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The endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic capabilities and launched the diversification of countless forms of algae. These primary plastids are found in members of the eukaryotic supergroup Archaeplastida. All known archaeplastids still retain some form of primary plastids, which are widely assumed to have a single origin. Here, we use single-cell genomics from natural samples combined with phylogenomics to infer the evolutionary origin of the phylum Picozoa, a globally distributed but seemingly rare group of marine microbial heterotrophic eukaryotes. Strikingly, the analysis of 43 single-cell genomes shows that Picozoa belong to Archaeplastida, specifically related to red algae and the phagotrophic rhodelphids. These picozoan genomes support the hypothesis that Picozoa lack a plastid, and further reveal no evidence of an early cryptic endosymbiosis with cyanobacteria. These findings change our understanding of plastid evolution as they either represent the first complete plastid loss in a free-living taxon, or indicate that red algae and rhodelphids obtained their plastids independently of other archaeplastids. The origin of primary plastids in an ancestor of Archaeplastida gave eukaryotes photosynthetic capabilities. This study used single-cell genomics and phylogenomics to infer the evolutionary origin of the plastid-lacking phylum Picozoa, a group of marine microbial heterotrophic eukaryotes, showing that they belong to the Archaeplastida and changing our understanding of plastid evolution.

In the human gut, temperate bacteriophages interact with bacteria through predation and horizontal gene transfer. Relying on taxonomic data, metagenomic studies have associated shifts in phage abundance with a number of human diseases. The temperate bacteriophage VEsP-1 with siphovirus morphology was isolated from a sample of river water using Enterococcus faecalis as a host. Starting from the whole genome sequence of VEsP-1, we retrieved related phage genomes in blastp searches of the tail protein and large terminase sequences, and blastn searches of the whole genome sequences, with matches compiled from several different databases, and visualized a part of viral dark matter sequence space. The genome network and phylogenomic analyses resulted in the proposal of a novel genus “Vespunovirus”, consisting of temperate, mainly metagenomic phages infecting Enterococcus spp.

Two new species of centrohelid heliozoans Acanthocystis costata and Choanocystis symna from a freshwater lake on Valamo Island and a freshwater pool in St. Petersburg (North-Western Russia) were studied with light and electron microscopy. Sequences of 18S rDNA were obtained for both species. Choanocystis symna has dumbbell-shaped plate scales (4.4-5.0 x 1.62-1.90 μm) and spine scales (3.9-6.7 μm) bearing from 3 to 5 (usually four) short teeth on the distal end. Acanthocystis costata has oval plate scales (1.3-3.7 x 0.9-1.9 μm), bearing numerous granules, as well as radial slits and spine scales (2.1-9.5 μm) with 4-6 teeth on the distal end. Acanthocystis costata and Acanthocystis nichollsi are similar in having slit-bearing plate scales and group together on the 18S rDNA tree. The presence of large particles of unknown nature was observed in food vacuoles of Acanthocystis costata.

The cell body of centrohelid heliozoans is covered with a layer of scales. These scales have species-specific morphology and, since they present in the trophic stage of the cell cycle can be termed \"trophic\" scales. Several species are known to form cysts; during this process they can produce specific \"cyst\" scales, different from trophic scales. The present paper describes morphology of cyst scales in two species of centrohelid heliozoans: Raineriophrys erinaceoides and Raphidiophrys heterophryoidea. The latter species has two types of cyst scales: scales of the first type resemble trophic scales in general structure but, their borders are broad, flattened and not enrolled. Scales of the second type are polygonal and connected to each other by special teeth, forming a single layer organized in a jig-saw puzzle-like manner. In Raineriophrys erinaceoides only one type of cyst scale was found. These scales are polygonal and completely different from trophic scales. It is unclear whether these scales form a puzzle-like layer or just overlap each other. Newly excysted individuals keep remnants of cyst scales in their cell coverings and at this stage cyst scales can easily be noted. The morphology of the cyst scales reported here is unlike any other previously reported. [PUBLICATION ABSTRACT]

ABSTRACT Meringosphaera is an enigmatic marine protist without clear phylogenetic affiliation, but it has long been suggested to be a chrysophytes-related autotroph. Microscopy-based reports indicate that it has a worldwide distribution, but no sequence data exists so far. We obtained the first 18S rDNA sequence for M. mediterranea (identified using light and electron microscopy) from the West Coast of Sweden. Observations of living cells revealed granulated axopodia and up to 6 globular photosynthesizing bodies about 2 μm in diameter, the nature of which requires further investigation. The ultrastructure of barbed undulating spine scales and patternless plate scales with a central thickening is in agreement with previous reports. Molecular phylogenetic analysis placed M. mediterranea inside the NC5 environmental clade of Centroplasthelida (Haptista) along with additional environmental sequences, together closely related to Choanocystidae. This placement is supported by similar scales in Meringosphaera and Choanocystidae. We searched the Tara Oceans 18S-V9 metabarcoding dataset which revealed four OTUs with 95.5-98.5% similarity, with oceanic distribution similar to that based on morphological observations. The current taxonomic position and species composition of the genus are discussed. The planktonic lifestyle of M. mediterranea contradicts the view of some authors that centrohelids enter the plankton only temporarily. Competing Interest Statement The authors have declared no competing interest.

Nuclearariids are a group of Opisthokonta, forming the deepest branch in Holomycota - one of the two major Opisthokonta clades, containing Fungi as a crawn group. They are the only members of Holomycota retaining the filose amoeboid state ancestral for Opisthokonta. The newly assembled genome of Nuclearia thermophila (Holomycota, Rotosphaerida) had a total length of 49 Mb, 15 321 protein-coding genes and a GC percentage of 44%. This is the first sequenced genome for this genus and the the third for Rotosphaerida as a whole. It was shown that N. thermophila shares more protein domains with Holozoa, than with the rest of Holomycota. Protein domains that were presumably acquired or lost by the common ancestors of the Holomycota and Holozoa groups were identified. The Holomycota ancestor had probably more gains and losses of protein domains compared to the Holozoa ancestor, which is particularly true for metabolism-related domains. However, this trend should be confirmed by studying the genomes of free-living organisms of the Teretosporea group.Competing Interest StatementThe authors have declared no competing interest.

The endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic capabilities and launched the diversification of countless forms of algae. These primary plastids are found in members of the eukaryotic supergroup Archaeplastida. All known archaeplastids still retain some form of primary plastids, which are widely assumed to have a single origin. Here, we used single-cell genomics from natural samples combined with phylogenomics to infer the evolutionary origin of the phylum Picozoa, a globally distributed but seemingly rare group of marine microbial heterotrophic eukaryotes. Strikingly, the analysis of single-cell genomes shows that Picozoa belong to Archaeplastida, specifically related to red algae and the phagotrophic rhodelphids. These picozoan genomes support the hypothesis that Picozoa lack a plastid, and further reveal no evidence of an early cryptic endosymbiosis with cyanobacteria. These findings change our understanding of plastid evolution as they either represent the first complete plastid loss in a free-living taxon, or indicate that red algae and rhodelphids obtained their plastids independently of other archaeplastids. Competing Interest Statement The authors have declared no competing interest. Footnotes * https://doi.org/10.6084/m9.figshare.c.5388176 * https://github.com/maxemil/picozoa-scripts

The Trichophyton rubrum species group consists of prevalent causative agents of human skin, nail and hair infections, including T. rubrum sensu stricto and T. violaceum, as well as other less well established or debatable taxa like T. soudanense, T. kuryangei and T. megninii. We aimed to describe genetic lineages in Russian T. rubrum sensu stricto, to find whether these lineages possess specific characteristics and to identify factors, shaping the population structure. We assessed polymorphism of 12 simple sequence repeat (SSR, or microsatellite) loci and TERG_02941 protein-coding gene in 70 T. rubrum isolates and also performed phylogenomic analysis. In both cases, two genetic lineages were found. The analysis of molecular variance (AMOVA) on the basis of SSR typing data indicated that 22-48% of the variability was between groups within T. rubrum. The pattern of phylogenetic changes in polymorphic protein-coding loci and SSR typing results revealed the pressure of strong directional selection, but its sources remained elusive. Our results suggest that Russian population of T. rubrum consists of two cosmopolitan genetic lineages, with no clear connection of population structure with types of infection, places of geographic origin, aldolase gene expression and urease activity.

Assembling the global eukaryotic tree of life has long been a major effort of Biology. In recent years, pushed by the new availability of genome-scale data for microbial eukaryotes, it has become possible to revisit many evolutionary enigmas. However, some of the most ancient nodes, which are essential for inferring a stable tree, have remained highly controversial. Among other reasons, the lack of adequate genomic datasets for key taxa has prevented the robust reconstruction of early diversification events. In this context, the centrohelid heliozoans are particularly relevant for reconstructing the tree of eukaryotes because they represent one of the last substantial groups that was missing large and diverse genomic data. Here, we filled this gap by sequencing high-quality transcriptomes for four centrohelid lineages, each corresponding to a different family. Combining these new data with a broad eukaryotic sampling, we produced a gene-rich taxon-rich phylogenomic dataset that enabled us to refine the structure of the tree. Specifically, we show that (i) centrohelids relate to haptophytes, confirming Haptista; (ii) Haptista relates to SAR; (iii) Cryptista share strong affinity with Archaeplastida; and (iv) Haptista + SAR is sister to Cryptista + Archaeplastida. The implications of this topology are discussed in the broader context of plastid evolution.

Assembling the global eukaryotic tree of life has long been a major effort of Biology. In recent years, pushed by the new availability of genome-scale data for microbial eukaryotes, it has become possible to revisit many evolutionary enigmas. However, some of the most ancient nodes, which are essential for inferring a stable tree, have remained highly controversial. Among other reasons, the lack of adequate genomic datasets for key taxa has prevented the robust reconstruction of early diversification events. In this context, the centrohelid heliozoans are particularly relevant for reconstructing the tree of eukaryotes because they represent one of the last substantial groups that was missing large and diverse genomic data. Here, we filled this gap by sequencing high-quality transcriptomes for four centrohelid lineages, each corresponding to a different family. Combining these new data with a broad eukaryotic sampling, we produced a gene-rich taxon-rich phylogenomic dataset that enabled us to refine the structure of the tree. Specifically, we show that (i) centrohelids relate to haptophytes, confirming Haptista; (ii) Haptista relates to SAR; (iii) Cryptista share strong affinity with Archaeplastida; and (iv) Haptista + SAR is sister to Cryptista + Archaeplastida. The implications of this topology are discussed in the broader context of plastid evolution.