Research Topics
| John M ArchibaldSummaryAffiliation: Dalhousie University Country: Canada Publications
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Detail Information
Publications
Treetrimmer: a method for phylogenetic dataset size reductionShinichiro Maruyama
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
BMC Res Notes 6:145. 2013..There is a need for bioinformatic tools with which to objectively carry out such pruning procedures...
Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenidsShinichiro Maruyama
Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo, Japan
BMC Evol Biol 11:105. 2011..However, the impact of endosymbiosis on the euglenophyte nuclear genome is not fully understood due to its complex nature as a 'hybrid' of a non-photosynthetic host cell and a secondary endosymbiont...- Plastid evolution: remnant algal genes in ciliatesJohn M Archibald
The Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
Curr Biol 18:R663-R665. 2008..A recent study has uncovered what could be the molecular signature of a photosynthetic ancestry for an important plastid-lacking lineage of microbial eukaryotes--the ciliates... 
Endosymbiosis: double-take on plastid originsJohn M Archibald
The Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, Halifax, Nova Scotia, B3H 1X5, Canada
Curr Biol 16:R690-2. 2006..New data reveal that a mysterious unicellular alga acquired its photosynthetic apparatus much more recently than other eukaryotes, affording a second look at the primary endosymbiotic origin of plastids...- Algal genomics: exploring the imprint of endosymbiosisJohn M Archibald
The Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, Halifax, Nova Scotia, Canada
Curr Biol 16:R1033-5. 2006..A genomic analysis of Cyanophora paradoxa - a deeply diverged unicellular alga - suggests that the abundance and functional diversity of nucleus-encoded genes of cyanobacterial origin differs in plants and algae... - Genome complexity in a lean, mean photosynthetic machineJohn M Archibald
Canadian Institute for Advanced Research, Program in Evolutionary Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5
Proc Natl Acad Sci U S A 103:11433-4. 2006 - The puzzle of plastid evolutionJohn M Archibald
The Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 1X5, Canada
Curr Biol 19:R81-8. 2009..Consequently, new models of plastid evolution involving ancient secondary and tertiary endosymbioses are needed to explain the full spectrum of photosynthetic eukaryotes... - Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogenyHameed Khan
Genome Atlantic and the Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
Mol Biol Evol 24:1832-42. 2007.... - Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and functionChristopher E Lane
Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5
Proc Natl Acad Sci U S A 104:19908-13. 2007..Nucleomorph proteins have the potential to reveal the minimal functional units required for basic eukaryotic cellular processes... - Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphsBruce A Curtis
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
Nature 492:59-65. 2012..Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph... - Complete sequence and analysis of the mitochondrial genome of Hemiselmis andersenii CCMP644 (Cryptophyceae)Eunsoo Kim
Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
BMC Genomics 9:215. 2008..Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte Rhodomonas salina. Here, the second complete mitochondrial genome of the cryptophyte alga Hemiselmis andersenii CCMP644 is presented... - Complete nucleomorph genome sequence of the nonphotosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene setGoro Tanifuji
Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
Genome Biol Evol 3:44-54. 2011..This result suggests that similar reductive processes have taken place in unrelated lineages of nucleomorph-containing algae... - Nucleomorph genome sequence of the cryptophyte alga Chroomonas mesostigmatica CCMP1168 reveals lineage-specific gene loss and genome complexityChrista E Moore
Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
Genome Biol Evol 4:1162-75. 2012..g., proteasome-mediated protein degradation, in the four cryptophyte lineages examined... - Complex array of endobionts in Petalomonas sphagnophila, a large heterotrophic euglenid protist from Sphagnum-dominated peatlandsEunsoo Kim
Department of Biochemistry and Molecular Biology, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Dalhousie University, Halifax, Nova Scotia, Canada
ISME J 4:1108-20. 2010..Our study adds significantly to the growing evidence for complex and dynamic protist-bacterial associations in nature... - The eukaryotic tree of life: endosymbiosis takes its TOLChristopher E Lane
The Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
Trends Ecol Evol 23:268-75. 2008.... - Novel nucleomorph genome architecture in the cryptomonad genus hemiselmisChristopher E Lane
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 1X5, Canada
J Eukaryot Microbiol 53:515-21. 2006..rufescens chromosomes indicate that recombination has been a major factor in shaping the karyotype and genomic structure of cryptomonad nucleomorphs... - Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Insight into the diversity and evolution of the cryptomonad nucleomorph genomeChristopher E Lane
Genome Atlantic and the Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
Mol Biol Evol 23:856-65. 2006..These results provide a glimpse into the genetic diversity of nucleomorph genomes in cryptomonads and set the stage for more comprehensive sequence-based studies in closely and distantly related taxa... - Genomic characterization of Neoparamoeba pemaquidensis (Amoebozoa) and its kinetoplastid endosymbiontGoro Tanifuji
Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, Nova Scotia B3H 4R2, Canada
Eukaryot Cell 10:1143-6. 2011..The genome of this "Ichthyobodo-related organism" was found to be unexpectedly large, with at least 11 chromosomes between 1.0 and 3.5 Mbp and a total genome size of at least 25 Mbp... - Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reductionJohn M Archibald
Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
J Hered 100:582-90. 2009..Such comparisons provide fascinating insight into the evolution of these highly derived organelles and, more generally, the potential causes and consequences of genome reduction in eukaryotes... - Actin gene family dynamics in cryptomonads and red algaeGoro Tanifuji
Department of Biochemistry and Molecular Biology, Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Dalhousie University, Halifax, Nova Scotia, Canada
J Mol Evol 71:169-79. 2010.... - Retrotransposons and tandem repeat sequences in the nuclear genomes of cryptomonad algaeHameed Khan
Genome Atlantic and the Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 1X5
J Mol Evol 64:223-36. 2007..The discovery of chromodomain-containing retroelements in cryptomonads further expands the known distribution of the so-called chromoviruses across the tree of eukaryotes... - Actin and ubiquitin protein sequences support a cercozoan/foraminiferan ancestry for the plasmodiophorid plant pathogensJohn M Archibald
Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, British Columbia V6T 1Z4, Canada
J Eukaryot Microbiol 51:113-8. 2004..Taken together, these results indicate that plasmodiophorids are indeed related to Cercozoa and Foraminifera, although the relationships amongst these groups remain unresolved... - Plastid evolution: gene transfer and the maintenance of 'stolen' organellesEunsoo Kim
Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3 H 1X5, Canada
BMC Biol 8:73. 2010..See research article http://www.biomedcentral.com/1471-2164/11/366... - Jumping genes and shrinking genomes--probing the evolution of eukaryotic photosynthesis with genomicsJohn M Archibald
Genome Atlantic and the Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
IUBMB Life 57:539-47. 2005..Here I discuss recent advances in our appreciation of the mosaic nature of the eukaryotic nuclear genome, and the ongoing role endosymbiosis plays in shaping its content... - Lateral transfer of introns in the cryptophyte plastid genomeHameed Khan
Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
Nucleic Acids Res 36:3043-53. 2008..e. nested group II/group III introns) in which the internal intron has lost its splicing capability, resulting in an amalgamation with the outer intron... - Organelle evolution: what's in a name?Patrick J Keeling
The Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
Curr Biol 18:R345-7. 2008.... - Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natansJohn M Archibald
Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
Proc Natl Acad Sci U S A 100:7678-83. 2003..These results underscore the importance of lateral gene transfer in contributing foreign proteins to eukaryotic cells and their organelles, and also suggest that its impact can vary from lineage to lineage... - Plastid-targeting peptides from the chlorarachniophyte Bigelowiella natansMatthew B Rogers
Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
J Eukaryot Microbiol 51:529-35. 2004..Consistent with this, the leader sequence from one B. natans protein was tested for function in the apicomplexan parasite, Toxoplasma gondii, and shown to direct the secretion of the protein... - Evolutionary dynamics of light-independent protochlorophyllide oxidoreductase genes in the secondary plastids of cryptophyte algaeAnna Fong
Dalhousie University, Department of Biochemistry and Molecular Biology, 5850 College Street, Sir Charles Tupper Medical Building, Halifax B3H 1X5, Canada
Eukaryot Cell 7:550-3. 2008..The presence of functional and nonfunctional copies of LIPOR genes in cryptophytes suggests that light-independent chlorophyll biosynthesis is a nonessential pathway in these organisms... - Phylogeny and nucleomorph karyotype diversity of chlorarachniophyte algaeTia D Silver
Department of Biochemistry and Molecular Biology, Canadian Institute for Advanced Research, Program in Evolutionary Biology, Dalhousie University, Halifax, Nova Scotia, Canada
J Eukaryot Microbiol 54:403-10. 2007..The significance of these phylogenetic and nucleomorph karyotype data is discussed... - Nucleomorph genomes: structure, function, origin and evolutionJohn M Archibald
The Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 1X5, Canada
Bioessays 29:392-402. 2007..It is now possible to speculate on the reasons that nucleomorphs persist in cryptomonads and chlorarachniophytes but have been lost in all other algae with plastids of secondary endosymbiotic origin... - Newly identified and diverse plastid-bearing branch on the eukaryotic tree of lifeEunsoo Kim
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5
Proc Natl Acad Sci U S A 108:1496-500. 2011..The rappemonads are unique, widespread, putatively photosynthetic algae that are absent from present-day ecosystem models and current versions of the tree of life... - Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arcticaInaki Ruiz-Trillo
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5
J Eukaryot Microbiol 53:379-84. 2006..Finally, to begin characterizing the Capsaspora genome, we have performed pulsed-field gel electrophoresis (PFGE) analyses, which indicate that its genome has at least 12 chromosomes with a total genome size in the range of 22-25 Mb... - Nucleomorph genomesChrista E Moore
The Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 1X5, Canada
Annu Rev Genet 43:251-64. 2009..In this article, we review the current state of knowledge with respect to the structure, function, origin, and evolution of nucleomorph genomes across the known diversity of cryptophyte and chlorarachniophyte algae... - Novel ubiquitin fusion proteins: ribosomal protein P1 and actinJohn M Archibald
Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Botany, University of British Columbia, Vancouver, Canada
J Mol Biol 328:771-8. 2003.... - Complex protein targeting to dinoflagellate plastidsNicola J Patron
Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Botany, University of British Columbia, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
J Mol Biol 348:1015-24. 2005..A four-residue phenylalanine-based motif is also a consistent feature of H. triquetra transit peptides, which is an ancient feature predating red algae and galucophytes that was lost in green plastids... - Broad distribution of TPI-GAPDH fusion proteins among eukaryotes: evidence for glycolytic reactions in the mitochondrion?Takuro Nakayama
Department of Biochemistry and Molecular Biology, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Dalhousie University, Halifax, Nova Scotia, Canada
PLoS ONE 7:e52340. 2012..These results suggest that part of the glycolytic pathway occurs inside mitochondria in these organisms, broadening our knowledge of the diversity of mitochondrial metabolism of protists... - Evolving a photosynthetic organelleTakuro Nakayama
Department of Biochemistry and Molecular Biology, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, Canada
BMC Biol 10:35. 2012..The question is how Paulinella can help us to understand the process by which an endosymbiont is converted into an organelle... - Recycled plastids: a 'green movement' in eukaryotic evolutionJohn M Archibald
Canadian Institute for Advanced Research, Dept Botany, University of British Columbia, Vancouver, Canada
Trends Genet 18:577-84. 2002.... - A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroupJohn M Archibald
Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
Mol Biol Evol 20:62-6. 2003..This character strongly suggests that Cercozoa and Foraminifera are close relatives and form a new "supergroup" of eukaryotes... - Nucleomorph ribosomal DNA and telomere dynamics in chlorarachniophyte algaeTia D Silver
Department of Biochemistry and Molecular Biology, Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Dalhousie University, Halifax, Nova Scotia, Canada
J Eukaryot Microbiol 57:453-9. 2010..CCMP2014. This feature may represent a useful evolutionary character for inferring the relationships among extant lineages... - Diversity, nomenclature, and taxonomy of protistsSina M Adl
Department of Biology, Dalhousie University, Halifax, NS, Canada
Syst Biol 56:684-9. 2007 - Gene duplication and gene conversion shape the evolution of archaeal chaperoninsJohn M Archibald
Program in Evolutionary Biology, Canadian Institute for Advanced Research Department of Biochemistry and Molecular Biology, Halifax, Nova Scotia, B3H 4H7 Canada
J Mol Biol 316:1041-50. 2002.... - Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signalsJohn M Archibald
Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4H7
J Mol Evol 55:232-45. 2002..Our approach is relatively insensitive to the presence of divergent sequences in the alignment, making it ideal for detecting recombination between both closely and distantly related genes... - Ultrastructure and molecular phylogeny of the cryptomonad Goniomonas avonlea sp. novEunsoo Kim
Canadian Institute for Advanced Research, Integrated Microbial Biodiversity Program, Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada
Protist 164:160-82. 2013..Our study adds to a growing body of evidence for the high level of diversity and antiquity of the genus Goniomonas... - Genome sequence of Shigella flexneri serotype 5a strain M90T SmNaoko T Onodera
Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
J Bacteriol 194:3022. 2012..von Seidlein et al., PLoS Med. 3:e353, 2006). We sequenced the genome of Shigella flexneri strain M90T Sm (serotype 5a) and compared it to the published genome sequence of S. flexneri strain 8401 (serotype 5b)... - Gene transfer: anything goes in plant mitochondriaJohn M Archibald
Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Department of Biochemistry and Molecular Biology, Sir Charles Tupper Medical Building, Dalhousie University, Halifax, NS B3H 1X5, Canada
BMC Biol 8:147. 2010..A model involving duplicative horizontal gene transfer and differential gene conversion is proposed as a hitherto unrecognized source of genetic diversity... - How do endosymbionts become organelles? Understanding early events in plastid evolutionDebashish Bhattacharya
Department of Biological Sciences and the Roy J Carver Center for Comparative Genomics, University of Iowa, Iowa City, IA 52242, USA
Bioessays 29:1239-46. 2007..Here we discuss the use of these terms in light of new data in order to highlight the unique aspects of plastids and mitochondria and underscore their central role in eukaryotic evolution... - The chaperonin genes of jakobid and jakobid-like flagellates: implications for eukaryotic evolutionJohn M Archibald
Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
Mol Biol Evol 19:422-31. 2002..In phylogenetic trees constructed from CCTalpha protein sequences, R. americana (but not M. jakobiformis) shows a weak but consistent affinity for the Heterolobosea and Euglenozoa... - Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogeniesDavid Longet
Dept of zoology and animal biology, University of Geneva, Sciences III, 30 Quai Ernest Ansermet, , Switzerland
Int J Syst Evol Microbiol 53:1735-9. 2003..Analysis of our data confirms a close relationship between Foraminifera and Cercozoa and points to Gromia as the closest relative of Foraminifera... - Comment on "The evolution of modern eukaryotic phytoplankton"Patrick J Keeling
Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
Science 306:2191; author reply 2191. 2004 - Widespread distribution of a unique marine protistan lineageMarie L Cuvelier
Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA 95039, USA
Environ Microbiol 10:1621-34. 2008..Given their broad thermal and geographic distribution, understanding the role these protists play in biogeochemical cycling within different habitats is essential... - MKKS/BBS6, a divergent chaperonin-like protein linked to the obesity disorder Bardet-Biedl syndrome, is a novel centrosomal component required for cytokinesisJun Chul Kim
Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
J Cell Sci 118:1007-20. 2005..Our findings provide the first insight into the nature and cellular function of BBS6, and shed light on the potential causes of several ailments, including obesity, retinal degeneration, kidney dysfunction and congenital heart disease...