Genomic divergence within non-photosynthetic cyanobacterial endosymbionts in rhopalodiacean diatoms

Organelle acquisitions via endosymbioses with prokaryotes were milestones in the evolution of eukaryotes. Still, quite a few uncertainties have remained for the evolution in the early stage of organellogenesis. In this respect, rhopalodiacean diatoms and their obligate cyanobacterial endosymbionts, called spheroid bodies, are emerging as new models for the study of organellogenesis. The genome for the spheroid body of Epithemia turgida, a rhopalodiacean diatom, has unveiled its unique metabolic nature lacking the photosynthetic ability. Nevertheless, the genome sequence of a spheroid body from a single lineage may not be sufficient to depict the evolution of these cyanobacterium-derived intracellular structures as a whole. Here, we report on the complete genome for the spheroid body of Rhopalodia gibberula, a lineage distinct from E. turgida, of which genome has been fully determined. Overall, features in genome structure and metabolic capacity, including a lack of photosynthetic ability, were highly conserved between the two spheroid bodies. However, our comparative genomic analyses revealed that the genome of the R. gibberula spheroid body exhibits a lower non-synonymous substitution rate and a slower progression of pseudogenisation than those of E. turgida, suggesting that a certain degree of diversity exists amongst the genomes of obligate endosymbionts in unicellular eukaryotes

Succession of Genetic Diversity of Botryococcus braunii (Trebouxiophyceae) in Two Japanese Reservoirs

AbstractBotryococcus braunii is a green colonial alga that produces large volumes of liquid hydrocarbon. Therefore, B. braunii is expected to be useful as an alternative fuel resource. Natural blooms of B. braunii have been recorded in several lakes and reservoirs. Elucidation of natural B. braunii blooming would provide important information for the development of an open-pond cultivation system. In this study, we periodically assessed the genetic diversity and colony density of B. braunii populations, along with several environmental parameters, in two Japanese reservoirs (provisionally called “N” and “S”) from December 2008 to December 2009. Reservoir N had low numbers of B. braunii colonies whereas Reservoir S was characterized by periodic density increases that occurred in December 2008, and in March, September, and December 2009. Population genetics analysis using specific environmental sequences (PGA-SES method) was conducted for B. braunii populations for the first time. Among the B. braunii-dominated samples of Reservoir S, high levels of genetic diversity were observed in December 2008 and March 2009, whereas the diversity levels in September and December 2009 were low. The results suggest that B. braunii periodicity can be categorized into a high genetic diversity type and a low genetic diversity type. The high genetic diversity type may be caused by simultaneous growth of many genotypes, whereas the low genetic diversity type seems to be explained by increases in the cell density of only a few adapted genotypes

A single origin of the photosynthetic organelle in different Paulinella lineages

<p>Abstract</p> <p>Background</p> <p>Gaining the ability to photosynthesize was a key event in eukaryotic evolution because algae and plants form the base of the food chain on our planet. The eukaryotic machines of photosynthesis are plastids (e.g., chloroplast in plants) that evolved from cyanobacteria through primary endosymbiosis. Our knowledge of plastid evolution, however, remains limited because the primary endosymbiosis occurred more than a billion years ago. In this context, the thecate "green amoeba" <it>Paulinella chromatophora </it>is remarkable because it very recently (i.e., minimum age of ≈ 60 million years ago) acquired a photosynthetic organelle (termed a "chromatophore"; i.e., plastid) <it>via </it>an independent primary endosymbiosis involving a <it>Prochlorococcus </it>or <it>Synechococcus</it>-like cyanobacterium. All data regarding <it>P. chromatophora </it>stem from a single isolate from Germany (strain M0880/a). Here we brought into culture a novel photosynthetic <it>Paulinella </it>strain (FK01) and generated molecular sequence data from these cells and from four different cell samples, all isolated from freshwater habitats in Japan. Our study had two aims. The first was to compare and contrast cell ultrastructure of the M0880/a and FK01 strains using scanning electron microscopy. The second was to assess the phylogenetic diversity of photosynthetic <it>Paulinella </it>to test the hypothesis they share a vertically inherited plastid that originated in their common ancestor.</p> <p>Results</p> <p>Comparative morphological analyses show that <it>Paulinella </it>FK01 cells are smaller than M0880/a and differ with respect to the number of scales per column. There are more distinctive, multiple fine pores on the external surface of FK01 than in M0880/a. Molecular phylogenetic analyses using multiple gene markers demonstrate these strains are genetically distinct and likely comprise separate species. The well-supported monophyly of the <it>Paulinella chromatophora </it>strains analyzed here using plastid-encoded 16S rRNA suggests strongly that they all share a common photosynthetic ancestor. The strain M0880/a is most closely related to Japanese isolates (Kanazawa-1, -2, and Kaga), whereas FK01 groups closely with a Kawaguchi isolate.</p> <p>Conclusion</p> <p>Our results indicate that <it>Paulinella chromatophora </it>comprises at least two distinct evolutionary lineages and likely encompasses a broader taxonomic diversity than previously thought. The finding of a single plastid origin for both lineages shows these taxa to be valuable models for studying post-endosymbiotic cell and genome evolution.</p

The draft genome of Kipferlia bialata reveals reductive genome evolution in fornicate parasites

The fornicata (fornicates) is a eukaryotic group known to consist of free-living and parasitic organisms. Genome datasets of two model fornicate parasites Giardia intestinalis and Spironucleus salmonicida are well annotated, so far. The nuclear genomes of G. intestinalis assemblages and S. salmonicida are small in terms of the genome size and simple in genome structure. However, an ancestral genomic structure and gene contents, from which genomes of the fornicate parasites have evolved, remains to be clarified. In order to understand genome evolution in fornicates, here, we present the draft genome sequence of a free-living fornicate, Kipferlia bialata, the divergence of which is earlier than those of the fornicate parasites, and compare it to the genomes of G. intestinalis and S. salmonicida. Our data show that the number of protein genes and introns in K. bialata genome are the most abundant in the genomes of three fornicates, reflecting an ancestral state of fornicate genome evolution. Evasion mechanisms of host immunity found in G. intestinalis and S. salmonicida are absent in the K. bialata genome, suggesting that the two parasites acquired the complex membrane surface proteins on the line leading to the common ancestor of G. intestinalis and S. salmonicida after the divergence from K. bialata. Furthermore, the mitochondrion related organelles (MROs) of K. bialata possess more complex suites of metabolic pathways than those in Giardia and in Spironucleus. In sum, our results unveil the process of reductive evolution which shaped the current genomes in two model fornicate parasites G. intestinalis and S. salmonicida

Rappemonads are haptophyte phytoplankton

20年以上謎だった生物の正体が判明 --光合成生物進化解明のカギに--. 京都大学プレスリリース. 2021-03-29.Rapidly accumulating genetic data from environmental sequencing approaches have revealed an extraordinary level of unsuspected diversity within marine phytoplankton, which is responsible for around 50% of global net primary production.However, the phenotypic identity of many of the organisms distinguished by environmental DNA sequences remains unclear. The rappemonads represent a plastid-bearing protistan lineage that to date has only been identified by environmental plastid 16S rRNA sequences.The phenotypic identity of this group, which does not confidently cluster in any known algal clades in 16S rRNA phylogenetic reconstructions, has remained unknown since the first report of environmental sequences over two decades ago. We show that rappemonads are closely related to a haptophyte microalga, Pavlomulina ranunculiformis gen. nov. et sp. nov., and belong to a new haptophyte class, the Rappephyceae. Organellar phylogenomic analyses provide strong evidence for the inclusion of this lineage within the Haptophyta as a sister group to the Prymnesiophyceae. Members of this new class have a cosmopolitan distribution in coastal and oceanic regions. The relative read abundance of Rappephyceae in a large environmental barcoding dataset was comparable to, or greater than, those of major haptophyte species, such as the bloom-forming Gephyrocapsa huxleyi and Prymnesium parvum, and this result indicates that they likely have a significant impact as primary producers. Detailed characterization of Pavlomulina allowed for reconstruction of the ancient evolutionary history of the Haptophyta, a group that is one of the most important components of extant marine phytoplankton communities

Evolving a photosynthetic organelle

The evolution of plastids from cyanobacteria is believed to represent a singularity in the history of life. The enigmatic amoeba Paulinella and its 'recently' acquired photosynthetic inclusions provide a fascinating system through which to gain fresh insight into how endosymbionts become organelles

Three-dimensional architecture and assembly mechanism of the egg-shaped shell in testate amoeba Paulinella micropora

Unicellular euglyphid testate amoeba Paulinella micropora with filose pseudopodia secrete approximately 50 siliceous scales into the extracellular template-free space to construct a shell isomorphic to that of its mother cell. This shell-constructing behavior is analogous to building a house with bricks, and a complex mechanism is expected to be involved for a single-celled amoeba to achieve such a phenomenon; however, the three-dimensional (3D) structure of the shell and its assembly in P. micropora are still unknown. In this study, we aimed to clarify the positional relationship between the cytoplasmic and extracellular scales and the structure of the egg-shaped shell in P. micropora during shell construction using focused ion beam scanning electron microscopy (FIB-SEM). 3D reconstruction revealed an extensive invasion of the electron-dense cytoplasm between the long sides of the positioned and stacked scales, which was predicted to be mediated by actin filament extension. To investigate the architecture of the shell of P. micropora, each scale was individually segmented, and the position of its centroid was plotted. The scales were arranged in a left-handed, single-circular ellipse in a twisted arrangement. In addition, we 3D printed individual scales and assembled them, revealing new features of the shell assembly mechanism of P. micropora. Our results indicate that the shell of P. micropora forms an egg shape by the regular stacking of precisely designed scales, and that the cytoskeleton is involved in the construction process

Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis

Endosymbiotic relationships between eukaryotic and prokaryotic cells are common in nature. Endosymbioses between two eukaryotes are also known; cyanobacterium-derived plastids have spread horizontally when one eukaryote assimilated another. A unique instance of a non-photosynthetic, eukaryotic endosymbiont involves members of the genus Paramoeba, amoebozoans that infect marine animals such as farmed fish and sea urchins. Paramoeba species harbor endosymbionts belonging to the Kinetoplastea, a diverse group of flagellate protists including some that cause devastating diseases. To elucidate the nature of this eukaryote-eukaryote association, we sequenced the genomes and transcriptomes of Paramoeba pemaquidensis and its endosymbiont Perkinsela sp. The endosymbiont nuclear genome is ~9.5 Mbp in size, the smallest of a kinetoplastid thus far discovered. Genomic analyses show that Perkinsela sp. has lost the ability to make a flagellum but retains hallmark features of kinetoplastid biology, including polycistronic transcription, trans-splicing, and a glycosome-like organelle. Mosaic biochemical pathways suggest extensive ‘cross-talk’ between the two organisms, and electron microscopy shows that the endosymbiont ingests amoeba cytoplasm, a novel form of endosymbiont-host communication. Our data reveal the cell biological and biochemical basis of the obligate relationship between Perkinsela sp. and its amoeba host, and provide a foundation for understanding pathogenicity determinants in economically important Paramoeba

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target