

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., Ko?ený, 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.

Archibald, J. M. 2011. Origin of eukaryotic cells: 40 years on. Symbiosis, 54, 69-86.

McInerney, J. O., Martin, W. F., Koonin, E. V., Allen, J. F., Galperin, 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.

Tanifuji, G., Kim, E., 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.

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.

Doolittle W. F., Lukes, J., Archibald, J. M., Keeling, P. J., & 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

Richards, T. A. & Archibald, J. M. 2011. Cell evolution: gene transfer agents and the origin of mitochondria. Curr. Biol. 21, R112-114. PubMed.

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. Correction

Lukes, J., Archibald, J. M., Keeling, P. J., Doolittle, W. F., & Gray, M. W., 2011. How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life. 63, 528-537. PubMed

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.

Hoef-Emden, K. & Archibald, J. M. 2011. Phylum Cryptophyta (Cryptomonads). In: Handbook of Protoctista, Second Edition. Margulis, L. (ed). Jones and Bartlett Publishers. In Press.

Archibald, J. M. & Richards, T. A. 2010. Gene transfer: anything goes in plant mitochondria. BMC Biology. 8,147. PubMed

Gray, M. W., Lukes, J., Archibald, J. M., Keeling, P. J., & Doolittle, W. F. 2010. Cell biology. Irremediable complexity? Science. 330, 920-921. PubMed

Curtis, B. A. & Archibald, J. M. 2010. A spliceosomal intron of mitochondrial DNA origin. Curr. Biol. 20, R919-920. PubMed

Silver, T. D., Moore, C. E. & Archibald, J. M. 2010. Nucleomorph ribosomal DNA and telomere dynamics in chlorarachniophyte algae. J. Euk. Microbiol. 57, 453-459. PubMed

Tanifuji, G. & Archibald, J. M. 2010. Actin gene family dynamics in cryptomonads and red algae. J. Mol. Evol. 71, 169-179. PubMed

Kim, E. & Archibald, J. M. 2010. Plastid evolution: gene transfer and the maintenance of 'stolen' organelles. BMC Biology. 8:73. PubMed

Curtis, B. & Archibald, J. M. 2010. Problems and progress in understanding the origins of mitochondria and plastids. In: Symbioses and stress. Seckbach, J. & Grube, M. (eds.). Springer-Verlag. pp. 41-62.

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. pp. 191-204.

Kim, E., Park, J. S., Simpson, A. G. B., Matsunaga, S., Watanabe, M., Murakami, A., Sommerfeld, K., Onodera, N. T., & 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

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 accelerated evolutionary rate.Genome Biol. Evol. 2009, 439-448. doi:10.1093/gbe/evp047.

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.

Elias, M. & Archibald, J. M. 2009. Sizing up the genomic footprint of endosymbiosis. BioEssays. 31, 1273-1279. PubMed

Moore, C. E. & Archibald, J. M. 2009. Nucleomorph genomes. Annu. Rev. Genet. 43: 251-264. PubMed

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.

Archibald, J. M. 2009. Genomics: Green evolution, green revolution. Science. 324, 191-192. (PDF)

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, 315-323. Link

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. (PDF)

Archibald, J. M. 2009. Secondary endosymbiosis. In: Encyclopedia of Microbiology, Third Edition. Schaechter, M. (ed.). Oxford: Elsevier. pp. 438-446.

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. doi: 10.1093/jhered/esp055

Archibald, J. M. 2009. The origin and spread of eukaryotic photosynthesis—evolving views in light of genomics. Bot. Marina. 52, 95-103. (PDF)

Kim, E. & Archibald, J. M. 2009. Diversity and evolution of plastids and their genomes. In: The chloroplast—interactions with the environment. Aronsson, H. &, Sandelius, A. S. (eds.). Springer-Verlag, Berlin. Pp. 1-39. (PDF)

Archibald, J. M. 2009. The puzzle of plastid evolution. Curr. Biol. 19, R81-R88. (PDF)

Archibald, J. M. 2008. The eocyte hypothesis and the origin of eukaryotic cells. Proc. Natl. Acad. Sci. USA. 51, 20049-20050. (PDF)

Hoef-Emden, K. & Archibald, J. M. 2008. Cryptomonads. Tree of Life web project. http://tolweb.org/Cryptomonads

Archibald, J. M. 2008. Plastid evolution: remnant algal genes in ciliates. Curr. Biol. 18, 663-665. (PDF)

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. (PDF)

Lane, C. E., & Archibald, J. M. 2008. The eukaryotic Tree of Life: endosymbiosis takes its TOL. Trends Ecol. Evol. 23, 268-275. (PDF)

Khan, H., & Archibald, J. M. 2008. Lateral transfer of introns in the cryptophyte plastid genome. Nucleic Acids Res. 36, 3043-3053. (PDF)

Cuvelier, M. L., Ortiz, A., Kim, Eunsoo, Moehlig, H., Richardson, D. E., Heidelberg, J. F., Archibald, J. M. & Worden, A. Z. 2008. Widespread distribution of a unique marine protistan lineage. Env. Microbiol. doi: 10.1111/j.1462-2920.2008.01580.x (PDF)

Keeling, P. J. & Archibald, J. M. 2008. Organelle Evolution: what's in a name? Curr. Biol. 18, R345-347. (PDF)

Lane, C. E. & Archibald, J. M. 2008. New members of the genus Hemiselmis (Cryptomonadales, Cryptophyceae). J. Phycol. 44, 339-450. (PDF)

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. (PDF)

Phipps, K., Donaher, N. A., Lane, C. E. & Archibald, J. M. 2008. Nucleomorph karyotype diversity in the freshwater cryptophyte genus Cryptomonas. J. Phycol. 44, 11-14. (PDF)

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. (PDF)

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. (PDF)

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. Euk. Microbiol. 54, 403-410. (PDF)

Archibald, J. M. 2007. Review of Genomics and Evolution of microbial eukaryotes (Katz and Bhattacharya eds.) Q. Rev. Biol., 82, 275-276. (PDF)

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. (PDF)

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. (PDF)

Archibald, J. M. 2007. Nucleomorph genomes: structure, function, origin and evolution. BioEssays, 29, 392-402. (PDF)

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(2), 223-236. (PDF)

Archibald, J. M. 2006. Algal genomics: exploring the imprint of endosymbiosis. Curr. Biol., 16, R1033-1035. (PDF)

Bhattacharya, D. & Archibald, J. M. 2006. Response to Theissen and Martin: "The difference between endosymbionts and organelles". Curr. Biol., 16, R1017-R1018. (PDF)

Lane, C. E. & Archibald, J. M. 2006. Novel nucleomorph genome architecture in the cryptomonad genus Hemiselmis. J. Eukaryot. Microbiol. 53(6), 515-521. (PDF)

Archibald, J. M. 2006. Endosymbiosis: double-take on plastid origins. Curr. Biol., 16, R690-R692. (PDF)

Ruiz-Trillo, I., Lane, C. E., Archibald, J. M. & Roger, A. J. 2006. Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica. J. Eukaryot. Microbiol. 53(5) 379-384. (PDF)

Archibald, J. M. 2006. Genome complexity in a lean, mean photosynthetic machine. Proc. Natl. Acad. Sci. USA,103, 11433-11434. (PDF)

Lane, C. E., Khan, H., MacKinnon, M., Fong, A., Theophilou, S., & Archibald, J. M. 2006. Insight into the diversity and evolution of the cryptomonad nucleomorph genome. Mol. Biol. Evol., 23, 856-865. (PDF)

Archibald, J. M. 2005. Jumping genes and shrinking genomes—probing the evolution of eukaryotic photosynthesis using genomics. IUBMB Life, 57, 539-547. (PDF) (Cover)

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. (PDF)

Kim, J. C., Ou, Y. Y., Badano, J. L., 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. (PDF)

Archibald, J. M. & Keeling, P. J. 2005. On the origin and evolution of plastids. In: Microbial Evolution: Concepts and Controversies. Sapp, J. (ed.). Oxford University Press, Oxford. Pp. 238-260.

Keeling, P. J., Archibald, J. M., Fast, N. M., & Palmer, J. D. 2004. Comment on "The Evolution of Modern Eukaryotic Phytoplankton". Science, 306, 2191. (PDF)

Archibald, J. M. & Keeling, P. J. 2004. The evolutionary history of plastids: a molecular phylogenetic perspective. In: Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics. Hirt, R. P. & Horner, D. (eds.). Taylor & Francis Books, London. Pp. 55-74.

Rogers. M. B., Archibald, J. M., Field, M. A., Li, C, Striepen, B. & Keeling, P. J. 2004. Plastid-targeting peptides from the chlorarachniophyte Bigelowiella natans. J. Eukaryot. Microbiol., 51, 529-535. (PDF)

Archibald, J. M. & Keeling, P. J. 2004. Actin and ubiquitin protein sequences support a cercozoan/foraminiferan ancestry for the plasmodiophorid plant pathogens. J. Eukaryot. Microbiol., 1, 113-118. (PDF)

Longet, D., Archibald, J. M., Keeling, P. J., & Pawlowski, J. 2003. Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies. Int. J. Syst. Evol. Microbiol. 53, 1735-1739. (PDF)

Archibald, J. M., Rogers, M., Toop, M. Ishida, K., & 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. (PDF) (Supplementary data ) (Commentary)

Archibald, J. M., Teh, E. M. & Keeling, P. J. 2003. Novel ubiquitin fusion proteins: ribosomal protein P1 and actin. J. Mol. Biol. 328, 771-778. (PDF)

Archibald, J. M. & Keeling, P. J. 2003. Plant genomes: cyanobacterial genes revealed. Heredity 90, 2-3. (PDF)

Archibald, J. M., Longet, D., Pawlowski, J. & Keeling, P. J. 2003. A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol. Biol. Evol. 20, 62-66. (PDF)

Archibald, J. M. & Keeling, P. J. 2002. Recycled plastids: a green movement in eukaryotic evolution. Trends Genet. 18, 577-584. (PDF)

Archibald, J. M. & 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. (PDF)

Archibald, J. M. & Roger, A. J. 2002. Gene duplication and gene conversion shape the evolution of archaeal chaperonins. J. Mol. Biol. 316, 1041-1050. (PDF)

Archibald, J. M., O’Kelly, C. J. & Doolittle, W. F. 2002. The chaperonin genes of jakobid and jakobid-like flagellates: implications for eukaryotic evolution. Mol. Biol. Evol. 19, 422-431. (PDF)

Archibald, J. M., Blouin, C. & Doolittle, W. F. 2001. Gene duplication and the evolution of group II chaperonins: implications for structure and function. J. Struct. Biol. 135, 157-169. (PDF)

Archibald, J. M., Cavalier-Smith, T., Maier, U.-G. & Douglas, S. 2001. Molecular chaperones encoded by a reduced eukaryotic nucleus: the cryptomonad nucleomorph. J. Mol. Evol. 52: 490-501. (PDF)

Archibald, J. M., Logsdon, J. M. Jr. & Doolittle, W. F. 2000. Origin and evolution of eukaryotic chaperonins: phylogenetic evidence for ancient duplications in CCT genes. Mol. Biol. Evol. 17, 1456-1466. (PDF)

Archibald, J. M., Logsdon, J. M. Jr. & Doolittle, W. F. 1999. Recurrent paralogy in the evolution of archaeal chaperonins. Curr. Biol. 9, 1053-1056. (PDF) (Supplementary data )

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Last updated: January 2014