Sergey Karpov

SUMMARY,Fungal parasites infect both the freshwater and marine algae, regulating their abundance Sanchytriomycota is a small group of zoosporic fungi parasitizing freshwater algae. Up to now they had been presented by two monotypic genera, Amoeboradix and Sanchytrium, having extraordinary cellular organization of amoeboid zoospores with pseudocilium.,We isolated new strain of Sanchytrium tribonematis having a unique intron insertion in rDNAs and studied its highly polymorphic morphology and ultrastructure. The shape of cyst and sporangia varies greatly. Widely spread zoospores may lack pseudocilia, but have different pseudopodia. The kinetosome of the pseudocilium in X-141 varies in length from 900 to 1600 nm, covering all known kinetosomes of sanchytrids studied before. Thus, the length of the kinetosome does not distinguish two genera. On the basis of polymorphism and unique rDNA introns of the X-141 strain, we describe it here as a new species, Sanchytrium polymorphicus. Star-like glycogen granules have been found in the ER cisterns of the sporangium, which proposes their synthesis in this cellular compartment. In the cyst nucleus we found numerous small (36 nm) isodiametric vesicles resembling virions, which can probably belong to the family Polyomaviridae. This may explain the origin of unique introns in the rDNA of sanchytrids.

Holomycota, together with Holozoa, represents one of the two main branches of the supergroup Opisthokonta. Fungi, as well as three basal protist lineages Nuclearida, Rosellida, and Aphelida belong to Holomycota. Surprisingly, among all these holomycotan groups, only the most basal lineage, Nuclearida, lacks any traces of flagella in its life cycle and is represented by free-living amoebae, in contrast to the obligately parasitic and flagellated Rosellida and Aphelida, which evolved later. As the earliest-branching lineage, nucleariids play a key role in understanding the origin and diversification of Opisthokonta, which is presumed to have evolved from a uniflagellated ancestor. In this study, we describe the first known nucleariid that is parasitic on algae and possesses a flagellated stage in its life cycle. We studied the life cycle, and showed the ultrastructure of main life cycle stages of this parasite. The multigene phylogenetic tree based on the newly sequenced transcriptome demonstrated its basal position among nucleariids, forming a clade of environmental OTUs. This finding together with unique ultrastructural features, parasitic style of life, and presence of flagellum allowed us to describe a new species, genus, and family in the order Nuclearidida. We emended the diagnoses of the order, class, and phylum Nuclearida. Based on the ribosomal phylogenetic tree where the Insolitus nuclearius has a basal position among the nucleariids we discussed the evolution of this group from the uniflagellated ancestor and provided new insights into the early evolution of Holomycota in a whole, revising hypotheses regarding the opisthokont ancestor.

The recently discovered Provora supergroup has primarily been examined to determine their phylogenomic position in the eukaryotic tree. Their morphology is more poorly studied, and here we focus on their cellular organization and how it compares with that of other supergroups. These small eukaryovorous flagellates exhibit several ultrastructural features that are also found in a subset of taxa from a wide variety of deep-branching lineages (Stramenopiles, Alveolata, Hemimastigophora, Malawimonadidae, Discoba and Metamonada), including vesicles beneath the plasmalemma, two opposing vanes on the flagella, a ventral feeding groove and a fibrillar system resembling the excavate type. Additionally, we identified four main microtubular roots (r1–r4) and a singlet root between r1 and r2, which support the strong feeding apparatus resembling ‘jaws’. Their unique extrusive organelles (ampulosomes) have a similar organization to Hemimastigophora extrusomes, but most of their cell characteristics most closely resemble features of the TSAR + Haptista grouping. We also describe a new species, Nibbleromonas piranha sp. nov., and highlight features of its feeding behaviour, which can be so aggressive as to result in cannibalism.

Aphelids are a poorly known group of algal parasites that have raised considerable interest because of their pivotal phylogenetic position as a sister lineage to the kingdom Fungi. Recent breakthroughs in sampling, sequencing and bioinformatical analyses of environmental nucleic acids have revealed magnificent biodiversity of aphelids. Nevertheless, only 4 genera have been described (Aphelidium, Paraphelidium, Amoeboaphelidium and Pseudaphelidium); 18S rRNA gene sequences are published for all except for the marine genus Pseudaphelidium. Most of the environmental nucleic acid data is from analysis of freshwater samples. We isolated two new marine aphelid strains (X-138 and X-139), and herein describe the life cycle of Protaphelidium rhizoclonii gen. et sp. nov., a parasite of the green alga Rhizoclonium sp., and provide the first 18S rRNA gene sequences for cultivated marine aphelids. The new marine aphelid life cycle is mostly typical for aphelids, but also includes previously undescribed stages. Molecular phylogenetic analysis indicated that Protaphelidium rhizoclonii is a member of an environmental clade at the base of the aphelid tree.

Aphelids are a holomycotan group, represented exclusively by parasitoids infecting algae. They form a sister lineage to Fungi in the phylogenetic tree and represent a key group for reconstruction of the evolution of Holomycota and for analysis of the origin of Fungi. The newly assembled genome of Aphelidium insullamus (Holomycota, Aphelida) with a total length of 18.9 Mb, 7820 protein-coding genes and a GC percentage of 52.05% was obtained by a hybrid assembly based on Oxford Nanopore long reads and Illumina paired reads. In order to trace the origin and the evolution of fungal osmotrophy and its presence or absence in Aphelida, we analyzed the set of main fungal transmembrane transporters, which are proteins of the Major Facilitator superfamily (MFS), in the predicted aphelid proteomes. This search has shown an absence of a specific fungal protein family Drug:H⁺ antiporters-2 (DAH-2) and specific fungal orthologs of the sugar porters (SP) family, and the presence of common opisthokont’s orthologs of the SP family in four aphelid genomes. The repertoire of SP orthologs in aphelids turned out to be less diverse than in free-living opisthokonts, and one of the most limited among opisthokonts. We argue that aphelids do not show signs of similarity with fungi in terms of their osmotrophic abilities, despite the sister relationships of these groups. Moreover, the osmotrophic abilities of aphelids appear to be reduced in comparison with free-living unicellular opisthokonts. Therefore, we assume that the evolution of fungi-specific traits began after the separation of fungal and aphelid lineages, and there are no essential reasons to consider aphelids as a prototype of the fungal ancestor.

Aphelids are a holomycotan group, represented exclusively by parasitoids infecting algae. They form a sister lineage to Fungi in the phylogenetic tree and represent a key group for reconstruction of the evolution of Holomycota and for analysis of the origin of Fungi. The newly assembled genome of Aphelidium insullamus (Holomycota, Aphelida) with a total length of 18.9Mb, 7820 protein-coding genes and a GC percentage of 52.05% was obtained by a hybrid assembly based on Oxford Nanopore long reads and Illumina paired reads. In order to trace the origin and the evolution of fungal osmotrophy and its presence or absence in Aphelida, we analyzed the set of main fungal transmembrane transporters, which are proteins of the Major Facilitator superfamily (MFS), in the predicted aphelid proteomes. This search has shown an absence of a specific fungal protein family Drug:H+ antiporters-2 (DAH-2) and specific fungal orthologs of the sugar porters (SP) family, and the presence of common opisthokont's orthologs of the SP family in four aphelid genomes. The repertoire of SP orthologs in aphelids turned out to be less diverse than in free-living opisthokonts, and one of the most limited among opisthokonts. We argue that aphelids do not show signs of similarity with fungi in terms of their osmotrophic abilities, despite the sister relationships of these groups. Moreover, the osmotrophic abilities of aphelids appear to be reduced in comparison with free-living unicellular opisthokonts. Therefore, we assume that the evolution of fungi-specific traits began after the separation of fungal and aphelid lineages, and there are no essential reasons to consider aphelids as a prototype of the fungal ancestor.