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Geoffrey I Mcfadden - One of the best experts on this subject based on the ideXlab platform.
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The Cryptomonad nucleomorph.
Protoplasma, 2017Co-Authors: Geoffrey I McfaddenAbstract:The Cryptomonad nucleomorph is a vestigial nucleus of a eukaryotic red alga engulfed by a phagotrophic protist and retained as a photosynthetic endosymbiont. This review recounts the initial discovery and subsequent characterisation of the Cryptomonad nucleomorph focusing on the key role of Peter Sitte and his proteges in our understanding of secondary endosymbiosis to create complex plastids, one of the major transition events in the evolution of life on Earth.
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Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature’s smallest nucleus
Proceedings of the National Academy of Sciences of the United States of America, 2006Co-Authors: Paul R. Gilson, Claudio H. Slamovits, Patrick J. Keeling, Michael Reith, Geoffrey I McfaddenAbstract:The introduction of plastids into different heterotrophic protists created lineages of algae that diversified explosively, proliferated in marine and freshwater environments, and radically altered the biosphere. The origins of these secondary plastids are usually inferred from the presence of additional plastid membranes. However, two examples provide unique snapshots of secondary-endosymbiosis-in-action, because they retain a vestige of the endosymbiont nucleus known as the nucleomorph. These are chlorarachniophytes and Cryptomonads, which acquired their plastids from a green and red alga respectively. To allow comparisons between them, we have sequenced the nucleomorph genome from the chlorarachniophyte Bigelowiella natans: at a mere 373,000 bp and with only 331 genes, the smallest nuclear genome known and a model for extreme reduction. The genome is eukaryotic in nature, with three linear chromosomes containing densely packed genes with numerous overlaps. The genome is replete with 852 introns, but these are the smallest introns known, being only 18, 19, 20, or 21 nt in length. These pygmy introns are shown to be miniaturized versions of normal-sized introns present in the endosymbiont at the time of capture. Seventeen nucleomorph genes encode proteins that function in the plastid. The other nucleomorph genes are housekeeping entities, presumably underpinning maintenance and expression of these plastid proteins. Chlorarachniophyte plastids are thus serviced by three different genomes (plastid, nucleomorph, and host nucleus) requiring remarkable coordination and targeting. Although originating by two independent endosymbioses, chlorarachniophyte and Cryptomonad nucleomorph genomes have converged upon remarkably similar architectures but differ in many molecular details that reflect two distinct trajectories to hypercompaction and reduction.
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Cryptomonad evolution: Nuclear 18S rDNA phylogeny versus cell morphology and pigmentation
Journal of Phycology, 2002Co-Authors: James A Deane, Isabelle M. Strachan, Gary W. Saunders, David R. A. Hill, Geoffrey I McfaddenAbstract:A nuclearl8S rDNA phylogeny for Cryptomonad algae is presented, including 11 species yet to be investigated by molecular means. The phylogenetic positions of the Cryptomonad genera Campylomonas and Plagioselmis are assessed for the first time. Campylomonas groups most closely with morphologically similar species with the same accessory pigment from the genus Cryptomonas. Plagioselmis groups with the genera Teleaulax and Geminigera forming a clade whose members are united by unusual thylakoid arrangement. Nuclear 18S rDNA phylogeny divides Cryptomonads into seven major lineages, two of which consist of the monospecific genera Proteomonas and Falcomonas. Analysis of nuclearl8S rDNA sequence supports suggestions that a Falcomonas-like Cryptomonad gave rise to all other blue-green Cryptomonads. New sequence from the plastid-lacking Cryptomonad genus Goniomonas is also included, and the order of divergence of the major Cryptomonad lineages is discussed. The morphology, number, and pigmentation of the Cryptomonad plastidial complex are congruent with nuclear 18S rDNA phylogenies. Host cell features, such as periplast type, furrow/ gullet system, and cell shape, can be more variable and may be markedly different in species that are closely related by nuclear 18S rDNA phylogeny. Conversely, some species that are not closely related by molecular phylogeny may display a very similar, possibly primitive, periplast and furrow morphology.
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Jam packed genomes – a preliminary, comparative analysis of nucleomorphs
Genetica, 2002Co-Authors: Paul R. Gilson, Geoffrey I McfaddenAbstract:There are two ways eukaryotic cells can permanently acquire chloroplasts. They can take up a cyanobacterium and turn it into a chloroplast or they can engulf an alga that already has a chloroplast. The second method is far more common and there are at least seven major groups of protists that have obtained their chloroplasts, this way. In most cases little remains of the engulfed alga apart from its chloroplast, but in two groups, the Cryptomonads and chlorarachniophytes, a small remnant nucleus of the engulfed alga is still present. These tiny nuclei, called nucleomorphs, are the smallest and most compact eukaryotic genomes known and recently the nucleomorph of the Cryptomonad alga Guillardia theta , was completely sequenced (551 kilobases). The nucleomorph of the chlorarachniophyte Bigellowiella natans (380 kilobases), is also being sequenced and is about half complete. We discuss some of the similarities and differences that are emerging between these two nucleomorph genomes. Both genomes contain just three chromosomes that encode mainly housekeeping genes and a few proteins for chloroplast functions. The bulk of nucleomorph gene coding capacity, therefore, appears to be devoted to self perpetuation and creating gene and protein expression machineries to make a small number of essential chloroplast proteins. We discuss reasons why both nucleomorphs are extraordinarily compact and why their gene sequences are evolving rapidly.
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Evidence for nucleomorph to host nucleus gene transfer: light-harvesting complex proteins from Cryptomonads and chlorarachniophytes.
Protist, 2000Co-Authors: James A Deane, Vanessa Su, Martin Fraunholz, Uwe G. Maier, Dion G. Durnford, William Martin, Geoffrey I McfaddenAbstract:Summary Cryptomonads and chlorarachniophytes acquired photosynthesis independently by engulfing and retaining eukaryotic algal cells. The nucleus of the engulfed cells (known as a nucleomorph) is much reduced and encodes only a handful of the numerous essential plastid proteins normally encoded by the nucleus of chloroplast-containing organisms. In Cryptomonads and chlorarachniophytes these proteins are thought to be encoded by genes in the secondary host nucleus. Genes for these proteins were potentially transferred from the nucleomorph (symbiont nucleus) to the secondary host nucleus; nucleus to nucleus intracellular gene transfers. We isolated complementary DNA clones (cDNAs) for chlorophyll-binding proteins from a Cryptomonad and a chlorarachniophyte. In each organism these genes reside in the secondary host nuclei, but phylogenetic evidence, and analysis of the targeting mechanisms, suggest the genes were initially in the respective nucleomorphs (symbiont nuclei). Implications for origins of secondary endosymbiotic algae are discussed.
John M Archibald - One of the best experts on this subject based on the ideXlab platform.
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Retrotransposons and Tandem Repeat Sequences in the Nuclear Genomes of Cryptomonad Algae
2015Co-Authors: Sharen Bowman, John M ArchibaldAbstract:Abstract. The Cryptomonads are an enigmatic group of unicellular eukaryotic algae that possess two nuclear genomes, having acquired photosynthesis by the uptake and retention of a eukaryotic algal endo-symbiont. The endosymbiont nuclear genome, or nucleomorph, of the Cryptomonad Guillardia theta has been completely sequenced: at only 551 kilobases (kb) and with a gene density of 1 gene/kb, it is a model of compaction. In contrast, very little is known about the structure and composition of the crypto-monad host nuclear genome. Here we present the results of two small-scale sequencing surveys of fo-smid clone libraries from two distantly related cryp-tomonads, Rhodomonas salina CCMP1319 and Cryptomonas paramecium CCAP977/2A, corre
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Ultrastructure and molecular phylogeny of the Cryptomonad Goniomonas avonlea sp. nov.
Protist, 2012Co-Authors: Eunsoo Kim, John M ArchibaldAbstract:We describe a new species of Cryptomonad, Goniomonas avonlea sp. nov., using molecular phylogeny and comprehensive microscopic investigation. G. avonlea is a marine bacterivorous flagellate, measuring 8-11 μm long and 6-7 μm wide, with two subequal flagella that are directed anteriorly and posteriorly. G. avonlea is morphologically and genetically distinct from three other Goniomonas species that have been described to date. SEM and TEM show that G. avonlea shares ultrastructural features with other Goniomonas and Cryptomonads, including the presence of bipartite ejectisomes, double septa in the transition region, flat mitochondrial cristae, a furrow complex, a rhizostyle, rectangular periplast plates, and the infundibulum. The discharged large ejectisome is straight and has a unique loose, reticulate layer. The flagellar apparatus includes non-tubular roots, microtubular roots, and a compound root that is reminiscent of the multilayered structure (MLS) observed in the flagellate cells of streptophytes and a few other eukaryotes. Molecular phylogenies based on 18S and 28S rRNA genes suggest a specific affiliation of G. avonlea to marine Goniomonas species, and support the monophyly of Goniomonas to the exclusion of plastid-bearing Cryptomonads. Our study adds to a growing body of evidence for the high level of diversity and antiquity of the genus Goniomonas.
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Complete Nucleomorph Genome Sequence of the Nonphotosynthetic Alga Cryptomonas paramecium Reveals a Core Nucleomorph Gene Set
Genome Biology and Evolution, 2010Co-Authors: Goro Tanifuji, Travis J. Wheeler, Natalie Donaher, Marlena Dlutek, Naoko T Onodera, John M ArchibaldAbstract:Nucleomorphs are the remnant nuclei of algal endosymbionts that were engulfed by nonphotosynthetic host eukaryotes. These peculiar organelles are found in Cryptomonad and chlorarachniophyte algae, where they evolved from red and green algal endosymbionts, respectively. Despite their independent origins, Cryptomonad and chlorarachniophyte nucleomorph genomes are similar in size and structure: they are both
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Actin Gene Family Dynamics in Cryptomonads and Red Algae
Journal of Molecular Evolution, 2010Co-Authors: Goro Tanifuji, John M ArchibaldAbstract:Here we present evidence for a complex evolutionary history of actin genes in red algae and Cryptomonads, a group that acquired photosynthesis secondarily through the engulfment of a red algal endosymbiont. Four actin genes were found in the nuclear genome of the Cryptomonad, Guillardia theta , and in the genome of the red alga, Galdieria sulphuraria , a member of the Cyanidiophytina. Phylogenetic analyses reveal that the both organisms possess two distinct sequence types, designated “type-1” and “type-2.” A weak but consistent phylogenetic affinity between the Cryptomonad type-2 sequences and the type-2 sequences of G. sulphuraria and red algae belonging to the Rhodophytina was observed. This is consistent with the possibility that the Cryptomonad type-2 sequences are derived from the red algal endosymbiont that gave rise to the Cryptomonad nucleomorph and plastid. Red algae as a whole possess two very different actin sequence types, with G. sulphuraria being the only organism thus far known to possess both. The common ancestor of Rhodophytina and Cyanidiophytina may have had two actin genes, with differential loss explaining the distribution of these genes in modern-day groups. Our study provides new insight into the evolution and divergence of actin genes in Cryptomonads and red algae, and in doing so underscores the challenges associated with heterogeneity in actin sequence evolution and ortholog/paralog detection.
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Retrotransposons and Tandem Repeat Sequences in the Nuclear Genomes of Cryptomonad Algae
Journal of Molecular Evolution, 2007Co-Authors: Hameed Khan, Catherine Kozera, Bruce A. Curtis, Jillian Tarrant Bussey, Stan Theophilou, Sharen Bowman, John M ArchibaldAbstract:The Cryptomonads are an enigmatic group of unicellular eukaryotic algae that possess two nuclear genomes, having acquired photosynthesis by the uptake and retention of a eukaryotic algal endosymbiont. The endosymbiont nuclear genome, or nucleomorph, of the Cryptomonad Guillardia theta has been completely sequenced: at only 551 kilobases (kb) and with a gene density of ∼1 gene/kb, it is a model of compaction. In contrast, very little is known about the structure and composition of the Cryptomonad host nuclear genome. Here we present the results of two small-scale sequencing surveys of fosmid clone libraries from two distantly related Cryptomonads, Rhodomonas salina CCMP1319 and Cryptomonas paramecium CCAP977/2A, corresponding to ∼150 and ∼235 kb of sequence, respectively. Very few of the random end sequences determined in this study show similarity to known genes in other eukaryotes, underscoring the considerable evolutionary distance between the Cryptomonads and other eukaryotes whose nuclear genomes have been completely sequenced. Using a combination of fosmid clone end-sequencing, Southern hybridizations, and PCR, we demonstrate that Ty3-gypsy long-terminal repeat (LTR) retrotransposons and tandem repeat sequences are a prominent feature of the nuclear genomes of both organisms. The complete sequence of a 30.9-kb genomic fragment from R. salina was found to contain a full-length Ty3-gypsy element with near-identical LTRs and a chromodomain, a protein module suggested to mediate the site-specific integration of the retrotransposon. The discovery of chromodomain-containing retroelements in Cryptomonads further expands the known distribution of the so-called chromoviruses across the tree of eukaryotes.
Takeo Horiguchi - One of the best experts on this subject based on the ideXlab platform.
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kleptochloroplast enlargement karyoklepty and the distribution of the Cryptomonad nucleus in nusuttodinium gymnodinium aeruginosum dinophyceae
Protist, 2015Co-Authors: Ryo Onuma, Takeo HoriguchiAbstract:The unarmoured freshwater dinoflagellate Nusuttodinium (= Gymnodinium) aeruginosum retains a Cryptomonad-derived kleptochloroplast and nucleus, the former of which fills the bulk of its cell volume. The paucity of studies following morphological changes to the kleptochloroplast with time make it unclear how the kleptochloroplast enlarges and why the cell ultimately loses the Cryptomonad nucleus. We observed, both at the light and electron microscope level, morphological changes to the kleptochloroplast incurred by the enlargement process under culture conditions. The distribution of the Cryptomonad nucleus after host cell division was also investigated. The volume of the kleptochloroplast increased more than 20-fold, within 120 h of ingestion of the Cryptomonad. Host cell division was not preceded by Cryptomonad karyokinesis so that only one of the daughter cells inherited a Cryptomonad nucleus. The fate of all daughter cells originating from a single cell through five generations was closely monitored, and this observation revealed that the cell that inherited the Cryptomonad nucleus consistently possessed the largest kleptochloroplast for that generation. Therefore, this study suggests that some important Cryptomonad nucleus division mechanism is lost during ingestion process, and that the Cryptomonad nucleus carries important information for the enlargement of the kleptochloroplast.
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Kleptochloroplast Enlargement, Karyoklepty and the Distribution of the Cryptomonad Nucleus in Nusuttodinium (= Gymnodinium) aeruginosum (Dinophyceae).
Protist, 2015Co-Authors: Ryo Onuma, Takeo HoriguchiAbstract:The unarmoured freshwater dinoflagellate Nusuttodinium (= Gymnodinium) aeruginosum retains a Cryptomonad-derived kleptochloroplast and nucleus, the former of which fills the bulk of its cell volume. The paucity of studies following morphological changes to the kleptochloroplast with time make it unclear how the kleptochloroplast enlarges and why the cell ultimately loses the Cryptomonad nucleus. We observed, both at the light and electron microscope level, morphological changes to the kleptochloroplast incurred by the enlargement process under culture conditions. The distribution of the Cryptomonad nucleus after host cell division was also investigated. The volume of the kleptochloroplast increased more than 20-fold, within 120 h of ingestion of the Cryptomonad. Host cell division was not preceded by Cryptomonad karyokinesis so that only one of the daughter cells inherited a Cryptomonad nucleus. The fate of all daughter cells originating from a single cell through five generations was closely monitored, and this observation revealed that the cell that inherited the Cryptomonad nucleus consistently possessed the largest kleptochloroplast for that generation. Therefore, this study suggests that some important Cryptomonad nucleus division mechanism is lost during ingestion process, and that the Cryptomonad nucleus carries important information for the enlargement of the kleptochloroplast.
Ryo Onuma - One of the best experts on this subject based on the ideXlab platform.
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Changes in the transcriptome, ploidy, and optimal light intensity of a Cryptomonad upon integration into a kleptoplastic dinoflagellate
The ISME Journal, 2020Co-Authors: Ryo Onuma, Shunsuke Hirooka, Yu Kanesaki, Takayuki Fujiwara, Hirofumi Yoshikawa, Shin-ya MiyagishimaAbstract:Endosymbiosis of unicellular eukaryotic algae into previously nonphotosynthetic eukaryotes has established chloroplasts in several eukaryotic lineages. In addition, certain unicellular organisms in several different lineages ingest algae and utilize them as temporal chloroplasts (kleptoplasts) for weeks to months before digesting them. Among these organisms, the dinoflagellate Nusuttodinium aeruginosum ingests the Cryptomonad Chroomonas sp. and enlarges the kleptoplast with the aid of the Cryptomonad nucleus. To understand how the Cryptomonad nucleus is remodeled in the dinoflagellate, here we examined changes in the transcriptome and ploidy of the ingested nucleus. We show that, after ingestion, genes involved in metabolism, translation, and DNA replication are upregulated while those involved in sensory systems and cell motility are downregulated. In the dinoflagellate cell, the Cryptomonad nucleus undergoes polyploidization that correlates with an increase in the mRNA levels of upregulated genes. In addition, the ingested nucleus almost loses transcriptional responses to light. Because polyploidization and loss of transcriptional regulation are also known to have occurred during the establishment of endosymbiotic organelles, these changes are probably a common trend in endosymbiotic evolution. Furthermore, we show that the kleptoplast and dinoflagellate are more susceptible to high light than the free-living Cryptomonad but that the ingested nucleus reduces this damage.
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kleptochloroplast enlargement karyoklepty and the distribution of the Cryptomonad nucleus in nusuttodinium gymnodinium aeruginosum dinophyceae
Protist, 2015Co-Authors: Ryo Onuma, Takeo HoriguchiAbstract:The unarmoured freshwater dinoflagellate Nusuttodinium (= Gymnodinium) aeruginosum retains a Cryptomonad-derived kleptochloroplast and nucleus, the former of which fills the bulk of its cell volume. The paucity of studies following morphological changes to the kleptochloroplast with time make it unclear how the kleptochloroplast enlarges and why the cell ultimately loses the Cryptomonad nucleus. We observed, both at the light and electron microscope level, morphological changes to the kleptochloroplast incurred by the enlargement process under culture conditions. The distribution of the Cryptomonad nucleus after host cell division was also investigated. The volume of the kleptochloroplast increased more than 20-fold, within 120 h of ingestion of the Cryptomonad. Host cell division was not preceded by Cryptomonad karyokinesis so that only one of the daughter cells inherited a Cryptomonad nucleus. The fate of all daughter cells originating from a single cell through five generations was closely monitored, and this observation revealed that the cell that inherited the Cryptomonad nucleus consistently possessed the largest kleptochloroplast for that generation. Therefore, this study suggests that some important Cryptomonad nucleus division mechanism is lost during ingestion process, and that the Cryptomonad nucleus carries important information for the enlargement of the kleptochloroplast.
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Kleptochloroplast Enlargement, Karyoklepty and the Distribution of the Cryptomonad Nucleus in Nusuttodinium (= Gymnodinium) aeruginosum (Dinophyceae).
Protist, 2015Co-Authors: Ryo Onuma, Takeo HoriguchiAbstract:The unarmoured freshwater dinoflagellate Nusuttodinium (= Gymnodinium) aeruginosum retains a Cryptomonad-derived kleptochloroplast and nucleus, the former of which fills the bulk of its cell volume. The paucity of studies following morphological changes to the kleptochloroplast with time make it unclear how the kleptochloroplast enlarges and why the cell ultimately loses the Cryptomonad nucleus. We observed, both at the light and electron microscope level, morphological changes to the kleptochloroplast incurred by the enlargement process under culture conditions. The distribution of the Cryptomonad nucleus after host cell division was also investigated. The volume of the kleptochloroplast increased more than 20-fold, within 120 h of ingestion of the Cryptomonad. Host cell division was not preceded by Cryptomonad karyokinesis so that only one of the daughter cells inherited a Cryptomonad nucleus. The fate of all daughter cells originating from a single cell through five generations was closely monitored, and this observation revealed that the cell that inherited the Cryptomonad nucleus consistently possessed the largest kleptochloroplast for that generation. Therefore, this study suggests that some important Cryptomonad nucleus division mechanism is lost during ingestion process, and that the Cryptomonad nucleus carries important information for the enlargement of the kleptochloroplast.
Patrick J. Keeling - One of the best experts on this subject based on the ideXlab platform.
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multiple gene phylogenies support the monophyly of Cryptomonad and haptophyte host lineages
Current Biology, 2007Co-Authors: Nicola J Patron, Yuji Inagaki, Patrick J. KeelingAbstract:Cryptomonad algae acquired their plastids by the secondary endosymbiotic uptake of a eukaryotic red alga. Several other algal lineages acquired plastids through such an event [1], but Cryptomonads are distinguished by the retention of a relic red algal nucleus, the nucleomorph [2]. The nucleomorph (and its absence in other lineages) can reveal a great deal about the process and history of endosymbiosis, but only if we know the relationship between Cryptomonads and other algae, and this has been controversial. Several recent analyses have suggested a relationship between plastids of Cryptomonads and some or all other red alga-containing lineages [3-6], but we must also know whether host nuclear genes mirror this relationship to determine the number of endosymbiotic events, and this has not been demonstrated. We have carried out an expressed sequence tag (EST) survey of the Cryptomonad Guillardia theta. Phylogenetic analyses of 102 orthologous nucleus-encoded proteins (18,425 amino acid alignment positions) show a robust sister-group relationship between Cryptomonads and the haptophyte algae, which also have a red secondary plastid. 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.
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EFL GTPase in Cryptomonads and the Distribution of EFL and EF-1α in Chromalveolates
Protist, 2006Co-Authors: Gillian H. Gile, Nicola J Patron, Patrick J. KeelingAbstract:EFL (EF-like protein) is a member of the GTPase superfamily that includes several translation factors. Because it has only been found in a few eukaryotic lineages and its presence correlates with the absence of the related core translation factor EF-1alpha, its distribution is hypothesized to be the result of lateral gene transfer and replacement of EF-1alpha. In one supergroup of eukaryotes, the chromalveolates, two major lineages were found to contain EFL (dinoflagellates and haptophytes), while the others encode EF-1alpha (apicomplexans, ciliates, heterokonts and Cryptomonads). For each of these groups, this distribution was deduced from whole genome sequence or expressed sequence tag (EST) data from several species, with the exception of Cryptomonads from which only a single EF-1alpha PCR product from one species was known. By sequencing ESTs from two Cryptomonads, Guillardia theta and Rhodomonas salina, and searching for all GTPase translation factors, we revealed that EFL is present in both species, but, contrary to expectations, we found EF-1alpha in neither. On balance, we suggest the previously reported EF-1alpha from Rhodomonas salina is likely an artefact of contamination. We also identified EFL in EST data from two members of the dinoflagellate lineage, Karlodinium micrum and Oxyrrhis marina, and from an ongoing genomic sequence project from a third, Perkinsus marinus. Karlodinium micrum is a symbiotic pairing of two lineages that would have both had EFL (a dinoflagellate and a haptophyte), but only the dinoflagellate gene remains. Oxyrrhis marina and Perkinsus marinus are early diverging sister-groups to dinoflagellates, and together show that EFL originated early in this lineage. Phylogenetic analysis confirmed that these genes are all EFL homologues, and showed that Cryptomonad genes are not detectably related to EFL from other chromalveolates, which collectively form several distinct groups. The known distribution of EFL now includes a third group of chromalveolates, Cryptomonads. Of the six major subgroups of chromalveolates, EFL is found in half and EF-1alpha in the other half, and none as yet unambiguously possess both genes. 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.
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Comparative rates of evolution in endosymbiotic nuclear genomes
BMC Evolutionary Biology, 2006Co-Authors: Nicola J Patron, Matthew B. Rogers, Patrick J. KeelingAbstract:Background The nucleomorphs associated with secondary plastids of Cryptomonads and chlorarachniophytes are the sole examples of organelles with eukaryotic nuclear genomes. Although not as widespread as their prokaryotic equivalents in mitochondria and plastids, nucleomorph genomes share similarities in terms of reduction and compaction. 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. Results Here, we test whether the phylogenetically distinct nucleomorph genomes of the Cryptomonad, Guillardia theta , and the chlorarachniophyte, Bigelowiella natans , have experienced similar evolutionary pressures during their transformation to reduced organelles. We compared the evolutionary rates of genes from nuclear, nucleomorph, and plastid genomes, all of which encode proteins that function in the same cellular compartment, the plastid, and are thus subject to similar selection pressures. Furthermore, we investigated the divergence of nucleomorphs within Cryptomonads by comparing G. theta and Rhodomonas salina . Conclusion Chlorarachniophyte nucleomorph genes have accumulated errors at a faster rate than other genomes within the same cell, regardless of the compartment where the gene product functions. In contrast, most nucleomorph genes in Cryptomonads have evolved faster than genes in other genomes on average, but genes for plastid-targeted proteins are not overly divergent, and it appears that Cryptomonad nucleomorphs are not presently evolving rapidly and have therefore stabilized. Overall, these analyses suggest that the forces at work in the two lineages are different, despite the similarities between the structures of their genomes.
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Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature’s smallest nucleus
Proceedings of the National Academy of Sciences of the United States of America, 2006Co-Authors: Paul R. Gilson, Claudio H. Slamovits, Patrick J. Keeling, Michael Reith, Geoffrey I McfaddenAbstract:The introduction of plastids into different heterotrophic protists created lineages of algae that diversified explosively, proliferated in marine and freshwater environments, and radically altered the biosphere. The origins of these secondary plastids are usually inferred from the presence of additional plastid membranes. However, two examples provide unique snapshots of secondary-endosymbiosis-in-action, because they retain a vestige of the endosymbiont nucleus known as the nucleomorph. These are chlorarachniophytes and Cryptomonads, which acquired their plastids from a green and red alga respectively. To allow comparisons between them, we have sequenced the nucleomorph genome from the chlorarachniophyte Bigelowiella natans: at a mere 373,000 bp and with only 331 genes, the smallest nuclear genome known and a model for extreme reduction. The genome is eukaryotic in nature, with three linear chromosomes containing densely packed genes with numerous overlaps. The genome is replete with 852 introns, but these are the smallest introns known, being only 18, 19, 20, or 21 nt in length. These pygmy introns are shown to be miniaturized versions of normal-sized introns present in the endosymbiont at the time of capture. Seventeen nucleomorph genes encode proteins that function in the plastid. The other nucleomorph genes are housekeeping entities, presumably underpinning maintenance and expression of these plastid proteins. Chlorarachniophyte plastids are thus serviced by three different genomes (plastid, nucleomorph, and host nucleus) requiring remarkable coordination and targeting. Although originating by two independent endosymbioses, chlorarachniophyte and Cryptomonad nucleomorph genomes have converged upon remarkably similar architectures but differ in many molecular details that reflect two distinct trajectories to hypercompaction and reduction.
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A high frequency of overlapping gene expression in compacted eukaryotic genomes
Proceedings of the National Academy of Sciences of the United States of America, 2005Co-Authors: Bryony A. P. Williams, Claudio H. Slamovits, Nicola J Patron, Naomi M Fast, Patrick J. KeelingAbstract: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, gene-dense genomes. The best studied of these are the microsporidia, highly adapted fungal parasites, and the nucleomorphs, relict nuclei of endosymbiotic algae found in Cryptomonads and chlorarachniophytes. These systems are now models for the effects of compaction on the form and dynamics of the nuclear genome. Here we report a large-scale investigation of gene expression from compacted eukaryotic genomes. We have conducted EST surveys of the microsporidian Antonospora locustae and nucleomorphs of the Cryptomonad Guillardia theta and the chlorarachniophyte Bigelowiella natans. In all three systems we find a high frequency of mRNA molecules that encode sequence from more than one gene. There is no bias for these genes to be on the same strand, so it is unlikely that these mRNAs represent operons. Instead, compaction appears to have reduced the intergenic regions to such an extent that control elements like promoters and terminators have been forced into or beyond adjacent genes, resulting in long untranslated regions that encode other genes. Normally, transcriptional overlap can interfere with expression of a gene, but these genomes cope with high frequencies of overlap and with termination signals within expressed genes. 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.