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We explored photoprotective strategies in a cryptophyte alga Rhodomonas salina. This cryptophytic alga represents phototrophs where chlorophyll a/c antennas in thylakoids are combined with additional light-harvesting system formed by phycobiliproteins in the chloroplast lumen. The fastest response to excessive irradiation is induction of non-photochemical quenching (NPQ). The maximal NPQ appears already after 20 s of excessive irradiation. This initial phase of NPQ is sensitive to Ca 2+ channel inhibitor (diltiazem) and disappears, also, in the presence of non-actin, an ionophore for monovalent cations. The prolonged exposure to high light of R. salina cells causes photoinhibition of photosystem II (PSII) that can be further enhanced when Ca 2+ fluxes are inhibited by diltiazem. The light-induced reduction in PSII photochemical activity is smaller when compared with immotile diatom Phaeodactylum tricornutum. We explain this as a result of their different photoprotective strategies. Besides the protective role of NPQ, the motile R. salina also minimizes high light exposure by increased cell velocity by almost 25% percent (25% from 82 to 104 μm/s). We suggest that motility of algal cells might have a photoprotective role at high light because algal cell rotation around longitudinal axes changes continual irradiation to periodically fluctuating light.

Nucleomorphs are small nuclei that evolved from the nucleus of former eukaryotic endosymbionts of cryptophytes and chlorarachniophytes. These enigmatic organelles reside in their complex plastids and harbor the smallest and most compacted eukaryotic genomes investigated so far. Although the coding capacity of the nucleomorph genomes is small, a significant percentage of the encoded proteins (predicted nucleomorph-encoded proteins, pNMPs) is still not functionally annotated. We have analyzed pNMPs with unknown functions via Phyre2, a bioinformatic tool for prediction and modeling of protein structure, resulting in a functional annotation of 215 pNMPs out of 826 uncharacterized open reading frames of cryptophytes. The newly annotated proteins are predicted to participate in nucleomorph-specific functions such as chromosome organization and expression, as well as in modification and degradation of nucleomorph-encoded proteins. Additionally, we have functionally assigned nucleomorph-encoded, putatively plastid-targeted proteins among the reinvestigated pNMPs. Hints for a putative function in the periplastid compartment, the cytoplasm surrounding the nucleomorphs, emerge from the identification of pNMPs that might be homologs of endomembrane system-related proteins. These proteins are discussed in respect to their putative functions., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Background: The evolution of photosynthesis has been a major driver in eukaryotic diversification. Eukaryotes have acquired plastids (chloroplasts) either directly via the engulfment and integration of a photosynthetic cyanobacterium (primary endosymbiosis) or indirectly by engulfing a photosynthetic eukaryote (secondary or tertiary endosymbiosis). The timing and frequency of secondary endosymbiosis during eukaryotic evolution is currently unclear but may be resolved in part by studying cryptomonads, a group of single-celled eukaryotes comprised of both photosynthetic and non-photosynthetic species. While cryptomonads such as Guillardia theta harbor a red algal-derived plastid of secondary endosymbiotic origin, members of the sister group Goniomonadea lack plastids. Here, we present the genome of Goniomonas avonlea-the first for any goniomonad-to address whether Goniomonadea are ancestrally non-photosynthetic or whether they lost a plastid secondarily., Results: We sequenced the nuclear and mitochondrial genomes of Goniomonas avonlea and carried out a comparative analysis of Go. avonlea, Gu. theta, and other cryptomonads. The Go. avonlea genome assembly is ~ 92 Mbp in size, with 33,470 predicted protein-coding genes. Interestingly, some metabolic pathways (e.g., fatty acid biosynthesis) predicted to occur in the plastid and periplastidal compartment of Gu. theta appear to operate in the cytoplasm of Go. avonlea, suggesting that metabolic redundancies were generated during the course of secondary plastid integration. Other cytosolic pathways found in Go. avonlea are not found in Gu. theta, suggesting secondary loss in Gu. theta and other plastid-bearing cryptomonads. Phylogenetic analyses revealed no evidence for algal endosymbiont-derived genes in the Go. avonlea genome. Phylogenomic analyses point to a specific relationship between Cryptista (to which cryptomonads belong) and Archaeplastida., Conclusion: We found no convincing genomic or phylogenomic evidence that Go. avonlea evolved from a secondary red algal plastid-bearing ancestor, consistent with goniomonads being ancestrally non-photosynthetic eukaryotes. The Go. avonlea genome sheds light on the physiology of heterotrophic cryptomonads and serves as an important reference point for studying the metabolic "rewiring" that took place during secondary plastid integration in the ancestor of modern-day Cryptophyceae.

Twenty years ago an Arctic cryptophyte was isolated from Baffin Bay and given strain number CCMP2045. Here, it was described using morphology, water- and non-water soluble pigments and nuclear-encoded SSU rDNA. The influence of temperature, salinity, and light intensity on growth rates was also examined. Microscopy revealed typical cryptophyte features but the chloroplast color was either green or red depending on the light intensity provided. Phycoerythrin (Cr-PE 566) was only produced when cells were grown under low-light conditions (5 μmol photons · m -2  · s -1 ). Non-water-soluble pigments included chlorophyll a, c 2 and five major carotenoids. Cells measured 8.2 × 5.1 μm and a tail-like appendage gave them a comma-shape. The nucleus was located posteriorly and a horseshoe-shaped chloroplast contained a single pyrenoid. Ejectosomes of two sizes and a nucleomorph anterior to the pyrenoid were discerned in TEM. SEM revealed a slightly elevated vestibular plate in the vestibulum. The inner periplast component consisted of slightly overlapping hexagonal plates arranged in 16-20 oblique rows. Antapical plates were smaller and their shape less profound. Temperature and salinity studies revealed CCMP2045 as stenothermal and euryhaline and growth was saturated between 5 and 20 μmol photons · m -2  · s -1 . The phylogeny based on SSU rDNA showed that CCMP2045 formed a distinct clade with CCMP2293 and Falcomonas sp. isolated from Spain. Combining pheno- and genotypic data, the Arctic cryptophyte could not be placed in an existing family and genus and therefore Baffinellaceae fam. nov. and Baffinella frigidus gen. et sp. nov. were proposed., (© 2018 Phycological Society of America.)

Mesodinium rubrum Lohmann is a mixotrophic ciliate and one of the best studied species exhibiting acquired phototrophy. To investigate the fate of cryptophyte organelles in the ciliate subjected to starvation, we conducted ultrastructural studies of a Korean strain of M. cf. rubrum during a 10 week starvation experiments. Ingested cells of the cryptophyte Teleaulax amphioxeia were first enveloped by ciliate membrane, and then prey organelles, including ejectisomes, flagella, basal bodies and flagellar roots, were digested. Over time, prey nuclei protruded into the cytoplasm of the ciliate, their size and volume increased, and their number decreased, suggesting that the cryptophyte nuclei likely fused with each other in the ciliate cytoplasm. At 4 weeks of starvation, M. cf. rubrum cells without cryptophyte nuclei started to appear. At 10 weeks of starvation, only two M. cf. rubrum cells still possessing a cryptophyte nucleus had relatively intact chloroplast-mitochondria complexes (CMCs), while M. cf. rubrum cells without cryptophyte nuclei had a few damaged CMCs. This is the first ultrastructural study demonstrating that cryptophyte nuclei undergo a dramatic change inside M. cf. rubrum in terms of size, shape, and number following their acquisition., (Copyright © 2016 Elsevier B.V. All rights reserved.)

Cryptomonadales have acquired their plastids by secondary endosymbiosis. A novel clade-CRY1-has been discovered at the base of the Cryptomonadales tree, but it remains unknown whether it contains plastids. Cryptomonadales are also an important component of phytoplankton assemblages. However, they cannot be readily identified in fixed samples, and knowledge on dynamics and distribution of specific taxa is scarce. We investigated the phenology of the CRY1 lineage, three cryptomonadales clades and a species Proteomonas sulcata in a brackish lagoon of the Baltic Sea (salinity 0.3-3.9) using fluorescence in situ hybridization. A newly design probe revealed that specimens of the CRY1 lineage were aplastidic. This adds evidence against the chromalveolate hypothesis, and suggests that the evolution of cryptomonadales' plastids might have been shorter than is currently assumed. The CRY1 lineage was the most abundant cryptomonad clade in the lagoon. All of the studied cryptomonads peaked in spring at the most freshwater station, except for P. sulcata that peaked in summer and autumn. Salinity and concentration of dissolved inorganic nitrogen most significantly affected their distribution and dynamics. Our findings contribute to the ecology and evolution of cryptomonads, and may advance understanding of evolutionary relationships within the eukaryotic tree of life., (© 2016 Phycological Society of America.)

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 120h 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., (Copyright © 2015 Elsevier GmbH. All rights reserved.)

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., (© The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Three-dimensional profiling and tracking by digital holography microscopy (DHM) provide label-free and quantitative analysis of the characteristics and dynamic processes of objects, since DHM can record real-time data for microscale objects and produce a single hologram containing all the information about their three-dimensional structures. Here, we have utilized DHM to visualize suspended microspheres and microfibers in three dimensions, and record the four-dimensional trajectories of free-swimming cells in the absence of mechanical focus adjustment. The displacement of microfibers due to interactions with cells in three spatial dimensions has been measured as a function of time at subsecond and micrometer levels in a direct and straightforward manner. It has thus been shown that DHM is a highly efficient and versatile means for quantitative tracking and analysis of cell motility.

Cryptospores, recovered from Ordovician through Devonian rocks, differ from trilete spores in possessing distinctive configurations (i.e. hilate monads, dyads, and permanent tetrads). Their affinities are contentious, but knowledge of their relationships is essential to understanding the nature of the earliest land flora. This review brings together evidence about the source plants, mostly obtained from spores extracted from minute, fragmented, yet exceptionally anatomically preserved fossils. We coin the term 'cryptophytes' for plants that produced the cryptospores and show them to have been simple terrestrial organisms of short stature (i.e. millimetres high). Two lineages are currently recognized. Partitatheca shows a combination of characters (e.g. spo-rophyte bifurcation, stomata, and dyads) unknown in plants today. Lenticulatheca encompasses discoidal sporangia containing monads formed from dyads with ultrastructure closer to that of higher plants, as exemplified by Cooksonia. Other emerging groupings are less well characterized, and their precise affinities to living clades remain unclear. Some may be stem group embryophytes or tracheophytes. Others are more closely related to the bryophytes, but they are not bryophytes as defined by extant representatives. Cryptophytes encompass a pool of diversity from which modern bryophytes and vascular plants emerged, but were competitively replaced by early tracheophytes. Sporogenesis always produced either dyads or tetrads, indicating strict genetic control. The long-held consensus that tetrads were the archetypal condition in land plants is challenged., (© 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.)

Cryptomonads are unicellular, biflagellate algae. Generally, cryptomonad cells cannot be preserved well because of their fragile nature, and an improved methodology should be developed to identify cryptomonads from natural habitats. In this study, we tried using several cytological fixatives, including glutaraldehyde, formaldehyde, and their combinations to preserve field samples collected from various waters, and the currently used fixative, Lugol's solution was tested for comparison. Results showed that among the fixatives tested, glutaraldehyde preserved the samples best, and the optimal concentration of glutaraldehyde was 2%. The cell morphology was well preserved by glutaraldehyde. Cells kept their original color, volume, and shape, and important taxonomic features such as furrow/gullet complex, ejectosomes, as well as flagella could be observed clearly, whereas these organelles frequently disappeared in Lugol's solution preserved samples. The osmotic adjustments and buffers tested could not preserve cell density significantly higher. Statistical calculation showed the cell density in the samples preserved by 2% glutaraldehyde remained stable after 43 days of the fixation procedure. In addition, DNA was extracted from glutaraldehyde preserved samples by grinding with liquid nitrogen and the 18S rDNA sequence was amplified by PCR. The sequence was virtually identical to the reference sequence, and phylogenetic analyses showed very close relationship between it and sequences from the same organism. To sum up, the present study demonstrated that 2% unbuffered glutaraldehyde, without osmotic adjustments, can preserve cryptomonads cells for identification, in terms of both light microscopy and phylogenetic analyses based on DNA sequences.

Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote-eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.

The cell envelopes of Cryptomonas and Chroomonas exhibited significant fluorescence using FITC-labelled concanavalin A and wheat germ agglutinin when the cells were fixed prior to lectin binding. The periplast became intensely labelled in Chroomonas whereas Cryptomonas showed fluorescing granula in its gullet/furrow region and on the cell surface. Lectin labelling followed by fixation showed only label of periplast remnants of lysed cells and of the flagella of Chroomonas. Isolated periplasts of Cryptomonas and Chroomonas were intensively labelled with both concanavalin A and wheat germ agglutinin. Glycostaining of gels, onto which total cell protein extracts were loaded, showed a glycoprotein of high molecular weight for Cryptomonas and Chroomonas and an additional glycoprotein for Cryptomonas species.

Trichocysts are ejectile organelles found in cryptomonads, dinoflagellates, and peniculine ciliates. The fine structure of trichocysts differs considerably among lineages, and their evolutionary relationships are unclear. The biochemical makeup of the trichocyst constituents has been studied in the ciliate Paramecium, but there have been no investigations of cryptomonads and dinoflagellates. Furthermore, morphological similarity between the contents of cryptomonad trichocysts and the R-bodies of the endosymbiotic bacteria of Paramecium has been reported. In this study, we identified the proteins of the trichocyst constituents in a red cryptomonad, Pyrenomonas helgolandii, and found their closest relationships to be with rebB that comprises the R-bodies of Caedibacter taeniospiralis (gammaproteobacteria), which is an endosymbiont of Paramecium. In addition, the biochemical makeups of the trichocysts are entirely different between cryptomonads and peniculine ciliates, and therefore, cryptomonad trichocysts have an evolutionary origin independent from the peniculine ciliate trichocysts.

Photosynthesis uses light as a source of energy but its excess can result in production of harmful oxygen radicals. To avoid any resulting damage, phototrophic organisms can employ a process known as non-photochemical quenching (NPQ), where excess light energy is safely dissipated as heat. The mechanism(s) of NPQ vary among different phototrophs. Here, we describe a new type of NPQ in the organism Rhodomonas salina, an alga belonging to the cryptophytes, part of the chromalveolate supergroup. Cryptophytes are exceptional among photosynthetic chromalveolates as they use both chlorophyll a/c proteins and phycobiliproteins for light harvesting. All our data demonstrates that NPQ in cryptophytes differs significantly from other chromalveolates - e.g. diatoms and it is also unique in comparison to NPQ in green algae and in higher plants: (1) there is no light induced xanthophyll cycle; (2) NPQ resembles the fast and flexible energetic quenching (qE) of higher plants, including its fast recovery; (3) a direct antennae protonation is involved in NPQ, similar to that found in higher plants. Further, fluorescence spectroscopy and biochemical characterization of isolated photosynthetic complexes suggest that NPQ in R. salina occurs in the chlorophyll a/c antennae but not in phycobiliproteins. All these results demonstrate that NPQ in cryptophytes represents a novel class of effective and flexible non-photochemical quenching.

Cryptophytes like the cryptomonad Guillardia theta are part of the marine phytoplankton and therefore major players in global carbon and biogeochemical cycles. Despite the importance for the cell in being able to cope with large changes in illumination on a daily basis, very little is known about photoprotection mechanisms in cryptophytes. Here, we show that Guillardia theta is able to perform non-photochemical quenching, although none of the usual xanthophyll cycle pigments (e.g., zeaxanthin, diadinoxanthin, diatoxanthin) are present at detectable levels. Instead, acclimation to high light intensity seems to involve an increase of alloxanthin. Guillardia theta has genes for 2 one-helix "light-harvesting-like" proteins, related to some cyanobacterial genes which are induced in response to high light stress. Both the plastid-encoded gene (hlipP) and the nucleomorph-encoded gene (HlipNm) are expressed, but transcript levels decrease rather than increase during high light exposure, suggesting that they are not involved in a high light stress response. The HlipNm protein was detected with a specific antibody; expression was constant, independent of the light exposure., (Copyright © 2011 Elsevier B.V. All rights reserved.)

Background: Dinophysis is exceptional among dinoflagellates, possessing plastids derived from cryptophyte algae. Although Dinophysis can be maintained in pure culture for several months, the genus is mixotrophic and needs to feed either to acquire plastids (a process known as kleptoplastidy) or obtain growth factors necessary for plastid maintenance. Dinophysis does not feed directly on cryptophyte algae, but rather on a ciliate (Myrionecta rubra) that has consumed the cryptophytes and retained their plastids. Despite the apparent absence of cryptophyte nuclear genes required for plastid function, Dinophysis can retain cryptophyte plastids for months without feeding., Results: To determine if this dinoflagellate has nuclear-encoded genes for plastid function, we sequenced cDNA from Dinophysis acuminata, its ciliate prey M. rubra, and the cryptophyte source of the plastid Geminigera cryophila. We identified five proteins complete with plastid-targeting peptides encoded in the nuclear genome of D. acuminata that function in photosystem stabilization and metabolite transport. Phylogenetic analyses show that the genes are derived from multiple algal sources indicating some were acquired through horizontal gene transfer., Conclusions: These findings suggest that D. acuminata has some functional control of its plastid, and may be able to extend the useful life of the plastid by replacing damaged transporters and protecting components of the photosystem from stress. However, the dearth of plastid-related genes compared to other fully phototrophic algae suggests that D. acuminata does not have the nuclear repertoire necessary to maintain the plastid permanently.

Marine goniomonads have a worldwide distribution but ultrastructural information has not been available so far. An isolate of the heterotrophic marine nanoflagellate Goniomonas (G. aff. amphinema) from North Wales (UK) has been studied, providing information on its morphology and cellular structure using video, electron, laser scanning confocal microscopy (LSCM), and atomic force microscopy. Here, we describe a new feature, a granular area, potentially involved in particle capture and feeding. The binding of the lectin wheat germ agglutinin to the granular area of cells with discharged ejectisomes indicates the adhesive nature of this novel feature. The presence of a microtubular intracellular cytopharynx, apparently also used for feeding, has been revealed by LSCM. The small subunit rRNA gene of the isolate has been sequenced (1,788 bp). Phylogenetic results corroborate significant genetic divergence within the marine members of Goniomonas. This work highlights the need for integrated morphological, ultrastructural, and molecular investigation when describing and studying heterotrophic nanoflagellates.

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.

Unicellular cryptophyte algae employ antenna proteins with phycobilin chromophores in their photosynthetic machinery. The mechanism of light harvesting in these organisms is significantly different than the energy funneling processes in phycobilisomes utilized by cyanobacteria and red algae. One of the most striking features of cryptophytes is the location of the water-soluble phycobiliproteins, which are contained within the intrathylakoid spaces and are not on the stromal side of the lamellae as in the red algae and cyanobacteria. Studies of mobility of phycobiliproteins at the lumenal side of the thylakoid membranes and how their diffusional behavior may influence the energy funneling steps in light harvesting are reported. Confocal microscopy and fluorescence recovery after photobleaching (FRAP) are used to measure the diffusion coefficient of phycoerythrin 545 (PE545), the primary light harvesting protein of Rhodomonas CS24, in vivo. It is concluded that the diffusion of PE545 in the lumen is inhibited, suggesting possible membrane association or aggregation as a potential source of mobility hindrance.

Nucleomorphs are the remnant nuclei of algal endosymbionts in cryptophytes and chlorarachniophytes, two evolutionarily distinct unicellular eukaryotic lineages that acquired photosynthesis secondarily by the engulfment of red and green algae, respectively. At less than one million base pairs in size, nucleomorph genomes are the most highly reduced nuclear genomes known, with three small linear chromosomes and a gene density similar to that seen in prokaryotes. The independent origin of nucleomorphs in cryptophytes and chlorarachniophytes presents an interesting opportunity to study the reductive evolutionary forces that have led to their remarkable convergence upon similar genome architectures and coding capacities. In this article, we review the current state of knowledge with respect to the structure, function, origin, and evolution of nucleomorph genomes across the known diversity of cryptophyte and chlorarachniophyte algae.

Plastid genes encoding light-independent protochlorophyllide oxidoreductase (LIPOR) subunits were isolated from cryptophyte algae, the first example of such genes in plastids of secondary endosymbiotic origin. The presence of functional and nonfunctional copies of LIPOR genes in cryptophytes suggests that light-independent chlorophyll biosynthesis is a nonessential pathway in these organisms.

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.