Corradi, Nicolas, Haag, Karen L, Pombert, Jean-François, Ebert, Dieter, Keeling, Patrick J
Abstract Background The highly compacted 2.9-Mb genome of Encephalitozoon cuniculi placed the microsporidia in the spotlight, encoding a mere 2,000 proteins and a highly reduced suite of biochemical...
A well-resolved global phylogeny of eukaryotes has been a major goal in understanding eukaryotic evolution and biodiversity because eukaryotic macroevolutionary events can only be interpreted...
Genomic survey of the non-cultivatable opportunistic human pathogen, Enterocytozoon bieneusi (2009)
Akiyoshi, Donna E., Morrison, Hilary G., Lei, Shi, Feng, Xiaochuan, Zhang, Quanshun, Corradi, Nicolas, ...
© 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Pathogens 5 (2009): e1000261,...
Evolution of Ultrasmall Spliceosomal Introns in Highly Reduced Nuclear Genomes (2009)
Slamovits, Claudio H., Keeling, Patrick J.
Intron reduction and loss is a significant component of genome compaction in many eukaryotic lineages, including yeasts, microsporidia, and some nucleomorphs. Nucleomorphs are the extremely reduced...
MINIREVIEWS Simplicity and Complexity of Microsporidian Genomes (2008)
Patrick J. Keeling, Claudio H. Slamovits
The adaptation to a parasitic lifestyle typically precipitates a number of profound changes to various levels of biological organization, including cell structure, genetics and genomics, metabolism,...
Williams, Bryony AP, Lee, Renny CH, Becnel, James J, Weiss, Louis M, Fast, Naomi M, Keeling, Patrick J
Abstract Background Microsporidia are well known models of extreme nuclear genome reduction and compaction. The smallest microsporidian genomes have received the most attention, but genomes of...
Nucleus-Encoded Periplastid-Targeted EFL in Chlorarachniophytes (2008)
Gile, Gillian H., Keeling, Patrick J.
Chlorarachniophytes are cercozoan amoeboflagellates that acquired photosynthesis by enslaving a green alga, which has retained a highly reduced nucleus called a nucleomorph. The nucleomorph lacks...
Plastid-Derived Genes in the Nonphotosynthetic Alveolate Oxyrrhis marina (2008)
Slamovits, Claudio H., Keeling, Patrick J.
Reconstructing the history of plastid acquisition and loss in the alveolate protists is a difficult problem because our knowledge of the distribution of plastids in extant lineages is incomplete due...
Jackson, Christopher J, Norman, John E, Schnare, Murray N, Gray, Michael W, Keeling, Patrick J, Waller, Ross F
Abstract Background Dinoflagellates comprise an ecologically significant and diverse eukaryotic phylum that is sister to the phylum containing apicomplexan endoparasites. The mitochondrial genome of...
Imanian, Behzad, Keeling, Patrick J
Abtract Background The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum are distinguished by the presence of a tertiary plastid derived from a diatom endosymbiont. The diatom is fully...
Horizontal transfer of a eukaryotic plastid-targeted protein gene to cyanobacteria (2007)
Rogers, Matthew B, Patron, Nicola J, Keeling, Patrick J
Abstract Background Horizontal or lateral transfer of genetic material between distantly related prokaryotes has been shown to play a major role in the evolution of bacterial and archaeal genomes,...
Rogers, Matthew B, Watkins, Russell F, Harper, James T, Durnford, Dion G, Gray, Michael W, Keeling, Patrick J
Abstract Background Lateral gene transfer is increasingly invoked to explain phylogenetic results that conflict with our understanding of organismal relationships. In eukaryotes, the most common...
Complex distribution of EFL and EF-1α proteins in the green algal lineage (2007)
Noble, Geoffrey P, Rogers, Matthew B, Keeling, Patrick J
Abstract Background EFL (or elongation factor-like) is a member of the translation superfamily of GTPase proteins. It is restricted to eukaryotes, where it is found in a punctate distribution that is...
BMC Biology BioMed Central (2007)
Christopher J Jackson, John E Norman, Murray N Schnare, Michael W Gray, Patrick J Keeling, Ross F Waller, ...
Research article Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria
Rogers, Matthew B., Gilson, Paul R., Su, Vanessa, McFadden, Geoffrey I., Keeling, Patrick J.
Chlorarachniophytes are amoeboflagellate cercozoans that acquired a plastid by secondary endosymbiosis. Chlorarachniophytes are the last major group of algae for which there is no completely...
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. (2006)
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Jonathan A. Eisen, Robert S. Coyne, Martin Wu, Dongying Wu, Mathangi Thiagarajan, Jennifer R. Wortman, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Comparative rates of evolution in endosymbiotic nuclear genomes (2006)
Patron, Nicola J, Rogers, Matthew B, Keeling, Patrick J
Abstract Background The nucleomorphs associated with secondary plastids of cryptomonads and chlorarachniophytes are the sole examples of organelles with eukaryotic nuclear genomes. Although not as...
A high density of ancient spliceosomal introns in oxymonad excavates (2006)
Slamovits, Claudio H, Keeling, Patrick J
Abstract Background Certain eukaryotic genomes, such as those of the amitochondriate parasites Giardia and Trichomonas , have very low intron densities, so low that canonical spliceosomal introns...
De Koning, Audrey P, Keeling, Patrick J
Abstract Background Loss of photosynthesis has occurred independently in several plant and algal lineages, and represents a major metabolic shift with potential consequences for the content and...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Eisen, Jonathan A., Coyne, Robert S., Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R., ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006)
Eisen, Jonathan A., Coyne, Robert S., Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R., ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Waller, Ross F., Slamovits, Claudio H., Keeling, Patrick J.
The number of cases of lateral or horizontal gene transfer in eukaryotic genomes is growing steadily, but in most cases, neither the donor nor the recipient is known, and the biological implications...
Gould, Sven B., Sommer, Maik S., Kroth, Peter G., Gile, Gillian H., Keeling, Patrick J., Maier, Uwe-G.
The complex plastid of the cryptophyte Guillardia theta and of the diatom Phaeodactylum tricornutum can both be traced back to an engulfed eukaryotic red alga. The eukaryotic origin of these plastids...
Waller, Ross F., Slamovits, Claudio H., Keeling, Patrick J.
The number of cases of lateral, or horizontal gene transfer in eukaryotic genomes is growing steadily, but in most cases neither the donor nor recipient are known and the biological implications of...
Gould, Sven B., Sommer, Maik S., Kroth, Peter G., Gile, Gillian H., Keeling, Patrick J., Maier, Uwe-G.
The complex plastid of the cryptophyte Guillardia theta and of the diatom Phaeodactylum tricornutum can both be traced back to an engulfed eukaryotic red alga. The eukaryotic origin of these plastids...
Rogers, Matthew B., Gilson, Paul R., Su, Vanessa, McFadden, Geoffrey I., Keeling, Patrick J.
Chlorarachniophytes are amoeboflagellate cercozoans that acquired a plastid by secondary endosymbiosis. Chlorarachniophytes are the last major group of algae for which there is no completely...
MICHELLE L. McEWAN, PATRICK J. KEELING
The dinoflagellate Kryptoperidinium foliaceum has replaced its ancestral peridinin-containing plastid with a fucoxanthin-containing diatom plastid via tertiary endosymbiosis. The diatom endosymbiont...
Plastid-Targeting Peptides from the Chlorarachniophyte Bigelowiella natans (2004)
MATTHEW B. ROGERS, JOHN M. ARCHIBALD, MATTHEW A. FIELD, CATHERINE LI, BORIS STRIEPEN, PATRICK J. KEELING
Chlorarachniophytes are marine amoeboflagellate protists that have acquired their plastid (chloroplast) through secondary endosymbiosis with a green alga. Like other algae, most of the proteins...
Symbiotic Innovation in the Oxymonad Streblomastix strix (2004)
BRIAN S. LEANDER, PATRICK J. KEELING
Streblomastix strix is an enigmatic oxymonad found exclusively in the hindgut of the damp-wood termite Zootermopsis. Streblomastix has a number of unusual morphological characters and forms a complex...
CLAUDIO H. SLAMOVITS, PATRICK J. KEELING
Nosema locustae is a microsporidian parasite of grasshopper pests that is used as a biological control agent, and is one of the emerging model systems for microsporidia. Due largely to its...
JOHN M. ARCHIBALD, PATRICK J. KEELING
The plasmodiophorids are a group of eukaryotic intracellular parasites that cause disease in a variety of economically significant crops. Plasmodiophorids have traditionally been considered fungi but...
BRIAN S. LEANDER, OLGA N. KUVARDINA, VLADIMIR V. ALESHIN, ALEXANDER P. MYLNIKOV, PATRICK J. KEELING
The molecular phylogeny of colpodellids provides a framework for inferences about the earliest stages in apicomplexan evolution and the characteristics of the last common ancestor of apicomplexans...
Harper, James T., Keeling, Patrick J.
Plastids (the photosynthetic organelles of plants and algae) originated through endosymbiosis between a cyanobacterium and a eukaryote, and subsequently spread to other eukaryotes by secondary...
Archibald, John M., Longet, David, Pawlowski, Jan, Keeling, Patrick J.
Ubiquitin is a 76 amino acid protein with a remarkable degree of evolutionary conservation. Ubiquitin plays an essential role in a large number of eukaryotic cellular processes by targeting proteins...
Harper, James T., Keeling, Patrick J.
Plastids (the photosynthetic organelles of plants and algae) originated through endosymbiosis between a cyanobacterium and a eukaryote and subsequently spread to other eukaryotes by secondary...
Harper, James T., Keeling, Patrick J.
Plastids (the photosynthetic organelles of plants and algae) originated through endosymbiosis between a cyanobacterium and a eukaryote, and subsequently spread to other eukaryotes by secondary...
OLGA N. KUVARDINA, BRIAN S. LEANDER, VLADIMIR V. ALESHIN, ALEXANDER P. MYL’NIKOV, PATRICK J. KEELING, TIMUR G. SIMDYANOV
In an attempt to reconstruct early alveolate evolution, we have examined the phylogenetic position of colpodellids by analyzing small subunit rDNA sequences from Colpodella pontica Myl’nikov 2000...
Re-examining Alveolate Evolution Using Multiple Protein Molecular Phylogenies (2002)
NAOMI M. FAST, LINGRU XUE, SCOTT BINGHAM, PATRICK J. KEELING
Alveolates are a diverse group of protists that includes three major lineages: ciliates, apicomplexa, and dinoflagellates. Among these three, it is thought that the apicomplexa and dinoflagellates...
Brinkman, Fiona S.L., Blanchard, Jeffrey L., Cherkasov, Artem, Av-Gay, Yossef, Brunham, Robert C., Fernandez, Rachel C., ...
Brinkman, Fiona S.L., Blanchard, Jeffrey L., Cherkasov, Artem, Av-Gay, Yossef, Brunham, Robert C., Fernandez, Rachel C., ...
An Evaluation of Hsp90 as a Mediator of Cortical Patterning in Tetrahymena (2001)
JOSEPH FRANKEL, NORMAN E. WILLIAMS, E. MARLO NELSEN, PATRICK J. KEELING
This study asks two questions: 1) whether Hsp90 is involved in the regulation of cortical patterning in Tetrahymena, and 2) if it is, whether specific defects in this regulation can be attributed to...
Foraminifera and Cercozoa Are Related in Actin Phylogeny: Two Orphans Find a Home? (2001)
In recent years, the increased sampling of protein-coding genes from diverse eukaryotes has revealed that many aspects of each gene tree are at odds with other phylogenies. This has led to the belief...
Fast, Naomi M., Kissinger, Jessica C., Roos, David S., Keeling, Patrick J.
The phylum Apicomplexa encompasses a large number of intracellular protozoan parasites, including the causative agents of malaria (Plasmodium), toxoplasmosis (Toxoplasma), and many other human and...
Evidence from Beta-Tubulin Phylogeny that Microsporidia Evolved from Within the Fungi (2000)
Keeling, Patrick J., Luker, Melissa A., Palmer, Jeffrey D.
Microsporidia are obligate intracellular parasites that were thought to be an ancient eukaryotic lineage based on molecular phylogenies using ribosomal RNA and translation elongation factors....
Symbiotic Origin of a Novel Actin Gene in the Cryptophyte Pyrenomonas helgolandii (2000)
Stibitz, Thomas B., Keeling, Patrick J., Bhattacharya, Debashish
Cryptophytes are photosynthetic protists that have acquired their plastids through the secondary symbiotic uptake of a red alga. A remarkable feature of cryptophytes is that they maintain a reduced...
Lateral Gene Transfer and Metabolic Adaptation in the Human Parasite Trichomonas vaginalis (2000)
De Koning, Audrey P., Brinkman, Fiona S. L., Jones, Steven J. M., Keeling, Patrick J.
Nuclear-encoded proteins target to the plastid in Toxoplasma gondii and Plasmodium falciparum
Waller, Ross F., Keeling, Patrick J., Donald, Robert G. K., Striepen, Boris, Handman, Emanuela, Lang-Unnasch, Naomi, ...
A vestigial, nonphotosynthetic plastid has been identified recently in protozoan parasites of the phylum Apicomplexa. The apicomplexan plastid, or “apicoplast,” is indispensable, but the complete...
Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase
Keeling, Patrick J., Palmer, Jeffrey D.
Enolase genes from land plants and apicomplexa (intracellular parasites, including the malarial parasite, Plasmodium) share two short insertions. This observation has led to the suggestion that the...
Archibald, John M., Rogers, Matthew B., Toop, Michael, Ishida, Ken-ichiro, Keeling, Patrick J.
Chlorarachniophytes are amoeboflagellate algae that acquired photosynthesis secondarily by engulfing a green alga and retaining its plastid (chloroplast). An important consequence of secondary...
Brinkman, Fiona S.L., Blanchard, Jeffrey L., Cherkasov, Artem, Av-Gay, Yossef, Brunham, Robert C., Fernandez, Rachel C., ...
An unusually high proportion of proteins encoded in Chlamydia genomes are most similar to plant proteins, leading to proposals that a Chlamydia ancestor obtained genes from a plant or plant-like host...
Fast, Naomi M., Law, Joyce S., Williams, Bryony A. P., Keeling, Patrick J.
Microsporidia constitute a group of extremely specialized intracellular parasites that infect virtually all animals. They are highly derived, reduced fungi that lack several features typical of other...
De Koning, Audrey P., Keeling, Patrick J.
Plastids are the organelles of plants and algae that house photosynthesis and many other biochemical pathways. Plastids contain a small genome, but most of their proteins are encoded in the nucleus...
Patron, Nicola J., Rogers, Matthew B., Keeling, Patrick J.
Plastids (photosynthetic organelles of plants and algae) are known to have spread between eukaryotic lineages by secondary endosymbiosis, that is, by the uptake of a eukaryotic alga by another...
Keeling, Patrick J., Inagaki, Yuji
Translation elongation factor 1α (EF-1α, or EF-Tu in bacteria) is a highly conserved core component of the translation machinery that is shared by all cellular life. It is part of a large...
A high frequency of overlapping gene expression in compacted eukaryotic genomes
Williams, Bryony A. P., Slamovits, Claudio H., Patron, Nicola J., Fast, Naomi M., Keeling, Patrick J.
The gene density of eukaryotic nuclear genomes is generally low relative to prokaryotes, but several eukaryotic lineages (many parasites or endosymbionts) have independently evolved highly compacted,...
Slamovits, Claudio H., Keeling, Patrick J.
In pyrophosphate-dependent glycolysis, the ATP/ADP-dependent enzymes phosphofructokinase (PFK) and pyruvate kinase are replaced by the pyrophosphate-dependent PFK and pyruvate phosphate dikinase...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature’s smallest nucleus
Gilson, Paul R., Su, Vanessa, Slamovits, Claudio H., Reith, Michael E., Keeling, Patrick J., McFadden, Geoffrey I.
The introduction of plastids into different heterotrophic protists created lineages of algae that diversified explosively, proliferated in marine and freshwater environments, and radically altered...
Nuclear-encoded proteins target to the plastid in Toxoplasma gondii and Plasmodium falciparum
Waller, Ross F., Keeling, Patrick J., Donald, Robert G. K., Striepen, Boris, Handman, Emanuela, Lang-Unnasch, Naomi, ...
A vestigial, nonphotosynthetic plastid has been identified recently in protozoan parasites of the phylum Apicomplexa. The apicomplexan plastid, or “apicoplast,” is indispensable, but the complete...
Lateral transfer at the gene and subgenic levels in the evolution of eukaryotic enolase
Keeling, Patrick J., Palmer, Jeffrey D.
Enolase genes from land plants and apicomplexa (intracellular parasites, including the malarial parasite, Plasmodium) share two short insertions. This observation has led to the suggestion that the...
Archibald, John M., Rogers, Matthew B., Toop, Michael, Ishida, Ken-ichiro, Keeling, Patrick J.
Chlorarachniophytes are amoeboflagellate algae that acquired photosynthesis secondarily by engulfing a green alga and retaining its plastid (chloroplast). An important consequence of secondary...
Brinkman, Fiona S.L., Blanchard, Jeffrey L., Cherkasov, Artem, Av-Gay, Yossef, Brunham, Robert C., Fernandez, Rachel C., ...
An unusually high proportion of proteins encoded in Chlamydia genomes are most similar to plant proteins, leading to proposals that a Chlamydia ancestor obtained genes from a plant or plant-like host...
Fast, Naomi M., Law, Joyce S., Williams, Bryony A. P., Keeling, Patrick J.
Microsporidia constitute a group of extremely specialized intracellular parasites that infect virtually all animals. They are highly derived, reduced fungi that lack several features typical of other...
De Koning, Audrey P., Keeling, Patrick J.
Plastids are the organelles of plants and algae that house photosynthesis and many other biochemical pathways. Plastids contain a small genome, but most of their proteins are encoded in the nucleus...
Patron, Nicola J., Rogers, Matthew B., Keeling, Patrick J.
Plastids (photosynthetic organelles of plants and algae) are known to have spread between eukaryotic lineages by secondary endosymbiosis, that is, by the uptake of a eukaryotic alga by another...
Keeling, Patrick J., Inagaki, Yuji
Translation elongation factor 1α (EF-1α, or EF-Tu in bacteria) is a highly conserved core component of the translation machinery that is shared by all cellular life. It is part of a large...
A high frequency of overlapping gene expression in compacted eukaryotic genomes
Williams, Bryony A. P., Slamovits, Claudio H., Patron, Nicola J., Fast, Naomi M., Keeling, Patrick J.
The gene density of eukaryotic nuclear genomes is generally low relative to prokaryotes, but several eukaryotic lineages (many parasites or endosymbionts) have independently evolved highly compacted,...
Slamovits, Claudio H., Keeling, Patrick J.
In pyrophosphate-dependent glycolysis, the ATP/ADP-dependent enzymes phosphofructokinase (PFK) and pyruvate kinase are replaced by the pyrophosphate-dependent PFK and pyruvate phosphate dikinase...
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
Eisen, Jonathan A, Coyne, Robert S, Wu, Martin, Wu, Dongying, Thiagarajan, Mathangi, Wortman, Jennifer R, ...
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct...
Microsporidian mitosomes retain elements of the general mitochondrial targeting system
Burri, Lena, Williams, Bryony A. P., Bursac, Dejan, Lithgow, Trevor, Keeling, Patrick J.
Microsporidia are intracellular parasites that infect a variety of animals, including humans. As highly specialized parasites, they are characterized by a number of unusual adaptations, many of which...
A complex and punctate distribution of three eukaryotic genes derived by lateral gene transfer
Rogers, Matthew B, Watkins, Russell F, Harper, James T, Durnford, Dion G, Gray, Michael W, Keeling, Patrick J
Corradi, Nicolas, Akiyoshi, Donna E., Morrison, Hilary G., Feng, Xiaochuan, Weiss, Louis M., Tzipori, Saul, ...
Jackson, Christopher J, Norman, John E, Schnare, Murray N, Gray, Michael W, Keeling, Patrick J, Waller, Ross F
Williams, Bryony AP, Lee, Renny CH, Becnel, James J, Weiss, Louis M, Fast, Naomi M, Keeling, Patrick J
Genomic Survey of the Non-Cultivatable Opportunistic Human Pathogen, Enterocytozoon bieneusi
Akiyoshi, Donna E., Morrison, Hilary G., Lei, Shi, Feng, Xiaochuan, Zhang, Quanshun, Corradi, Nicolas, ...
Enterocytozoon bieneusi is the most common microsporidian associated with human disease, particularly in the immunocompromised population. In the setting of HIV infection, it is associated with...
Gile, Gillian H., Faktorová, Drahomíra, Castlejohn, Christina A., Burger, Gertraud, Lang, B. Franz, Farmer, Mark A., ...