Biology subjects

Kolisko, M.

Publications and source records attributed to Kolisko, M..

6 recordsLinked to original sources

bioRxiv2026

The genome assembly of Sphaerospora molnari provides novel insights into the rapid evolution and diversification of unique lineage-specific gene groups in myxozoan parasites

BackgroundMyxozoans are ancient cnidarian parasites with highly derived genomes characterized by an extremely accelerated rate of nucleotide substitution, abundant orphan and lineage-specific genes without further characterization. Genome data are limited to two out of the four main evolutionary lineages, assemblies are highly fragmented and often show significant levels of host contamination. ResultsWe present a near chromosome-scale myxozoan genome, based on Oxford Nanopore-reads of Sphaerospora molnari, a member of the previously uncharacterized group of blood-feeding myxozoans, thereby addressing a key gap in the subphylums phylogeny. The haploid genome assembly spans 40.17 Mb in 40 contigs, harbors 14,957 genes and shows the smallest mitogenome of myxozoans (14,015 bp). Gene gain/gene loss analyses showed that myxozoans have small ancestral gene repertoires and show highly lineage-specific genome compositions. Using comparative analyses focusing on identifying unique but diversified gene compartments in S. molnari, we discovered taxonomically restricted protist genes related to red blood cell attachment (Plasmodium ETRAMPs) and surface protein variation (Plasmodium variant surface antigen families RIFIN and STEVOR, as well as Metamonada variant-specific surface proteins, VSPs), raising questions about their origins and evolution. A genomic trait shared between several myxozoans is the significant expansion of DNA transposable elements belonging to the mutator-like elements (MULEs), and while the simple copy-paste mechanism of these transposases may suggest frequent uncontrolled mutation, we demonstrate domestication of MULEs into transcription factors. Analyses of the gene fragments of chimeric MULEs (pack-MULES) of S. molnari show that these coincide with highly diversified gene groups in this lineage, including alien genes, suggesting MULEs as a driving force for gene evolution in myxozoans. ConclusionsParasitic lifestyle shifts drive exceptionally rapid genome evolution in myxozoans, primarily through nonadaptive mutation and gene transfer via MULEs, with adaptive refinement through MULE domestication and selection. In S. molnari, these processes underpin unique erythrocyte exploitation and immune evasion strategies essential for survival in the hosts bloodstream.

genomics↗

bioRxiv2024

Multiple plastid losses within photosynthetic stramenopiles revealed by comprehensive phylogenomics

Ochrophyta is a vast and morphologically diverse group of algae with complex plastids, including familiar taxa with fundamental ecological importance (diatoms or kelp), and a wealth of lesser-known and obscure organisms. The sheer diversity of ochrophytes poses a challenge for reconstructing their phylogeny, with major gaps in sampling and an unsettled placement of particular taxa yet to be tackled. We sequenced transcriptomes from 25 strategically selected representatives and used these data to build the most taxonomically comprehensive ochrophyte-centered phylogenomic supermatrix to date. We employed a combination of approaches to reconstruct and critically evaluate the relationships among ochrophytes. While generally congruent with previous analyses, the updated ochrophyte phylogenomic tree resolved the position of several taxa with previously uncertain placement, and supported a redefinition of the class Synchromophyceae. Our results indicated that the heterotrophic plastid-lacking heliozoan Actinophrys sol is not a sister lineage of ochrophytes, as proposed recently, but rather phylogenetically nested among them. In addition, we found Picophagus flagellatus to be a secondarily heterotrophic ochrophyte lacking all hallmark plastid genes, yet exhibiting mitochondrial proteins that seem to be genetic footprints of lost plastid organelle. We thus document, for the first time, plastid loss in two separate ochrophyte lineages. Altogether, our study provides a new framework for reconstructing trait evolution in ochrophytes and demonstrates that plastid loss is more common than previously thought. Issue Section: Discoveries

evolutionary biology↗

bioRxiv2021

A free-living protist that lacks canonical eukaryotic DNA replication and segregation systems

Cells must replicate and segregate their DNA with precision. In eukaryotes, these processes are part of a regulated cell-cycle that begins at S-phase with the replication of DNA and ends after M-phase. Previous studies showed that these processes were present in the last eukaryotic common ancestor and the core parts of their molecular systems are conserved across eukaryotic diversity. However, some unicellular parasites, such as the metamonad Giardia intestinalis, have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a high-quality draft genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. We found that parasitic and free-living metamonads harbor a conspicuously incomplete set of canonical proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and other replisome components, most structural kinetochore subunits including the Ndc80 complex, as well as several canonical cell-cycle checkpoint proteins. Carpediemonas is the first eukaryote known to have lost this large suite of conserved complexes, suggesting that it has a highly unusual cell cycle and that unlike any other known eukaryote, it must rely on novel or alternative set of mechanisms to carry out these fundamental processes.

evolutionary biology↗

bioRxiv2019

Multiple independent origins of apicomplexan-like parasites

Apicomplexans are a diverse group of globally important parasites, that include pathogens like Plasmodium, the causative agent of malaria. Despite their current obligate parasitic nature, apicomplexans evolved from photosynthetic algae and retain a remnant plastid (chloroplast). Such a complex evolutionary transition was unexpected, but here we show that it occurred at least three times independently. Using single-cell genomics and transcriptomics from diverse uncultivated parasites, we find that two genera previously classified within the Apicomplexa, Piridium and Platyproteum, form separately branching lineages in phylogenomic analyses. Both retain cryptic plastids with genomic and metabolic features convergent with apicomplexans. These findings suggest a predilection in this lineage for both the loss of photosynthesis and the transition to a morphologically similar parasitic lifestyle, resulting in multiple lineages of highly convergent animal parasites.

evolutionary biology↗

bioRxiv2018

Phylogeny, evidence for a cryptic plastid, and distribution of Chytriodinium parasites (Dinophyceae) infecting copepods

Spores of the dinoflagellate Chytriodinium are known to infest copepod eggs causing their lethality. Despite the potential to control the population of such an ecologically important host, knowledge about Chytriodinium parasites is limited: we know little about phylogeny, parasitism, abundance, or geographical distribution. We carried out genome sequence surveys on four manually isolated sporocytes from the same sporangium to analyse the phylogenetic position of Chytriodinium based on SSU and concatenated SSU/LSU rRNA gene sequences, and also characterize two genes related to the plastidial heme pathway, hemL and hemY. The results suggest the presence of a cryptic plastid in Chytriodinium and a photosynthetic ancestral state of the parasitic Chytriodinium/Dissodinium clade. Finally, by mapping Tara Oceans V9 SSU amplicon data to the recovered SSU rRNA gene sequences from the sporocytes, we show that globally, Chytriodinium parasites are most abundant within the pico/nano- and mesoplankton of the surface ocean and almost absent within microplankton, a distribution indicating that they generally exist either as free-living spores or host-associated sporangia.

microbiology↗

bioRxiv2018

EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors, and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is a community driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the complete eukaryotic tree of life and microbial ecologists that actively use environmental sequencing data for the purpose of developing reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous sequence data mining and annotation by providing protocols, guidelines and tools to do so.

microbiology↗