P J Keeling

Summary

Affiliation: University of British Columbia
Country: Canada

Publications

  1. ncbi request reprint Nucleus-to-nucleus gene transfer and protein retargeting into a remnant cytoplasm of cryptophytes and diatoms
    Sven B Gould
    Philipps Universitat Marburg, Marburg, Germany
    Mol Biol Evol 23:2413-22. 2006
  2. ncbi request reprint Alveolate and chlorophycean mitochondrial cox2 genes split twice independently
    Ross F Waller
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
    Gene 383:33-7. 2006
  3. doi request reprint Role of horizontal gene transfer in the evolution of photosynthetic eukaryotes and their plastids
    Patrick J Keeling
    Botany Department, University of British Columbia, Vancouver, BC, Canada
    Methods Mol Biol 532:501-15. 2009
  4. pmc Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions
    Nicolas Corradi
    Canadian Institute for Advanced Research, The Biodiversity Research Centre, University of British Columbia, University Boulevard, Vancouver, BC V6T 1Z4, Canada
    Genome Biol 10:R106. 2009
  5. pmc Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities
    Bryony A P Williams
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
    BMC Genomics 9:200. 2008
  6. pmc Complex phylogenetic distribution of a non-canonical genetic code in green algae
    Ellen Cocquyt
    Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium
    BMC Evol Biol 10:327. 2010
  7. pmc Complex distribution of EFL and EF-1alpha proteins in the green algal lineage
    Geoffrey P Noble
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, BC, Canada
    BMC Evol Biol 7:82. 2007
  8. pmc A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer
    Matthew B Rogers
    Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    BMC Evol Biol 7:89. 2007
  9. pmc A high density of ancient spliceosomal introns in oxymonad excavates
    Claudio H Slamovits
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
    BMC Evol Biol 6:34. 2006
  10. pmc Comparative rates of evolution in endosymbiotic nuclear genomes
    Nicola J Patron
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada
    BMC Evol Biol 6:46. 2006

Detail Information

Publications96

  1. ncbi request reprint Nucleus-to-nucleus gene transfer and protein retargeting into a remnant cytoplasm of cryptophytes and diatoms
    Sven B Gould
    Philipps Universitat Marburg, Marburg, Germany
    Mol Biol Evol 23:2413-22. 2006
    ..tricornutum. Furthermore, the described cryptophyte PPC proteins possibly allow the elucidation of the processes by which proteins are involved in different levels of host control over its eukaryotic organelle...
  2. ncbi request reprint Alveolate and chlorophycean mitochondrial cox2 genes split twice independently
    Ross F Waller
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
    Gene 383:33-7. 2006
    ....
  3. doi request reprint Role of horizontal gene transfer in the evolution of photosynthetic eukaryotes and their plastids
    Patrick J Keeling
    Botany Department, University of British Columbia, Vancouver, BC, Canada
    Methods Mol Biol 532:501-15. 2009
    ..g., cytosolic genes or genes left over from the replacement of an earlier plastid), some from the plastid of other algal lineages, and some from completely unrelated sources...
  4. pmc Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions
    Nicolas Corradi
    Canadian Institute for Advanced Research, The Biodiversity Research Centre, University of British Columbia, University Boulevard, Vancouver, BC V6T 1Z4, Canada
    Genome Biol 10:R106. 2009
    ....
  5. pmc Genome sequence surveys of Brachiola algerae and Edhazardia aedis reveal microsporidia with low gene densities
    Bryony A P Williams
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
    BMC Genomics 9:200. 2008
    ..The smallest microsporidian genomes have received the most attention, but genomes of different species range in size from 2.3 Mb to 19.5 Mb and the nature of the larger genomes remains unknown...
  6. pmc Complex phylogenetic distribution of a non-canonical genetic code in green algae
    Ellen Cocquyt
    Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium
    BMC Evol Biol 10:327. 2010
    ....
  7. pmc Complex distribution of EFL and EF-1alpha proteins in the green algal lineage
    Geoffrey P Noble
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, BC, Canada
    BMC Evol Biol 7:82. 2007
    ..This distribution singles out green algae as a particularly promising group to understand the origin of EFL and the effects of its presence on EF-1alpha...
  8. pmc A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer
    Matthew B Rogers
    Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    BMC Evol Biol 7:89. 2007
    ..Ideally such an observation would involve a single eukaryote or a small group of related eukaryotes encoding a gene from a specific bacterial lineage...
  9. pmc A high density of ancient spliceosomal introns in oxymonad excavates
    Claudio H Slamovits
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
    BMC Evol Biol 6:34. 2006
    ..Here we have used environmental expressed sequence tag (EST) sequencing to identify 17 genes from the uncultivable oxymonad Streblomastix strix, to survey intron densities in this most poorly studied excavate group...
  10. pmc Comparative rates of evolution in endosymbiotic nuclear genomes
    Nicola J Patron
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada
    BMC Evol Biol 6:46. 2006
    ..They also differ in several aspects, not least in that they encode proteins that target to the plastid, and so function in a different compartment from that in which they are encoded...
  11. pmc The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum retain functionally overlapping mitochondria from two evolutionarily distinct lineages
    Behzad Imanian
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
    BMC Evol Biol 7:172. 2007
    ..This redundancy raises the question of whether the organelles share any functions in common or have distributed functions between them...
  12. pmc Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists
    Fabien Burki
    Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    BMC Evol Biol 10:377. 2010
    ..Phyllostaurus sp.), Phytomyxea (Spongospora subterranea, Plasmodiophora brassicae) and Gromiida (Gromia sphaerica)...
  13. pmc Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria
    Christopher J Jackson
    School of Botany, The University of Melbourne, Victoria 3010, Australia
    BMC Biol 5:41. 2007
    ..Here, we investigate structure, content and expression of dinoflagellate mitochondrial genomes...
  14. pmc Horizontal transfer of a eukaryotic plastid-targeted protein gene to cyanobacteria
    Matthew B Rogers
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, BC, Canada
    BMC Biol 5:26. 2007
    ..In particular, gene flow from eukaryotes to prokaryotes is rarely documented with strong support, which is unusual since prokaryotic genomes appear to readily accept foreign genes...
  15. pmc The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured
    Audrey P de Koning
    Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
    BMC Biol 4:12. 2006
    ..To investigate such changes, we sequenced the complete plastid genome of the parasitic, non-photosynthetic green alga, Helicosporidium...
  16. ncbi request reprint Polymorphic insertions and deletions in parabasalian enolase genes
    Patrick J Keeling
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529 6270 University Blvd, Vancouver, British Columbia V6T 1Z4, Canada
    J Mol Evol 58:550-6. 2004
    ....
  17. doi request reprint 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
    ....
  18. ncbi request reprint Shrink it or lose it: balancing loss of function with shrinking genomes in the microsporidia
    Patrick J Keeling
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, Vancouver, BC, Canada
    Virulence 2:67-70. 2011
    ....
  19. pmc Simplicity and complexity of microsporidian genomes
    Patrick J Keeling
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529 6270 University Blvd, Vancouver, BC V6T 1Z4, Canada
    Eukaryot Cell 3:1363-9. 2004
  20. ncbi request reprint 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
  21. ncbi request reprint Genomics. Deep questions in the tree of life
    Patrick J Keeling
    Botany Department, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
    Science 317:1875-6. 2007
  22. ncbi request reprint Comparative genomics of microsporidia
    Patrick J Keeling
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
    Folia Parasitol (Praha) 52:8-14. 2005
    ....
  23. ncbi request reprint Ostreococcus tauri: seeing through the genes to the genome
    Patrick J Keeling
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
    Trends Genet 23:151-4. 2007
    ..By contrast, O. tauri has retained a large complement of genes. Studying O. tauri should shed light on forces, other than parasitism and endosymbiosis, that result in densely packed genomes...
  24. ncbi request reprint Causes and effects of nuclear genome reduction
    Patrick J Keeling
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
    Curr Opin Genet Dev 15:601-8. 2005
    ..In these genomes, normally weak forces might become more significant drivers of genome evolution...
  25. ncbi request reprint Evidence from SSU rRNA phylogeny that Octomitus is a sister lineage to Giardia
    Patrick J Keeling
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, 3529 6270 University Blvd, Vancouver, BC, Canada V6T 1Z4
    Protist 157:205-12. 2006
    ..Phylogenetic analysis showed Octomitus to be the sister to Giardia with strong support, together occupying one side of the deepest split in the diplomonad tree...
  26. doi request reprint Horizontal gene transfer in eukaryotic evolution
    Patrick J Keeling
    Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z, Canada
    Nat Rev Genet 9:605-18. 2008
    ..Major recent trends include the important role of HGT in adaptation to certain specialized niches and the highly variable impact of HGT in different lineages...
  27. doi request reprint Chromalveolates and the evolution of plastids by secondary endosymbiosis
    Patrick J Keeling
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, BC, Canada
    J Eukaryot Microbiol 56:1-8. 2009
    ..Collectively, these data are most easily reconciled with a single origin of the chromalveolate plastids, although the phylogeny of chromalveolate host lineages (and potentially Rhizaria) remain to be reconciled with this plastid data...
  28. ncbi request reprint Characterisation of a non-canonical genetic code in the oxymonad Streblomastix strix
    Patrick J Keeling
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
    J Mol Biol 326:1337-49. 2003
    ....
  29. ncbi request reprint Congruent evidence from alpha-tubulin and beta-tubulin gene phylogenies for a zygomycete origin of microsporidia
    Patrick J Keeling
    Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
    Fungal Genet Biol 38:298-309. 2003
    ..While the tubulin phylogenies do not provide a decisive conclusion, they do further narrow the probable origin of microsporidia to a zygomycete-like ancestor...
  30. ncbi request reprint Microsporidia: biology and evolution of highly reduced intracellular parasites
    Patrick J Keeling
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver BC, V6T 1Z4, Canada
    Annu Rev Microbiol 56:93-116. 2002
    ....
  31. pmc Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase
    P J Keeling
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Proc Natl Acad Sci U S A 98:10745-50. 2001
    ....
  32. ncbi request reprint Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home?
    P J Keeling
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    Mol Biol Evol 18:1551-7. 2001
    ..The union of Cercozoa and Foraminifera suggested by actin phylogeny represents a novel step in the long process of determining the broad relationships between all major eukaryotic groups...
  33. pmc The reduced genome of the parasitic microsporidian Enterocytozoon bieneusi lacks genes for core carbon metabolism
    Patrick J Keeling
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
    Genome Biol Evol 2:304-9. 2010
    ..Altogether, E. bieneusi appears to have no fully functional pathway to generate ATP from glucose. Therefore, this intracellular parasite relies on transporters to import ATP from its host...
  34. pmc The endosymbiotic origin, diversification and fate of plastids
    Patrick J Keeling
    Botany Department, Canadian Institute for Advanced Research, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
    Philos Trans R Soc Lond B Biol Sci 365:729-48. 2010
    ..The many twists and turns of plastid evolution each represent major evolutionary transitions, and each offers a glimpse into how genomes evolve and how cells integrate through gene transfers and protein trafficking...
  35. doi request reprint Functional and ecological impacts of horizontal gene transfer in eukaryotes
    Patrick J Keeling
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
    Curr Opin Genet Dev 19:613-9. 2009
    ..Most, but not all, of the functionally significant HGT to eukaryotes comes from bacteria, in part due to chance, but probably also because bacteria have greater metabolic diversity to offer...
  36. ncbi request reprint Evidence from beta-tubulin phylogeny that microsporidia evolved from within the fungi
    P J Keeling
    Department of Biology, Indiana University at Bloomington, USA
    Mol Biol Evol 17:23-31. 2000
    ..e., with chytrids), suggesting that the affiliation between microsporidian and fungal tubulins is not an artifact of long-branch attraction...
  37. ncbi request reprint Diplonemid glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and prokaryote-to-eukaryote lateral gene transfer
    Q Qian
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada
    Protist 152:193-201. 2001
    ....
  38. ncbi request reprint The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomes
    Claudio H Slamovits
    Department of Botany, University of British Columbia, Vancouver, BC, Canada
    J Mol Biol 372:356-68. 2007
    ..Overall, the combination of characteristics found in the Oxyrrhis genome allows us to plot the sequence of many events that led to the extreme organisation of apicomplexan and dinoflalgellate mitochondrial genomes...
  39. ncbi request reprint HSP90, tubulin and actin are retained in the tertiary endosymbiont genome of Kryptoperidinium foliaceum
    Michelle L McEwan
    Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
    J Eukaryot Microbiol 51:651-9. 2004
    ....
  40. pmc Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast
    Fiona S L Brinkman
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada, V5A 1S6
    Genome Res 12:1159-67. 2002
    ....
  41. pmc A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids
    Jan Janouskovec
    Department of Botany, University of British Columbia, Vancouver, BC, Canada
    Proc Natl Acad Sci U S A 107:10949-54. 2010
    ..g., ciliates, Cryptosporidium, and Phytophthora)...
  42. ncbi request reprint Lateral gene transfer and the complex distribution of insertions in eukaryotic enolase
    James T Harper
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, British Columbia, 3529 6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
    Gene 340:227-35. 2004
    ..Of these, lateral gene transfer is the easiest to detect and some well-supported cases of eukaryote-to-eukaryote lateral transfer are evident from the phylogeny...
  43. doi request reprint Environmental PCR survey to determine the distribution of a non-canonical genetic code in uncultivable oxymonads
    Audrey P de Koning
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
    Environ Microbiol 10:65-74. 2008
    ..Overall, we propose that the non-canonical genetic code arose once in a common ancestor of Streblomastix and a subgroup of polymastigids...
  44. pmc Gene replacement of fructose-1,6-bisphosphate aldolase supports the hypothesis of a single photosynthetic ancestor of chromalveolates
    Nicola J Patron
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529 6270 University Blvd, Vancouver, British Columbia V6T 1Z4, Canada
    Eukaryot Cell 3:1169-75. 2004
    ..The chromalveolate enzymes form a strongly supported group in FBA phylogeny, and their common possession of this unexpected plastid characteristic provides new evidence for their close relationship and a common origin for their plastids...
  45. ncbi request reprint Alpha and beta subunits of pyruvate dehydrogenase E1 from the microsporidian Nosema locustae: mitochondrion-derived carbon metabolism in microsporidia
    N M Fast
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
    Mol Biochem Parasitol 117:201-9. 2001
    ..We propose that microsporidia may utilise a unique pyruvate decarboxylation pathway involving PDH, demonstrating once again the diversity of core metabolism in amitochondriate eukaryotes...
  46. ncbi request reprint Dinoflagellate nuclear SSU rRNA phylogeny suggests multiple plastid losses and replacements
    J F Saldarriaga
    Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
    J Mol Evol 53:204-13. 2001
    ..Eight independent instances of plastid loss and three of replacement can be inferred from existing data, but as more non-photosynthetic lineages are characterized these numbers will surely grow...
  47. ncbi request reprint Lateral gene transfer of a multigene region from cyanobacteria to dinoflagellates resulting in a novel plastid-targeted fusion protein
    Ross F Waller
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, Vancouver, British Columbia, Canada
    Mol Biol Evol 23:1437-43. 2006
    ....
  48. pmc Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans
    John 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...
  49. ncbi request reprint On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes
    James T Harper
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
    Int J Syst Evol Microbiol 55:487-96. 2005
    ..Whereas these results are consistent with the monophyly of chromalveolates inferred from plastid data, testing this hypothesis is going to require a substantial increase in data from a wide variety of organisms...
  50. ncbi request reprint A tertiary plastid uses genes from two endosymbionts
    Nicola J Patron
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada V6T 1Z4
    J Mol Biol 357:1373-82. 2006
    ..micrum are different from those found in either dinoflagellates or haptophytes, pointing to a plastid with an evolutionarily chimeric proteome, and a massive remodelling of protein trafficking during plastid replacement...
  51. ncbi request reprint Multiple protein phylogenies show that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage
    Juan F Saldarriaga
    Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
    Int J Syst Evol Microbiol 53:355-65. 2003
    ..Together, these two organisms can be instrumental in reconstructing the early evolution of dinoflagellates and apicomplexans by helping to reveal aspects of the ancestors of both groups...
  52. ncbi request reprint The phylogeny of colpodellids (Alveolata) using small subunit rRNA gene sequences suggests they are the free-living sister group to apicomplexans
    Olga N Kuvardina
    Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Botany, University of British Columbia, Vancouver BC V6T 1Z4, Canada
    J Eukaryot Microbiol 49:498-504. 2002
    ..This ancestor also very likely contained a plastid, but it is presently not certain whether it was photosynthetic, and it is not clear whether extant perkinsids or colpodellids have retained the organelle...
  53. ncbi request reprint Nuclear-encoded, plastid-targeted genes suggest a single common origin for apicomplexan and dinoflagellate plastids
    N M Fast
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    Mol Biol Evol 18:418-26. 2001
    ....
  54. ncbi request reprint Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages
    Nicola J Patron
    Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
    Curr Biol 17:887-91. 2007
    ..This relationship demonstrates that loss of nucleomorphs must have taken place in haptophytes independently of any other red alga-containing lineages and that the ancestor of both already contained a red algal endosymbiont...
  55. doi request reprint The distribution of Elongation Factor-1 Alpha (EF-1alpha), Elongation Factor-Like (EFL), and a non-canonical genetic code in the ulvophyceae: discrete genetic characters support a consistent phylogenetic framework
    Gillian H Gile
    Department of Botany, University of British Columbia, Vancouver, BC, Canada
    J Eukaryot Microbiol 56:367-72. 2009
    ..crinalis (Siphonocladales), whereas Caulerpales use the universal code. This supports a sister relationship between Siphonocladales and Dasycladales and further refines our understanding of ulvophycean phylogeny...
  56. ncbi request reprint Mitochondrial genome of a tertiary endosymbiont retains genes for electron transport proteins
    Behzad Imanian
    Genetics Graduate Program, Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
    J Eukaryot Microbiol 54:146-53. 2007
    ..Ultrastructural examination confirmed the endosymbiont mitochondria retain normal tubular cristae. Overall, these data suggest the endosymbiont mitochondria have not reduced at the genomic or functional level...
  57. doi request reprint Nucleus-encoded periplastid-targeted EFL in chlorarachniophytes
    Gillian H Gile
    Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    Mol Biol Evol 25:1967-77. 2008
    ..Taken together, the data suggest that the system that directs proteins to the PPC in chlorarachniophytes uses a bipartite targeting sequence, as does the PPC-targeting system that evolved independently in cryptomonads...
  58. ncbi request reprint Surface morphology of Saccinobaculus (Oxymonadida): implications for character evolution and function in oxymonads
    Kevin J Carpenter
    Botany Department, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, V6T 1Z4 Canada
    Protist 159:209-21. 2008
    ....
  59. ncbi request reprint Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids
    James T Harper
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    Mol Biol Evol 20:1730-5. 2003
    ....
  60. ncbi request reprint Genome compaction and stability in microsporidian intracellular parasites
    Claudio H Slamovits
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
    Curr Biol 14:891-6. 2004
    ....
  61. ncbi request reprint Microsporidian mitochondrial proteins: expression in Antonospora locustae spores and identification of genes coding for two further proteins
    Bryony A P Williams
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    J Eukaryot Microbiol 52:271-6. 2005
    ..In yeast mitochondria, this protein is part of a trimeric complex that processes proteins targeted to the inner membrane and the intermembrane space, and its substrate in A. locustae is presently unknown...
  62. pmc A high frequency of overlapping gene expression in compacted eukaryotic genomes
    Bryony A P Williams
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
    Proc Natl Acad Sci U S A 102:10936-41. 2005
    ..These findings also point to serious practical difficulties in studying expression in compacted genomes, because many techniques, such as arrays or serial analysis of gene expression will be misleading...
  63. pmc Pyruvate-phosphate dikinase of oxymonads and parabasalia and the evolution of pyrophosphate-dependent glycolysis in anaerobic eukaryotes
    Claudio H Slamovits
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, 3529 6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
    Eukaryot Cell 5:148-54. 2006
    ....
  64. doi request reprint Morphology, phylogeny, and diversity of Trichonympha (Parabasalia: Hypermastigida) of the wood-feeding cockroach Cryptocercus punctulatus
    Kevin J Carpenter
    Canadian Institute for Advanced Research, Botany Department, University of British Columbia, Vancouver, BC, Canada
    J Eukaryot Microbiol 56:305-13. 2009
    ..The monophyly of symbiotic bacteria of Trichonympha raises the intriguing possibility of three-way co-speciation among bacteria, Trichonympha, and insect hosts...
  65. ncbi request reprint Phylogenetic history of plastid-targeted proteins in the peridinin-containing dinoflagellate Heterocapsa triquetra
    Ross F Waller
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver
    Int J Syst Evol Microbiol 56:1439-47. 2006
    ..We also identified two cases of apparent lateral, or horizontal, gene transfer, one from the green plastid lineage and one from a bacterial lineage unrelated to plastids or cyanobacteria...
  66. doi request reprint Nuclear genome sequence survey of the Dinoflagellate Heterocapsa triquetra
    Michelle McEwan
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, BC, Canada
    J Eukaryot Microbiol 55:530-5. 2008
    ..Another 5% of the survey was long, complex repeats, some highly represented. By far the greatest fraction of the survey (89.5%) is made up of non-repeated sequence with no similarity to any other known sequence...
  67. doi request reprint Alpha- and beta-tubulin phylogenies support a close relationship between the microsporidia Brachiola algerae and Antonospora locustae
    Renny C H Lee
    Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    J Eukaryot Microbiol 55:388-92. 2008
    ..Also, an uncultivated microsporidian that infects cyclopoid copepods is shown to be related to Edhazardia aedis...
  68. ncbi request reprint Molecular phylogenies of Parabasalia inferred from four protein genes and comparison with rRNA trees
    Delphine Gerbod
    Department of Biology, Indiana University, Bloomington, IN 47405, USA
    Mol Phylogenet Evol 31:572-80. 2004
    ..e., species-specific) and not a problem for phylogeny reconstruction. Only for enolase are there more ancient duplications that may confound phylogenetic interpretation...
  69. ncbi request reprint Actin and ubiquitin protein sequences support a cercozoan/foraminiferan ancestry for the plasmodiophorid plant pathogens
    John 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...
  70. ncbi request reprint The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans: evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts
    Matthew B Rogers
    Botany Department, University of British Columbia, British Columbia, Canada
    Mol Biol Evol 24:54-62. 2007
    ..The B. natans plastid is thus not closely related to that of Euglena, which suggests that plastids originated independently in these 2 groups and the Cabozoa hypothesis is false...
  71. doi request reprint Plastid-derived genes in the nonphotosynthetic alveolate Oxyrrhis marina
    Claudio H Slamovits
    Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    Mol Biol Evol 25:1297-306. 2008
    ....
  72. ncbi request reprint EFL GTPase in cryptomonads and the distribution of EFL and EF-1alpha in chromalveolates
    Gillian H Gile
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, V6 T 1Z4 Canada
    Protist 157:435-44. 2006
    ..Phylogenetic analysis indicates EFL likely arose early within each subgroup where it is found, but suggests it may have originated multiple times within chromalveolates as a whole...
  73. ncbi request reprint Plastid-derived Type II fatty acid biosynthetic enzymes in chromists
    Kim Ryall
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, V6T 1Z4 Vancouver, BC, Canada
    Gene 313:139-48. 2003
    ..On the other hand, the strongly supported plastid fab I clade is related to cyanobacteria, and contains genes from chlamydiales...
  74. ncbi request reprint Expressed sequence tag (EST) survey of the highly adapted green algal parasite, Helicosporidium
    Audrey P de Koning
    Botany Department, Canadian Institute for Advanced Research, University of British Columbia, 3529 6270 University Boulevard, Vancouver, Canada BC, V6T 1Z4
    Protist 156:181-90. 2005
    ..Overall, these data multiply the available molecular information from Helicosporidium 100-fold, which should provide the basis for new insights into these unusual but interesting parasites...
  75. ncbi request reprint Re-examining alveolate evolution using multiple protein molecular phylogenies
    Naomi M Fast
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver
    J Eukaryot Microbiol 49:30-7. 2002
    ..Altogether, these results support the sisterhood of apicomplexa and dinoflagellates, but point out that the relationship is not as strong as is often assumed...
  76. pmc Distribution and phylogeny of EFL and EF-1alpha in Euglenozoa suggest ancestral co-occurrence followed by differential loss
    Gillian H Gile
    Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 4:e5162. 2009
    ..However, differential loss may play a role in EFL evolution, and this possibility has been less widely discussed...
  77. pmc Nucleus-encoded genes for plastid-targeted proteins in Helicosporidium: functional diversity of a cryptic plastid in a parasitic alga
    Audrey P de Koning
    3529 6270 University Blvd, Vancouver, BC V6T 1Z4, Canada
    Eukaryot Cell 3:1198-205. 2004
    ..These two parasites represent different evolutionary trajectories in plastid metabolic adaptation...
  78. pmc The inadequacy of morphology for species and genus delineation in microbial eukaryotes: an example from the parabasalian termite symbiont coronympha
    James T Harper
    Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 4:e6577. 2009
    ..Here we have used molecular markers to assess the species delineations in two related but morphologically distinct genera of uncultivated symbionts found in the hindgut of termites...
  79. ncbi request reprint Cryptic organelles in parasitic protists and fungi
    Bryony A P Williams
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada
    Adv Parasitol 54:9-68. 2003
    ..The apicomplexan plastid is now very well characterised and has been shown to function in the biosynthesis of fatty acids, isopentenyl diphosphate and heme, activities also found in photosynthetic plastids...
  80. pmc Molecular phylogeny and description of the novel katablepharid Roombia truncata gen. et sp. nov., and establishment of the Hacrobia taxon nov
    Noriko Okamoto
    Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 4:e7080. 2009
    ..Katablepharids are one such non-photosynthetic lineage closely related to cryptophytes. Despite their evolutionary and ecological importance, katablepharids are poorly investigated...
  81. pmc Bacterial catalase in the microsporidian Nosema locustae: implications for microsporidian metabolism and genome evolution
    Naomi M Fast
    Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
    Eukaryot Cell 2:1069-75. 2003
    ..locustae catalase may play some functional role in the spore. There is no evidence that the N. locustae catalase functions in a cryptic peroxisome...
  82. ncbi request reprint Molecular phylogeny and surface morphology of Colpodella edax (Alveolata): insights into the phagotrophic ancestry of apicomplexans
    Brian S Leander
    Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    J Eukaryot Microbiol 50:334-40. 2003
    ..Three flagella were present in some individuals, a peculiar feature also found in the microgametes of some apicomplexans...
  83. doi request reprint mRNA processing in Antonospora locustae spores
    Nicolas Corradi
    Department of Botany, University of British Columbia, 3529 6270, Vancouver, BC, V6T 1Z4, Canada
    Mol Genet Genomics 280:565-74. 2008
    ..locustae spores. Those transcripts were found to overlap up to four open reading frames in different strands, adding a novel layer of complexity in the mRNA transcription of this microsporidian species...
  84. pmc The mitochondrial genome of the entomoparasitic green alga helicosporidium
    Jean Francois Pombert
    Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 5:e8954. 2010
    ..Here we describe the complete mitochondrial genome sequence of the same strain, Helicosporidium sp. ATCC 50920 isolated from the black fly Simulium jonesi...
  85. ncbi request reprint Symbiotic innovation in the oxymonad Streblomastix strix
    Brian S Leander
    Canadian Institute for Advanced Research, Program in Evolutionary Biology, Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
    J Eukaryot Microbiol 51:291-300. 2004
    ..strix from a long slender cell to a teardrop-shaped cell, where the axostyle was compacted and became bifurcated near the posterior end...
  86. ncbi request reprint Novel ubiquitin fusion proteins: ribosomal protein P1 and actin
    John 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
    ....
  87. ncbi request reprint Recycled plastids: a 'green movement' in eukaryotic evolution
    John M Archibald
    Canadian Institute for Advanced Research, Dept Botany, University of British Columbia, Vancouver, Canada
    Trends Genet 18:577-84. 2002
    ....
  88. ncbi request reprint Molecular phylogeny and surface morphology of marine aseptate gregarines (Apicomplexa): Selenidium spp. and Lecudina spp
    B S Leander
    Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Botany, 3529 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
    J Parasitol 89:1191-205. 2003
    ..The trophozoites from the 2 species of Selenidium shared novel transverse striations but differed from one another in overall cell morphologies and writhing behavior...
  89. ncbi request reprint Sulfolobus islandicus plasmids pRN1 and pRN2 share distant but common evolutionary ancestry
    P J Keeling
    Department of Biology, Indiana University, Bloomington 47405, USA
    Extremophiles 2:391-3. 1998
    ..Two of these reading frames are likely related to replication, one encoding a large protein with a helicase domain similar to viral helicases, and the other a copy number control protein, CopG...
  90. ncbi request reprint Phylogeny of gregarines (Apicomplexa) as inferred from small-subunit rDNA and beta-tubulin
    Brian S Leander
    Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Botany, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
    Int J Syst Evol Microbiol 53:345-54. 2003
    ....
  91. ncbi request reprint Comment on "A green algal apicoplast ancestor"
    Ross F Waller
    Department of Biochemistry and, Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
    Science 301:49; author reply 49. 2003
  92. ncbi request reprint Complex protein targeting to dinoflagellate plastids
    Nicola 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...
  93. ncbi request reprint A transcriptional fusion of genes encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and enolase in dinoflagellates
    Kiyotaka Takishita
    Japan Agency for Marine Earth Science and Technology JAMSTEC, Yokosuka, Kanagawa 237 0061, Japan
    J Eukaryot Microbiol 52:343-8. 2005
    ....
  94. pmc Complete nucleotide sequence of the chlorarachniophyte nucleomorph: nature's smallest nucleus
    Paul R Gilson
    Infection and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3050, Australia
    Proc Natl Acad Sci U S A 103:9566-71. 2006
    ....
  95. pmc Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote
    Jonathan A Eisen
    The Institute for Genomic Research, Rockville, Maryland, United States of America
    PLoS Biol 4:e286. 2006
    ..thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance...
  96. doi request reprint Evolutionary biology: bridge over troublesome plastids
    Patrick J Keeling
    Nature 451:896-7. 2008