Causes and effects of nuclear genome reduction

Comparative genomics of Ascetosporea gives new insight into the evolutionary basis for animal parasitism in Rhizaria

BACKGROUND

Ascetosporea (Endomyxa, Rhizaria) is a group of unicellular parasites infecting aquatic invertebrates. They are increasingly being recognized as widespread and important in marine environments, causing large annual losses in invertebrate aquaculture. Despite their importance, little molecular data of Ascetosporea exist, with only two genome assemblies published to date. Accordingly, the evolutionary origin of these parasites is unclear, including their phylogenetic position and the genomic adaptations that accompanied the transition from a free-living lifestyle to parasitism. Here, we sequenced and assembled three new ascetosporean genomes, as well as the genome of a closely related amphizoic species, to investigate the phylogeny, origin, and genomic adaptations to parasitism in Ascetosporea.

RESULTS

Using a phylogenomic approach, we confirm the monophyly of Ascetosporea and show that Paramyxida group with Mikrocytida, with Haplosporida being sister to both groups. We report that the genomes of these parasites are relatively small (12-36 Mb) and gene-sparse (~ 2300-5200 genes), while containing surprisingly high amounts of non-coding sequence (~ 70-90% of the genomes). Performing gene-tree aware ancestral reconstruction of gene families, we demonstrate extensive gene losses at the origin of parasitism in Ascetosporea, primarily of metabolic functions, and little gene gain except on terminal branches. Finally, we highlight some functional gene classes that have undergone expansions during evolution of the group.

CONCLUSIONS

We present important new genomic information from a lineage of enigmatic but important parasites of invertebrates and illuminate some of the genomic innovations accompanying the evolutionary transition to parasitism in this lineage. Our results and data provide a genetic basis for the development of control measures against these parasites.

A Small Genome amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba

This study investigates the genomic characteristics of Echinamoeba silvestris, a small-sized amoeba within the Tubulinea clade of the Amoebozoa supergroup. Despite Tubulinea's significance in various fields, genomic data for this clade have been scarce. E. silvestris presents the smallest free-living amoeba genome within Tubulinea and Amoebozoa to date. Comparative analysis reveals intriguing parallels with parasitic lineages in terms of genome size and predicted gene numbers, emphasizing the need to understand the consequences of reduced genomes in free-living amoebae. Functional categorization of predicted genes in E. silvestris shows similar percentages of ortholog groups to other amoebae in various categories, but a distinctive feature is the extensive gene contraction in orphan (ORFan) genes and those involved in biological processes. Notably, among the few genes that underwent expansion, none are related to cellular components, suggesting adaptive processes that streamline biological processes and cellular components for efficiency and energy conservation. Additionally, our investigation into noncoding and repetitive elements sheds light on the evolution of genome size in amoebae, with E. silvestris distinguished by low percentage of repetitive elements. Furthermore, the analysis reveals that E. silvestris has the lowest mean number of introns per gene among the species studied, providing further support for its observed compact genome. Overall, this research underscores the diversity within Tubulinea, highlights knowledge gaps in Amoebozoa genomics, and positions E. silvestris as a valuable addition to genomic data sets, prompting further exploration of complexities in Amoebozoa diversity and genome evolution.

A Small Genome Amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba

This study investigates the genomic characteristics of Echinamoeba silvestris , a small-sized amoeba within the Tubulinea clade of the Amoebozoa supergroup. Despite Tubulinea's significance in various fields, genomic data for this clade have been scarce . E. silvestris presents the smallest free-living amoeba genome within Tubulinea and Amoebozoa to date. Comparative analysis reveals intriguing parallels with parasitic lineages in terms of genome size and predicted gene numbers, emphasizing the need to understand the consequences of reduced genomes in free-living amoebae. Functional categorization of predicted genes in E. silvestris shows similar percentages of ortholog groups to other amoebae in various categories, but a distinctive feature is the extensive gene contraction in orphan (ORFan) genes and those involved in biological processes. Notably, among the few genes that underwent expansion, none are related to cellular components, suggesting adaptive processes that streamline biological processes and cellular components for efficiency and energy conservation. The investigation delves into genomic structural evidence, including gene content and repetitive elements, illuminating the distinctive genomic traits of E. silvestris and providing reinforcement for its compact genome size. Overall, this research underscores the diversity within Tubulinea, highlights knowledge gaps in Amoebozoa genomics, and positions E. silvestris as a valuable addition to genomic datasets, prompting further exploration of complexities in Amoebozoa diversity and genome evolution.

Phagocytosis underpins the biotrophic lifestyle of intracellular parasites in the class Phytomyxea (Rhizaria)

Phytomyxea are intracellular biotrophic parasites infecting plants and stramenopiles, including the agriculturally impactful Plasmodiophora brassicae and the brown seaweed pathogen Maullinia ectocarpii. They belong to the clade Rhizaria, where phagotrophy is the main mode of nutrition. Phagocytosis is a complex trait of eukaryotes, well documented for free-living unicellular eukaryotes and specific cellular types of animals. Data on phagocytosis in intracellular, biotrophic parasites are scant. Phagocytosis, where parts of the host cell are consumed at once, is seemingly at odds with intracellular biotrophy. Here we provide evidence that phagotrophy is part of the nutritional strategy of Phytomyxea, using morphological and genetic data (including a novel transcriptome of M. ectocarpii). We document intracellular phagocytosis in P. brassicae and M. ectocarpii by transmission electron microscopy and fluorescent in situ hybridization. Our investigations confirm molecular signatures of phagocytosis in Phytomyxea and hint at a small specialized subset of genes used for intracellular phagocytosis. Microscopic evidence confirms the existence of intracellular phagocytosis, which in Phytomyxea targets primarily host organelles. Phagocytosis seems to coexist with the manipulation of host physiology typical of biotrophic interactions. Our findings resolve long debated questions on the feeding behaviour of Phytomyxea, suggesting an unrecognized role for phagocytosis in biotrophic interactions.

Genome sequence of Ophryocystis elektroscirrha, an apicomplexan parasite of monarch butterflies: cryptic diversity and response to host-sequestered plant chemicals

Apicomplexa are ancient and diverse organisms which have been poorly characterized by modern genomics. To better understand the evolution and diversity of these single-celled eukaryotes, we sequenced the genome of Ophryocystis elektroscirrha, a parasite of monarch butterflies, Danaus plexippus. We contextualize our newly generated resources within apicomplexan genomics before answering longstanding questions specific to this host-parasite system. To start, the genome is miniscule, totaling only 9 million bases and containing fewer than 3,000 genes, half the gene content of two other sequenced invertebrate-infecting apicomplexans, Porospora gigantea and Gregarina niphandrodes. We found that O. elektroscirrha shares different orthologs with each sequenced relative, suggesting the true set of universally conserved apicomplexan genes is very small indeed. Next, we show that sequencing data from other potential host butterflies can be used to diagnose infection status as well as to study diversity of parasite sequences. We recovered a similarly sized parasite genome from another butterfly, Danaus chrysippus, that was highly diverged from the O. elektroscirrha reference, possibly representing a distinct species. Using these two new genomes, we investigated potential evolutionary response by parasites to toxic phytochemicals their hosts ingest and sequester. Monarch butterflies are well-known to tolerate toxic cardenolides thanks to changes in the sequence of their Type II ATPase sodium pumps. We show that Ophryocystis completely lacks Type II or Type 4 sodium pumps, and related proteins PMCA calcium pumps show extreme sequence divergence compared to other Apicomplexa, demonstrating new avenues of research opened by genome sequencing of non-model Apicomplexa.

Beyond being an energy supplier, ATP synthase is a sculptor of mitochondrial cristae

Mitochondrial F₁F_O-ATP synthase plays a key role in cellular bioenergetics; this enzyme is present in all eukaryotic linages except in amitochondriate organisms. Despite its ancestral origin, traceable to the alpha proteobacterial endosymbiotic event, the actual structural diversity of these complexes, due to large differences in their polypeptide composition, reflects an important evolutionary divergence between eukaryotic lineages. We discuss the effect of these structural differences on the oligomerization of the complex and the shape of mitochondrial cristae.

A Large-Scale Genome-Based Survey of Acidophilic Bacteria Suggests That Genome Streamlining Is an Adaption for Life at Low pH

The genome streamlining theory suggests that reduction of microbial genome size optimizes energy utilization in stressful environments. Although this hypothesis has been explored in several cases of low-nutrient (oligotrophic) and high-temperature environments, little work has been carried out on microorganisms from low-pH environments, and what has been reported is inconclusive. In this study, we performed a large-scale comparative genomics investigation of more than 260 bacterial high-quality genome sequences of acidophiles, together with genomes of their closest phylogenetic relatives that live at circum-neutral pH. A statistically supported correlation is reported between reduction of genome size and decreasing pH that we demonstrate is due to gene loss and reduced gene sizes. This trend is independent from other genome size constraints such as temperature and G + C content. Genome streamlining in the evolution of acidophilic bacteria is thus supported by our results. The analyses of predicted Clusters of Orthologous Genes (COG) categories and subcellular location predictions indicate that acidophiles have a lower representation of genes encoding extracellular proteins, signal transduction mechanisms, and proteins with unknown function but are enriched in inner membrane proteins, chaperones, basic metabolism, and core cellular functions. Contrary to other reports for genome streamlining, there was no significant change in paralog frequencies across pH. However, a detailed analysis of COG categories revealed a higher proportion of genes in acidophiles in the following categories: "replication and repair," "amino acid transport," and "intracellular trafficking". This study brings increasing clarity regarding the genomic adaptations of acidophiles to life at low pH while putting elements, such as the reduction of average gene size, under the spotlight of streamlining theory.

Convergent Loss of Chemoreceptors across Independent Origins of Slave-Making in Ants

The evolution of an obligate parasitic lifestyle often leads to the reduction of morphological and physiological traits, which may be accompanied by loss of genes and functions. Slave-making ants are social parasites that exploit the work force of closely related ant species for social behaviors such as brood care and foraging. Recent divergence between these social parasites and their hosts enables comparative studies of gene family evolution. We sequenced the genomes of eight ant species, representing three independent origins of ant slavery. During the evolution of eusociality, chemoreceptor genes multiplied due to the importance of chemical communication in insect societies. We investigated the evolutionary fate of these chemoreceptors and found that slave-making ant genomes harbored only half as many gustatory receptors as their hosts', potentially mirroring the outsourcing of foraging tasks to host workers. In addition, parasites had fewer odorant receptors and their loss shows striking patterns of convergence across independent origins of parasitism, in particular in orthologs often implicated in sociality like the 9-exon odorant receptors. These convergent losses represent a rare case of convergent molecular evolution at the level of individual genes. Thus, evolution can operate in a way that is both repeatable and reversible when independent ant lineages lose important social traits during the transition to a parasitic lifestyle.

Substantial intraspecific genome size variation in golden-brown algae and its phenotypic consequences

BACKGROUND AND AIMS

While nuclear DNA content variation and its phenotypic consequences have been well described for animals, vascular plants and macroalgae, much less about this topic is known regarding unicellular algae and protists in general. The dearth of data is especially pronounced when it comes to intraspecific genome size variation. This study attempts to investigate the extent of intraspecific variability in genome size and its adaptive consequences in a microalgal species.

METHODS

Propidium iodide flow cytometry was used to estimate the absolute genome size of 131 strains (isolates) of the golden-brown alga Synura petersenii (Chrysophyceae, Stramenopiles), identified by identical internal transcribed spacer (ITS) rDNA barcodes. Cell size, growth rate and genomic GC content were further assessed on a sub-set of strains. Geographic location of 67 sampling sites across the Northern hemisphere was used to extract climatic database data and to evaluate the ecogeographical distribution of genome size diversity.

KEY RESULTS

Genome size ranged continuously from 0.97 to 2.02 pg of DNA across the investigated strains. The genome size was positively associated with cell size and negatively associated with growth rate. Bioclim variables were not correlated with genome size variation. No clear trends in the geographical distribution of strains of a particular genome size were detected, and strains of different genome size occasionally coexisted at the same locality. Genomic GC content was significantly associated only with genome size via a quadratic relationship.

CONCLUSIONS

Genome size variability in S. petersenii was probably triggered by an evolutionary mechanism operating via gradual changes in genome size accompanied by changes in genomic GC content, such as, for example, proliferation of transposable elements. The variation was reflected in cell size and relative growth rate, possibly with adaptive consequences.

Genome size evolution: towards new model systems for old questions

Genome size (GS) variation is a fundamental biological characteristic; however, its evolutionary causes and consequences are the topic of ongoing debate. Whether GS is a neutral trait or one subject to selective pressures, and how strong these selective pressures are, may remain open questions. Fundamentally, the genomic sequences responsible for this variation directly impact the potential evolutionary outcomes and, equally, are the targets of different evolutionary pressures. For example, duplications and deletions of genic regions (large or small) can have immediate and drastic phenotypic effects, while an expansion or contraction of non-coding DNA is less likely to cause catastrophic phenotypic effects. However, in the long term, the accumulation or deletion of ncDNA is likely to have larger effects. Modern sequencing technologies are allowing for the dissection of these proximate causes, but a combination of these new technologies with more traditional evolutionary experiments and approaches could revolutionize this debate and potentially resolve many of these arguments. Here, I discuss an ambitious way forward for GS research, putting it in context of historical debates, theories and sometimes contradictory evidence, and highlighting the promise of combining new sequencing technologies and analytical developments with more traditional experimental evolution approaches.

Combining morphology, behaviour and genomics to understand the evolution and ecology of microbial eukaryotes

Microbial eukaryotes (protists) are structurally, developmentally and behaviourally more complex than their prokaryotic cousins. This complexity makes it more difficult to translate genomic and metagenomic data into accurate functional inferences about systems ranging all the way from molecular and cellular levels to global ecological networks. This problem can be traced back to the advent of the cytoskeleton and endomembrane systems at the origin of eukaryotes, which endowed them with a range of complex structures and behaviours that still largely dominate how they evolve and interact within microbial communities. But unlike the diverse metabolic properties that evolved within prokaryotes, the structural and behavioural characteristics that strongly define how protists function in the environment cannot readily be inferred from genomic data, since there is generally no simple correlation between a gene and a discrete activity or function. A deeper understanding of protists at both cellular and ecological levels, therefore, requires not only high-throughput genomics but also linking such data to direct observations of natural history and cell biology. This is challenging since these observations typically require cultivation, which is lacking for most protists. Potential remedies with current technology include developing a more phylogenetically diverse range of model systems to better represent the diversity, as well as combining high-throughput, single-cell genomics with microscopic documentation of the subject cells to link sequence with structure and behaviour. This article is part of a discussion meeting issue 'Single cell ecology'.

The Biochemistry and Evolution of the Dinoflagellate Nucleus

Dinoflagellates are known to possess a highly aberrant nucleus-the so-called dinokaryon-that exhibits a multitude of exceptional biological features. These include: (1) Permanently condensed chromosomes; (2) DNA in a cholesteric liquid crystalline state, (3) extremely large DNA content (up to 200 pg); and, perhaps most strikingly, (4) a deficit of histones-the canonical building blocks of all eukaryotic chromatin. Dinoflagellates belong to the Alveolata clade (dinoflagellates, apicomplexans, and ciliates) and, therefore, the biological oddities observed in dinoflagellate nuclei are derived character states. Understanding the sequence of changes that led to the dinokaryon has been difficult in the past with poor resolution of dinoflagellate phylogeny. Moreover, lack of knowledge of their molecular composition has constrained our understanding of the molecular properties of these derived nuclei. However, recent advances in the resolution of the phylogeny of dinoflagellates, particularly of the early branching taxa; the realization that divergent histone genes are present; and the discovery of dinoflagellate-specific nuclear proteins that were acquired early in dinoflagellate evolution have all thrown new light nature and evolution of the dinokaryon.

Causes and Effects of Loss of Classical Nonhomologous End Joining Pathway in Parasitic Eukaryotes

We report frequent losses of components of the classical nonhomologous end joining pathway (C-NHEJ), one of the main eukaryotic tools for end joining repair of DNA double-strand breaks, in several lineages of parasitic protists. Moreover, we have identified a single lineage among trypanosomatid flagellates that has lost Ku70 and Ku80, the core C-NHEJ components, and accumulated numerous insertions in many protein-coding genes. We propose a correlation between these two phenomena and discuss the possible impact of the C-NHEJ loss on genome evolution and transition to the parasitic lifestyle.IMPORTANCE Parasites tend to evolve small and compact genomes, generally endowed with a high mutation rate, compared with those of their free-living relatives. However, the mechanisms by which they achieve these features, independently in unrelated lineages, remain largely unknown. We argue that the loss of the classical nonhomologous end joining pathway components may be one of the crucial steps responsible for characteristic features of parasite genomes.

Multilocus Sequence Typing and Population Genetic Analysis of Enterocytozoon bieneusi: Host Specificity and Its Impacts on Public Health

Microsporidia comprise a large class of unicellular eukaryotic pathogens that are medically and agriculturally important, but poorly understood. There have been nearly 1,500 microsporidian species described thus far, which are variable in biology, genetics, genomics, and host specificity. Among those, Enterocytozoon bieneusi is the well-known species responsible for the most recorded cases of human microsporidian affections. The pathogen can colonize a broad range of mammals and birds and most of the animals surveyed share some genotypes with humans, posing a threat to public health. Based on DNA sequence analysis of the ribosomal internal transcribed spacer (ITS) and phylogenetic analysis, several hundreds of E. bieneusi genotypes have been defined and clustered into different genetic groups with varied levels of host specificity. However, single locus-based typing using ITS might have insufficient resolution to discriminate among E. bieneusi isolates with complex genetic or hereditary characteristics and to assess the elusive reproduction or transmission modes of the organism, highlighting the need for exploration and application of multilocus sequence typing (MLST) and population genetic tools. The present review begins with a primer on microsporidia and major microsporidian species, briefly introduces the recent advances on E. bieneusi ITS genotyping and phylogeny, summarizes recent MLST and population genetic data, analyzes the inter- and intragroup host specificity at the MLST level, and interprets the public health implications of host specificity in zoonotic or cross-species transmission of this ubiquitous fungus.

Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions

Phylogenetic methods unearth evolutionary history when supported by three starting points of reason: (1) the continuity axiom begs the existence of a "model" of evolutionary change, (2) the singularity axiom defines the historical ground plan (phylogeny) in which biological entities (taxa) evolve, and (3) the memory axiom demands identification of biological attributes (characters) with historical information. Axiom consequences are interlinked, making the retrodiction enterprise an endeavor of reciprocal fulfillment. In particular, establishing direction of evolutionary change (character polarization) roots phylogenies and enables testing the existence of historical memory (homology). Unfortunately, rooting phylogenies, especially the "tree of life," generally follow narratives instead of integrating empirical and theoretical knowledge of retrodictive exploration. This stems mostly from a focus on molecular sequence analysis and uncertainties about rooting methods. Here, we review available rooting criteria, highlighting the need to minimize both ad hoc and auxiliary assumptions, especially argumentative ad hocness. We show that while the outgroup comparison method has been widely adopted, the generality criterion of nesting and additive phylogenetic change embodied in Weston rule offers the most powerful rooting approach. We also propose a change of focus, from phylogenies that describe the evolution of biological systems to those that describe the evolution of parts of those systems. This weakens violation of character independence, helps formalize the generality criterion of rooting, and provides new ways to study the problem of evolution.

Genomics and evolution of Pneumocystis species

The genus Pneumocystis comprises highly diversified fungal species that cause severe pneumonia in individuals with a deficient immune system. These fungi infect exclusively mammals and present a strict host species specificity. These species have co-diverged with their hosts for long periods of time (> 100 MYA). Details of their biology and evolution are fragmentary mainly because of a lack of an established long-term culture system. Recent genomic advances have unlocked new areas of research and allow new hypotheses to be tested. We review here new findings of the genomic studies in relation with the evolutionary trajectory of these fungi and discuss the impact of genomic data analysis in the context of the population genetics. The combination of slow genome decay and limited expansion of specific gene families and introns reflect intimate interactions of these species with their hosts. The evolutionary adaptation of these organisms is profoundly influenced by their population structure, which in turn is determined by intrinsic features such as their self-fertilizing mating system, high host specificity, long generation times, and transmission mode. Essential key questions concerning their adaptation and speciation remain to be answered. The next cornerstone will consist in the establishment of a long-term culture system and genetic manipulation that should allow unravelling the driving forces of Pneumocystis species evolution.

Phylogenomic analysis of integral diiron membrane histidine motif-containing enzymes in ciliates provides insights into their function and evolutionary relationships

The Integral Membrane Histidine Motif-containing Enzymes (IMHME) are a class of binuclear non-heme iron proteins widely distributed among prokaryotes and eukaryotes. They are characterized by a conserved tripartite motif consisting of eight to ten histidine residues. Their known function is the activation of the dioxygen moiety to serve as efficient catalysts for reactions of hydroxylation, desaturation or reduction. To date most studies on IMHME were carried out in metazoan, phototrophic or parasitic organisms, whereas genome-wide analysis in heterotrophic free living protozoa, such as the Ciliophora phylum, has not been undertaken. In the seven fully sequenced genomes available we retrieved 118 putative sequences of the IMHME type, albeit with large differences in number among the ciliates: 11 sequences in Euplotes octocarinatus, 7 in Ichthyophthirius multifiliis, 13 in Oxytricha trifallax, 18 in Stylonychia lemnae, 25 in Tetrahymena thermophila, 31 in Paramecium tetraurelia and 13 in Pseudocohnilembus persalinus. The pool of putative sequences was classified in 16 orthologous groups from which 11 were related to fatty acid desaturase (FAD) and 5 to the fatty acid hydroxylase (FAH) superfamilies. Noteworthy, a large diversity on the number and type of FAD / FAH proteins were found among the ciliates, a feature that, in principle, may be attributed to peculiarities of the evolutionary process, such as gene expansion and reduction, but also to horizontal gene transfer, as we demonstrate in this work. We identified twelve putative enzymatic activities, from which four were newly assigned activities: sphingolipid Δ4-desaturase, ω3/Δ15 fatty acid desaturase, a large group of alkane 1-monooxygenases, and acylamide-delta-3(E)-desaturase, although unequivocal allocation would require additional experiments. We also combined the phylogenetics analysis with lipids analysis, thereby allowing the detection of two enzymatic activities not previously reported: a C-5 sterol desaturase in P. tetraurelia and a delta-9 fatty acid desaturase in Cohnilembus reniformis. The analysis revealed a significant lower number of FAD's sequences in the spirotrichea ciliates than in the oligohymenophorea, emphasizing the importance of fatty acids trophic transfer among aquatic organisms as a source of variation in metabolic activity, individual and population growth rates, and reproduction.

The Genome of Nosema sp. Isolate YNPr: A Comparative Analysis of Genome Evolution within the Nosema/Vairimorpha Clade

The microsporidian parasite designated here as Nosema sp. Isolate YNPr was isolated from the cabbage butterfly Pieris rapae collected in Honghe Prefecture, Yunnan Province, China. The genome was sequenced by Illumina sequencing and compared to those of two related members of the Nosema/Vairimorpha clade, Nosema ceranae and Nosema apis. Based upon assembly statistics, the Nosema sp. YNPr genome is 3.36 x 10⁶bp with a G+C content of 23.18% and 2,075 protein coding sequences. An “ACCCTT” motif is present approximately 50-bp upstream of the start codon, as reported from other members of the clade and from Encephalitozoon cuniculi, a sister taxon. Comparative small subunit ribosomal DNA (SSU rDNA) analysis as well as genome-wide phylogenetic analysis confirms a closer relationship between N. ceranae and Nosema sp. YNPr than between the two honeybee parasites N. ceranae and N. apis. The more closely related N. ceranae and Nosema sp. YNPr show similarities in a number of structural characteristics such as gene synteny, gene length, gene number, transposon composition and gene reduction. Based on transposable element content of the assemblies, the transposon content of Nosema sp. YNPr is 4.8%, that of N. ceranae is 3.7%, and that of N. apis is 2.5%, with large differences in the types of transposons present among these 3 species. Gene function annotation indicates that the number of genes participating in most metabolic activities is similar in all three species. However, the number of genes in the transcription, general function, and cysteine protease categories is greater in N. apis than in the other two species. Our studies further characterize the evolution of the Nosema/Vairimorpha clade of microsporidia. These organisms maintain variable but very reduced genomes. We are interested in understanding the effects of genetic drift versus natural selection on genome size in the microsporidia and in developing a testable hypothesis for further studies on the genomic ecology of this group.

The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases

Plasmodiophora brassicae causes clubroot, a major disease of Brassica oil and vegetable crops worldwide. P. brassicae is a Plasmodiophorid, obligate biotrophic protist in the eukaryotic kingdom of Rhizaria. Here we present the 25.5 Mb genome draft of P. brassicae, developmental stage-specific transcriptomes and a transcriptome of Spongospora subterranea, the Plasmodiophorid causing powdery scab on potato. Like other biotrophic pathogens both Plasmodiophorids are reduced in metabolic pathways. Phytohormones contribute to the gall phenotypes of infected roots. We report a protein (PbGH3) that can modify auxin and jasmonic acid. Plasmodiophorids contain chitin in cell walls of the resilient resting spores. If recognized, chitin can trigger defense responses in plants. Interestingly, chitin-related enzymes of Plasmodiophorids built specific families and the carbohydrate/chitin binding (CBM18) domain is enriched in the Plasmodiophorid secretome. Plasmodiophorids chitin synthases belong to two families, which were present before the split of the eukaryotic Stramenopiles/Alveolates/Rhizaria/Plantae and Metazoa/Fungi/Amoebozoa megagroups, suggesting chitin synthesis to be an ancient feature of eukaryotes. This exemplifies the importance of genomic data from unexplored eukaryotic groups, such as the Plasmodiophorids, to decipher evolutionary relationships and gene diversification of early eukaryotes.

Genome evolution in trypanosomatid parasites

A decade of genome sequencing has transformed our understanding of how trypanosomatid parasites have evolved and provided fresh impetus to explaining the origins of parasitism in the Kinetoplastida. In this review, I will consider the many ways in which genome sequences have influenced our view of genomic reduction in trypanosomatids; how species-specific genes, and the genomic domains they occupy, have illuminated the innovations in trypanosomatid genomes; and how comparative genomics has exposed the molecular mechanisms responsible for innovation and adaptation to a parasitic lifestyle.

The Cryptosporidium parvum ApiAP2 gene family: insights into the evolution of apicomplexan AP2 regulatory systems

We provide the first comprehensive analysis of any transcription factor family in Cryptosporidium, a basal-branching apicomplexan that is the second leading cause of infant diarrhea globally. AP2 domain-containing proteins have evolved to be the major regulatory family in the phylum to the exclusion of canonical regulators. We show that apicomplexan and perkinsid AP2 domains cluster distinctly from other chromalveolate AP2s. Protein-binding specificity assays of C. parvum AP2 domains combined with motif conservation upstream of co-regulated gene clusters allowed the construction of putative AP2 regulons across the in vitro life cycle. Orthologous Apicomplexan AP2 (ApiAP2) expression has been rearranged relative to the malaria parasite P. falciparum, suggesting ApiAP2 network rewiring during evolution. C. hominis orthologs of putative C. parvum ApiAP2 proteins and target genes show greater than average variation. C. parvum AP2 domains display reduced binding diversity relative to P. falciparum, with multiple domains binding the 5'-TGCAT-3', 5'-CACACA-3' and G-box motifs (5'-G[T/C]GGGG-3'). Many overrepresented motifs in C. parvum upstream regions are not AP2 binding motifs. We propose that C. parvum is less reliant on ApiAP2 regulators in part because it utilizes E2F/DP1 transcription factors. C. parvum may provide clues to the ancestral state of apicomplexan transcriptional regulation, pre-AP2 domination.

Secondary loss of a cis-spliced intron during the divergence of Giardia intestinalis assemblages

BACKGROUND

Giardia intestinalis is a parasitic unicellular eukaryote with a highly reduced genome, in which only six cis-spliced and four trans-spliced introns have been discovered. However, we anticipate that more cis- and trans-spliced introns likely remain unidentified in genes encoding hypothetical proteins that occupy ca. 2/3 of all of the open reading frames (ORFs) in the Giardia genome. Consequently, comprehensive surveys of introns in ORFs for hypothetical proteins are critical for better understanding of the intron evolution in this organism.

RESULTS

In this study, we identified two novel cis-spliced introns in the draft genome data of G. intestinalis strain WB, by surveying the conserved sequence motifs shared amongst the previously known introns. G. intestinalis strains can be divided into phylogenetically distinct assemblages A-H, and all the introns identified in past studies are shared among the published genome data from strains WB, DH, GS, and P15 representing assemblages A1, A2, B, and E, respectively. Nevertheless one of the two novel introns identified in this study was found to be absent in strain P15.

CONCLUSION

By considering the organismal relationship among G. intestinalis assemblages A1, A2, B, and E, one of the two introns identified in this study has highly likely been lost after the divergence of the assemblages. On the basis of a sequence comparison between the intron-bearing loci in WB, DH, and GS genomes and the homologous but intron-free locus in P15 genome, we propose that the loss of this particular intron was mediated by integration of the DNA fragment reverse-transcribed from mature mRNAs.

A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium

The evolution of an obligate parasitic lifestyle is often associated with genomic reduction, in particular with the loss of functions associated with increasing host-dependence. This is evident in many parasites, but perhaps the most extreme transitions are from free-living autotrophic algae to obligate parasites. The best-known examples of this are the apicomplexans such as Plasmodium, which evolved from algae with red secondary plastids. However, an analogous transition also took place independently in the Helicosporidia, where an obligate parasite of animals with an intracellular infection mechanism evolved from algae with green primary plastids. We characterised the nuclear genome of Helicosporidium to compare its transition to parasitism with that of apicomplexans. The Helicosporidium genome is small and compact, even by comparison with the relatively small genomes of the closely related green algae Chlorella and Coccomyxa, but at the functional level we find almost no evidence for reduction. Nearly all ancestral metabolic functions are retained, with the single major exception of photosynthesis, and even here reduction is not complete. The great majority of genes for light-harvesting complexes, photosystems, and pigment biosynthesis have been lost, but those for other photosynthesis-related functions, such as Calvin cycle, are retained. Rather than loss of whole function categories, the predominant reductive force in the Helicosporidium genome is a contraction of gene family complexity, but even here most losses affect families associated with genome maintenance and expression, not functions associated with host-dependence. Other gene families appear to have expanded in response to parasitism, in particular chitinases, including those predicted to digest the chitinous barriers of the insect host or remodel the cell wall of Helicosporidium. Overall, the Helicosporidium genome presents a fascinating picture of the early stages of a transition from free-living autotroph to parasitic heterotroph where host-independence has been unexpectedly preserved.

Helicosporidium is a highly-adapted obligate parasite of animals. Its evolutionary origins were unclear for almost a century, but molecular analysis ultimately and surprisingly showed that it is a green alga, which means it has undergone an evolutionary transition from autotrophy to parasitism comparable to that of the malaria parasite Plasmodium and its relatives. Such transitions are often associated with the loss of biological functions that are no longer necessary in their novel environment and with the development of molecular mechanisms, sometimes quite sophisticated, to invade and take advantage of their hosts. Yet, very little is actually known about the early stages of the transition of a free-living organism to an obligate intracellular parasite. Here we sequenced the genome and transcriptome of Helicosporidium, and use it to show that the outcome of this transition is quite different from that of Plasmodium.

The eukaryotic tree of life from a global phylogenomic perspective

Molecular phylogenetics has revolutionized our knowledge of the eukaryotic tree of life. With the advent of genomics, a new discipline of phylogenetics has emerged: phylogenomics. This method uses large alignments of tens to hundreds of genes to reconstruct evolutionary histories. This approach has led to the resolution of ancient and contentious relationships, notably between the building blocks of the tree (the supergroups), and allowed to place in the tree enigmatic yet important protist lineages for understanding eukaryote evolution. Here, I discuss the pros and cons of phylogenomics and review the eukaryotic supergroups in light of earlier work that laid the foundation for the current view of the tree, including the position of the root. I conclude by presenting a picture of eukaryote evolution, summarizing the most recent progress in assembling the global tree.

Overexpression of molecular chaperone genes in nucleomorph genomes

Chlorarachniophytes and cryptophytes possess complex plastids that were acquired by the ingestion of a green and red algal endosymbiont, respectively. The plastids are surrounded by four membranes, and a relict nucleus, called the nucleomorph, remains in the periplastidal compartment, which corresponds to the remnant cytoplasm of the endosymbiont. Nucleomorphs contain a greatly reduced genome that possesses only several hundred genes with high evolutionary rates. We examined the relative transcription levels of the genes of all proteins encoded by the nucleomorph genomes of two chlorarachniophytes and three cryptophytes using an RNA-seq transcriptomic approach. The genes of two heat shock proteins, Hsp70 and Hsp90, were highly expressed under normal conditions. It has been shown that molecular chaperone overexpression allows an accumulation of genetic mutations in bacteria. Our results suggest that overexpression of heat shock proteins in nucleomorph genomes may play a role in buffering the mutational destabilization of proteins, which might allow the high evolutionary rates of nucleomorph-encoded proteins.

Mitochondrial genome sequences and comparative genomics of Achlya hypogyna and Thraustotheca clavata

As a lineage, oomycetes have adapted to a wide range of lifestyles. Although the common ancestor of the group was likely a marine pathogen, extant members inhabit a spectrum from free-living saprobes to obligate biotrophs. The mitochondrial genomes of Achlya hypogyna and Thraustotheca clavata were sequenced to directly compare a facultative parasitic species (A. hypogyna) to a closely related free living saprobe (T. clavata). Both sequenced mitochondrial genomes are circular, with sizes of 46,869 bp for A. hypogyna and 47,381 bp for T. clavata. They share 63 common genes, indicating little influence of lifestyle on gene content, but small differences in total number and order of genes. Achlya hypogyna has a single copy of nad2, whereas T. clavata has one pseudogene (rps7) and two duplicated genes (nad5 and nad2), each with one full and one truncated copy. The genomes encode a total of 29 or 30 tRNAs (A. hypogyna and T. clavata, respectively) for 19 amino acids. Three unidentified open reading frames are conserved, and one is unique to T. clavata. Comparisons of these genomes with published sequences of the closely related Saprolegnia ferax mitochondrial genome, and four other more distantly related oomycetes, reveals no correlation in genome content or architecture with lifestyle.

Evolution of parasitism along convergent lines: from ecology to genomics

SUMMARY From hundreds of independent transitions from a free-living existence to a parasitic mode of life, separate parasite lineages have converged over evolutionary time to share traits and exploit their hosts in similar ways. Here, we first summarize the evidence that, at a phenotypic level, eukaryotic parasite lineages have all converged toward only six general parasitic strategies: parasitoid, parasitic castrator, directly transmitted parasite, trophically transmitted parasite, vector-transmitted parasite or micropredator. We argue that these strategies represent adaptive peaks, with the similarities among unrelated taxa within any strategy extending to all basic aspects of host exploitation and transmission among hosts and transcending phylogenetic boundaries. Then, we extend our examination of convergent patterns by looking at the evolution of parasite genomes. Despite the limited taxonomic coverage of sequenced parasite genomes currently available, we find some evidence of parallel evolution among unrelated parasite taxa with respect to genome reduction or compaction, and gene losses or gains. Matching such changes in parasite genomes with the broad phenotypic traits that define the convergence of parasites toward only six strategies of host exploitation is not possible at present. Nevertheless, as more parasite genomes become available, we may be able to detect clear trends in the evolution of parasitic genome architectures representing true convergent adaptive peaks, the genomic equivalents of the phenotypic strategies used by all parasites.

Microsporidia and 'the art of living together'

Parasitism, aptly defined as one of the 'living-together' strategies (Trager, 1986), presents a dynamic system in which the parasite and its host are under evolutionary pressure to evolve new and specific adaptations, thus enabling the coexistence of the two closely interacting partners. Microsporidia are very frequently encountered obligatory intracellular protistan parasites that can infect both animals and some protists and are a consummate example of various aspects of the 'living-together' strategy. Microsporidia, relatives of fungi in the superkingdom Opisthokonta, belong to the relatively small group of parasites for which the host cell cytoplasm is the site of both reproduction and maturation. The structural and physiological reduction of their vegetative stage, together with the manipulation of host cell physiology, enables microsporidia to live in the cytosolic environment for most of their life cycle in a way resembling endocytobionts. The ability to form structurally complex spores and the invention and assembly of a unique injection mechanism enable microsporidia to disperse within host tissues and between host organisms, resulting in long-lasting infections. Microsporidia have adapted their genomes to the intracellular way of life, evolved strategies how to obtain nutrients directly from the host and how to manipulate not only the infected cells, but also the hosts themselves. The enormous variability of host organisms and their tissues provide microsporidian parasites a virtually limitless terrain for diversification and ecological expansion. This review attempts to present a general overview of microsporidia, emphasising some less known and/or more recently discovered facets of their biology.

Decay of genes encoding the oomycete flagellar proteome in the downy mildew Hyaloperonospora arabidopsidis

Zoospores are central to the life cycles of most of the eukaryotic microbes known as oomycetes, but some genera have lost the ability to form these flagellated cells. In the plant pathogen Phytophthora infestans, genes encoding 257 proteins associated with flagella were identified by comparative genomics. These included the main structural components of the axoneme and basal body, proteins involved in intraflagellar transport, regulatory proteins, enzymes for maintaining ATP levels, and others. Transcripts for over three-quarters of the genes were up-regulated during sporulation, and persisted to varying degrees in the pre-zoospore stage (sporangia) and motile zoospores. Nearly all of these genes had orthologs in other eukaryotes that form flagella or cilia, but not species that lack the organelle. Orthologs of 211 of the genes were also absent from a sister taxon to P. infestans that lost the ability to form flagella, the downy mildew Hyaloperonospora arabidopsidis. Many of the genes retained in H. arabidopsidis were also present in other non-flagellates, suggesting that they play roles both in flagella and other cellular processes. Remnants of the missing genes were often detected in the H. arabidopsidis genome. Degradation of the genes was associated with local compaction of the chromosome and a heightened propensity towards genome rearrangements, as such regions were less likely to share synteny with P. infestans.

Back to basics: a revealing secondary reduction of the mitochondrial protein import pathway in diverse intracellular parasites

Mitochondria are present in all eukaryotes, but remodeling of their metabolic contribution has in some cases left them almost unrecognizable and they are referred to as mitochondria-like organelles, hydrogenosomes or, in the case where evolution has led to a great deal of simplification, as mitosomes. Mitochondria rely on the import of proteins encoded in the nucleus and the protein import machinery has been investigated in detail in yeast: several sophisticated molecular machines act in concert to import substrate proteins across the outer mitochondrial membrane and deliver them to a precise sub-mitochondrial compartment. Because these machines are so sophisticated, it has been a major challenge to conceptualize the first phase of their evolution. Here we review recent studies on the protein import pathway in parasitic species that have mitosomes: in the course of their evolution for highly specialized niches these parasites, particularly Cryptosporidia and Microsporidia, have secondarily lost numerous protein functions, in accordance with the evolution of their genomes towards a minimal size. Microsporidia are related to fungi, Cryptosporidia are apicomplexans and kin to the malaria parasite Plasmodium; and this great phylogenetic distance makes it remarkable that Microsporidia and Cryptosporidia have independently evolved skeletal protein import pathways that are almost identical. We suggest that the skeletal pathway reflects the protein import machinery of the first eukaryotes, and defines the essential roles of the core elements of the mitochondrial protein import machinery. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.

Red algal parasites: models for a life history evolution that leaves photosynthesis behind again and again

Many of the most virulent and problematic eukaryotic pathogens have evolved from photosynthetic ancestors, such as apicomplexans, which are responsible for a wide range of diseases including malaria and toxoplasmosis. The primary barrier to understanding the early stages of evolution of these parasites has been the difficulty in finding parasites with closely related free-living lineages with which to make comparisons. Parasites found throughout the florideophyte red algal lineage, however, provide a unique and powerful model to investigate the genetic origins of a parasitic lifestyle. This is because they share a recent common ancestor with an extant free-living red algal species and parasitism has independently arisen over 100 times within this group. Here, we synthesize the relevant hypotheses with respect to how these parasites have proliferated. We also place red algal research in the context of recent developments in understanding the genome evolution of other eukaryotic photosynthesizers turned parasites.

Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms

The functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. The molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden Markov models of structural recognition. Here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. We find there is a remarkable conservation in the distribution of domains with respect to the molecular functions they perform in the three superkingdoms of life. In general, most of the protein repertoire is spent in functions related to metabolic processes but there are significant differences in the usage of domains for regulatory and extra-cellular processes both within and between superkingdoms. Our results support the hypotheses that the proteomes of superkingdom Eukarya evolved via genome expansion mechanisms that were directed towards innovating new domain architectures for regulatory and extra/intracellular process functions needed for example to maintain the integrity of multicellular structure or to interact with environmental biotic and abiotic factors (e.g., cell signaling and adhesion, immune responses, and toxin production). Proteomes of microbial superkingdoms Archaea and Bacteria retained fewer numbers of domains and maintained simple and smaller protein repertoires. Viruses appear to play an important role in the evolution of superkingdoms. We finally identify few genomic outliers that deviate significantly from the conserved functional design. These include Nanoarchaeum equitans, proteobacterial symbionts of insects with extremely reduced genomes, Tenericutes and Guillardia theta. These organisms spend most of their domains on information functions, including translation and transcription, rather than on metabolism and harbor a domain repertoire characteristic of parasitic organisms. In contrast, the functional repertoire of the proteomes of the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum was no different than the rest of bacteria, failing to support claims of them representing a separate superkingdom. In turn, Protista and Bacteria shared similar functional distribution patterns suggesting an ancestral evolutionary link between these groups.

Splintrons in Giardia intestinalis: Spliceosomal introns in a split form

The divergent eukaryotic unicellular organism Giardia intestinalis is an intestinal parasite in humans and various animals. An analysis of a draft genome sequence suggested that G. intestinalis has a much simpler genome organization and gene repertoire than those of other model eukaryotic organisms (e.g., Arabidopsis and human). This general picture of the G. intestinalis genome seemingly agrees with the fact that only four spliceosomal (cis-spliced) introns have been identified in this organism to date. We have recently shown that G. intestinalis possesses a unique gene expression system incorporating spliceosome-mediated trans-splicing. Some protein-coding genes in G. intestinalis are split into multiple pieces in the genome and each gene fragment is independently transcribed. Two particular pre-mRNAs directly interact with each other by forming an intermolecular-stem structure and are then trans-spliced into a mature mRNA by spliceosomes. We believe that this trans-splicing secondarily arose from the system that excises canonical (cis-splicing) introns. Based on these findings, we suspect that similar phenomena-split genes and post-transcriptional assemblage of their transcripts via trans-splicing-may be prevalent in more distinct eukaryotic lineages than previously known, particularly in organisms possessing "intron-poor" genomes.

Non-coding RNAs in schistosomes: an unexplored world

Non-coding RNAs (ncRNAs) were recently given much higher attention due to technical advances in sequencing which expanded the characterization of transcriptomes in different organisms. ncRNAs have different lengths (22 nt to >1, 000 nt) and mechanisms of action that essentially comprise a sophisticated gene expression regulation network. Recent publication of schistosome genomes and transcriptomes has increased the description and characterization of a large number of parasite genes. Here we review the number of predicted genes and the coverage of genomic bases in face of the public ESTs dataset available, including a critical appraisal of the evidence and characterization of ncRNAs in schistosomes. We show expression data for ncRNAs in Schistosoma mansoni. We analyze three different microarray experiment datasets: (1) adult worms' large-scale expression measurements; (2) differentially expressed S. mansoni genes regulated by a human cytokine (TNF-α) in a parasite culture; and (3) a stage-specific expression of ncRNAs. All these data point to ncRNAs involved in different biological processes and physiological responses that suggest functionality of these new players in the parasite's biology. Exploring this world is a challenge for the scientists under a new molecular perspective of host-parasite interactions and parasite development.

Complete nucleomorph genome sequence of the nonphotosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set

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 <1 million base pairs in size (the smallest nuclear genomes known), comprised three chromosomes, and possess subtelomeric ribosomal DNA operons. Here, we report the complete sequence of one of the smallest cryptomonad nucleomorph genomes known, that of the secondarily nonphotosynthetic cryptomonad Cryptomonas paramecium. The genome is 486 kbp in size and contains 518 predicted genes, 466 of which are protein coding. Although C. paramecium lacks photosynthetic ability, its nucleomorph genome still encodes 18 plastid-associated proteins. More than 90% of the “conserved” protein genes in C. paramecium (i.e., those with clear homologs in other eukaryotes) are also present in the nucleomorph genomes of the cryptomonads Guillardia theta and Hemiselmis andersenii. In contrast, 143 of 466 predicted C. paramecium proteins (30.7%) showed no obvious similarity to proteins encoded in any other genome, including G. theta and H. andersenii. Significantly, however, many of these “nucleomorph ORFans” are conserved in position and size between the three genomes, suggesting that they are in fact homologous to one another. Finally, our analyses reveal an unexpected degree of overlap in the genes present in the independently evolved chlorarachniophyte and cryptomonad nucleomorph genomes: ∼80% of a set of 120 conserved nucleomorph genes in the chlorarachniophyte Bigelowiella natans were also present in all three cryptomonad nucleomorph genomes. This result suggests that similar reductive processes have taken place in unrelated lineages of nucleomorph-containing algae.

Red algae lose key mitochondrial genes in response to becoming parasitic

Red algal parasites are unusual because the vast majority of them parasitize species with which they share a recent common ancestor. This strategy has earned them the name “adelphoparasites,” from the Greek, adelpho, meaning “kin.” Intracellular adelphoparasites are very rare in nature, yet have independently evolved hundreds of times among the floridiophyte red algae. Much is known about the life history and infection cycle of these parasites but nearly nothing in known about their genomes. We sequenced the mitochondrial genomes of the free-living Gracilariopsis andersonii and its closely related parasite Gracilariophila oryzoides to determine what effect a parasitic lifestyle has on the genomes of red algal parasites. Whereas the parasite genome is similar to the host in many ways, the genes encoding essential proteins ATP8 and SDHC are pseudogenes in the parasite. The mitochondrial genome of parasite from a different class of red algae, Plocamiocolax puvinata, has lost the atp8 gene entirely, indicating that this gene is no longer critical in red algal parasite mitochondria.

Phylogenetic approach to the variability of the microsporidian Enterocytozoon bieneusi and its implications for inter- and intrahost transmission

Enterocytozoon bieneusi is a microsporidian parasite that infects many vertebrate animals, including humans. The rDNA internal transcribed spacer (ITS) shows a hypervariable sequence; however, so far no clear information has been inferred about strain evolution in this species. We reviewed all the sequences described and performed a phylogenetic study. Four groups of sequences strongly differentiated from each other were detected, although most of the isolates (94%) corresponded to group I. The highly diverse sequences of this group were analyzed using median-joining networks. The host species (humans, pets, swine, cattle, birds, and wild animals) and the continents of origin of the isolates were considered. Central haplotypes in the network were obtained from very diverse hosts and geographical origins. The results show that although E. bieneusi has a broad host specificity, transmission is not completely free: some strains were able to circulate within a given host species and were only occasionally transmitted to another host. Additionally, while not relevant for swine or cattle hosts, geography seems to be a relevant factor for human infection by E. bieneusi.

Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction

Nucleomorphs are the relic nuclei of algal endosymbionts that became permanent fixtures inside nonphotosynthetic eukaryotic host cells. These unusual organelles exist in only 2 lineages, the cryptophytes, which possess nucleomorphs and plastids (chloroplasts) derived from the uptake of a red algal endosymbiont, and the chlorarachniophytes, which harbor green algal derived nucleomorphs and plastids. Despite having evolved independently of one another, the nucleomorph genomes of cryptophytes and chlorarachniophytes are strikingly similar in size and basic structure. Both are <1 Mbp in size-the smallest nuclear genomes known-and are composed of only 3 chromosomes, each with its own subtelomeric rDNA repeats. Nucleomorph-containing algae thus represent an interesting system in which to study genome and chromosome evolution in eukaryotes. Here, we provide an overview of nucleomorph genome biology and focus on new information gleaned from comparisons of complete nucleomorph genome sequences, both within and between cryptophytes and chlorarachniophytes. Such comparisons provide fascinating insight into the evolution of these highly derived organelles and, more generally, the potential causes and consequences of genome reduction in eukaryotes.

Evolution of ultrasmall spliceosomal introns in highly reduced nuclear genomes

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 relicts of algal endosymbiont nuclei found in two lineages, cryptomonads and chlorarachniophytes. In cryptomonads, introns are rare or even lost altogether. In contrast, the nucleomorph of the chlorarachniophyte Bigelowiella natans contains the smallest nuclear genome known but paradoxically also retained over 800 tiny spliceosomal introns, ranging from 18 to 21 nt in length. Because introns have not been described in any other chlorarachniophyte nucleomorph, we do not know when these introns were reduced or whether they have been lost in other lineages. To gain insight into the evolution of these unique introns, we sequenced more than 150 spliceosomal introns in the nucleomorph of the chlorarachniophyte Gymnochlora stellata and compared size distribution, sequence features, and patterns of gain/loss. To clarify the possible relationship between intron size and splicing efficiency, we also analyzed the outcome of 580 splicing events. Overall, these data indicate that the radical intron size reduction took place in the ancestor of all extant chlorarachniophytes and that although most introns have been retained through this reductive process, intron loss has also occurred. We also show that intron size is not static, and splicing is not determined strictly by size, but that size does play a strong role in splicing efficiency, likely as part of a combination of sequence features and size.