Publications from John Archibald and the Archibald Lab
Kim, E., Park, J. S., Simpson, A. G. B., Matsunaga, S., Watanabe, M., Murakami, A., Sommerfeld, K., Onodera, N. T., & Archibald, J. M. Complex array of endobionts in Petalomonas sphagnophila, a large heterotrophic euglenid protist from Sphagnum-dominated peatlands. ISME Journal. Under Review.
Silver, T. D., Moore, C. E. & Archibald, J. M. Nucleomorph ribosomal DNA and telmere dynamics in chlorarachniophyte algae. J. Euk. Microbiol. Under Review.
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. 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. doi: 10.1002/bies.200900117
Moore, C. E. & Archibald, J. M. 2009. Nucleomorph genomes. Annu. Rev. Genet. 43: 251-254. 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.
Hopkins, J. & Archibald, J. M. 2009. Plastid evolution and the nuclear genomic 'footprint' of red and green algal endosymbionts. In: Red algae in the age of genomics. Seckbach, J. & Grube, M. (eds.). Springer-Verlag. In Press.
Archibald, J. M. 2009. Genomics: Green evolution, green revolution. Science. 324, 191-192. (PDF)
Hoef-Emden, K. & Archibald, J. M. 2009. Phylum Cryptophyta (Cryptomonads). In: Handbook of Protoctista, Second Edition. Margulis, L. (ed). Jones and Bartlett Publishers. In Press.
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.
Curtis, B. & Archibald, J. M. 2009. Problems and progress in understanding the origins of mitochondria and plastids. In: Symbiosis and stress. Seckbach, J. & Grube, M. (eds.). Springer-Verlag. In Press.
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 )
Last updated: December 23, 2009
