Biology subjects

Tashyreva, D.

Publications and source records attributed to Tashyreva, D..

4 recordsLinked to original sources

bioRxiv2026

Inverse relationship between mitochondrial and non-coding nuclear DNA content in free-living kinetoplastids

The evolution of genome size and eukaryotic genome organisation has puzzled evolutionary biologists for decades. Are differences in DNA content and protein-coding capacity of eukaryotic genomes a result of natural selection, or neutral processes? If they were shaped by natural selection, which features might be connected with these differences: cell volume, ecological strategy, availability of nutrients, etc.? Kinetoplastids are protists with compact nuclear genomes that almost entirely lack introns, but whose mitochondrial DNA content (kDNA) can rival that of their nuclei. We hypothesised that the reduction in non-protein coding nuclear DNA content during the evolution of kinetoplastids is connected with an increase in kDNA content: species with larger fractions of total cellular DNA that is allocated to kDNA will have concomitantly smaller fractions of non-coding DNA in the nuclear genome. We developed a framework for estimation of DNA content in both the mitochondria and nuclei from quantitative fluorescence microscopy data, and inferred the fraction of non-coding DNA in nuclear genomes based on the combination of transcriptomic and fluorescence imaging data. Across 10 genetically distant isolates from diverse free-living kinetoplastid lineages, there is indeed a trend towards a lower proportion of non-protein-coding nuclear DNA when kDNA proportion is higher relative to the total DNA in the cell. This observation is consistent with the hypothesis that in free-living kinetoplastids, mitochondrial and nuclear genomes might co-evolve in terms of their DNA content. This finding raises the possibility that natural selection acts on genome size evolution in kinetoplastids, and contributes evidence and methodology to address this question more broadly in eukaryotes.

evolutionary biology↗

bioRxiv2026

Absence of endosymbiotic gene transfer in symbiont-bearing diplonemids

Horizontal gene transfer (HGT) is one of the fundamental processes in the evolution of prokaryotic genomes, while its importance in eukaryotes is still debated. Some of the hallmark eukaryotic organelles, such as mitochondria and chloroplasts, are of an ancient endosymbiotic origin. The process of acquiring (and losing) new endosymbionts is dynamic and still ongoing in many lineages. Endosymbiotic gene transfer (EGT) between symbionts and their hosts has been considered as one of the major sources of overall HGTs in eukaryotes. Thanks to recent advances in genomics and microscopy, more and more endosymbionts are discovered in protists offering suitable models for the study of EGT and its impact on the host. Recently, the presence of holosporacean and chlamydiacean symbionts in the novel strains of marine euglenozoan flagellates of genus Rhynchopus has been discovered. Here, we present an analysis of the genomes and transcriptomes of five Rhynchopus strains and examine the extent of EGT/HGT and the role of endosymbiosis in shaping the nuclear genome of symbiont-bearing hosts. Our results have shown that there is no evidence of a recent EGT from either Holosporales or Chlamydiales symbionts. The absence of such transfers suggests that EGT or at least a stable retention of EGT genes is not a requisite for a successful endosymbiosis. Furthermore, our results show striking differences between patterns of detected HGTs among the Rhynchopus lineages pointing to a dynamic and largely neutral evolution of horizontally-acquired genes.

evolutionary biology↗

bioRxiv2022

Massive accumulation of strontium and barium in diplonemid protists

Barium (Ba) and strontium (Sr) are often used as proxies for the reconstruction of past marine productivity and global climate. The ability to accumulate Ba2+ and Sr2+ in the form of crystals is rare among eukaryotes. Here we report that unicellular heterotrophs called diplonemids (Euglenozoa), one of the most abundant groups of marine planktonic protists, accumulate conspicuous amounts of these trace elements in the form of intracellular barite (BaSO4) and celestite (SrSO4) crystals, in concentrations greater than in other known Ba/Sr-accumulating organisms. Moreover, these flagellates can uptake Sr2+ exclusively or together with Ba2+ and form (Ba,Sr)SO4. One species, Namystinia karyoxenos, is naturally capable of intracellular accumulation of Ba2+ and Sr2+ 42,000 and 10,000 times relative to the surrounding medium. Altering the amounts of both elements in the medium resulted in corresponding changes in the quantity and composition of crystals. Planktonic copepods fed with diplonemids produce celestite-rich fecal pellets, which facilitate deposition of these minerals on the seafloor. We propose that diplonemids, which emerged during the Neoproterozoic era, qualify as impactful players of Ba2+/Sr2+ cycling in the ocean that possibly contributed to sedimentary rock formation over long geological periods.

microbiology↗

bioRxiv2019

Highly reduced genomes of protist endosymbionts show evolutionary convergence

Genome evolution in bacterial endosymbionts is notoriously extreme: the combined effects of strong genetic drift and unique selective pressures result in highly reduced genomes with distinctive adaptations to hosts [1-4]. These processes are mostly known from animal endosymbionts, where nutritional endosymbioses represent the best-studied systems. However, eukaryotic microbes, or protists, also harbor diverse bacterial endosymbionts, but their genome reduction and functional relationships with their more diverse hosts are largely unexplored [5-7]. We sequenced the genomes of four bacterial endosymbionts from three species of diplonemids, poorly-studied but abundant and diverse heterotrophic protists [8-10]. The endosymbionts come from two intracellular families from different orders, Rickettsiaceae and Holosporaceae, that have invaded diplonemids multiple times, and their genomes have converged on an extremely small size (605-632 kbp), similar gene content (e.g., metabolite transporters and secretion systems), and reduced metabolic potential (e.g., loss of energy metabolism). These characteristics are generally found in both families, but the diplonemid endosymbionts have evolved greater extremes in parallel. Their modified type VI secretion systems are likely involved in the manipulation of host metabolism (e.g., interactions with host mitochondria) or defense against bacterial infections, although their similar effector/immunity proteins may also allow for co-occurring Holosporaceae species in one diplonemid host. Finally, modified cellular machinery like ATP synthase without oxidative phosphorylation and reduced flagella present in both diplonemid endosymbionts and nutritional animal endosymbionts indicates that intracellular mechanisms have converged in bacterial endosymbionts with various functions and from different eukaryotic hosts across the tree of life.

evolutionary biology↗