Background: Eukaryotes whole-genome sequencing is crucial for species identification, gene detection and protein-annotation. Oxford Nanopore sequencing serves as an affordable and rapid platform for sequencing eukaryotes, however the relatively higher error rates require computational and bioinformatic efforts to produce more accurate genome assemblies. Here, we evaluated the effect of read correction tools on eukaryotes genome completeness, gene detection and protein-annotation. Methods: Reads generated by ONT of four eukaryotes, C. albicans, C. gattii, S. cerevisiae, and P. falciparum, were assembled using minimap2 and underwent three rounds of read correction using flye, medaka and racon. The generates consensus FASTA files were compared for total length (bp), genome completeness, gene detection, and protein-annotation by QUAST, BUSCO, BRAKER1 and InterProScan, respectively. Results: genome completeness was dependent on assembly method rather than read correction tool, however, medaka performed better than flye and racon. Racon significantly performed better than flye and medaka in gene detection, while both racon and medaka significantly performed better than flye in protein-annotation. Conclusion: We show that three rounds of read correction significantly affects gene detection and protein-annotation which are dependent on assembly quality in preference to assembly completeness.

Interactome analyses have traditionally been applied to yeast, human and other model organisms due to the availability of protein-protein interactions data for these species. Recently these techniques have been applied to more diverse species using computational interaction prediction from genome sequence and other data types. This review describes the various types of computational interactome networks that can be created and how they have been used in diverse eukaryotic species, highlighting some of the key interactome studies in non-model organisms.

Ancient lakes are among the most interesting models for evolution studies, because their biodiversity is the result of a complex combination of migration and speciation. Here, we investigate the origin of single celled planktonic eukaryotes from the oldest lake in the world – Lake Baikal. By using 18S rDNA metabarcoding we recovered 1,427 Operational Taxonomic Units (OTUs) belonging to protists populating surface waters (1-50 meters) and belonging to pico- and nano-plankton size fractions. The recovered communities resembled other lacustrine freshwater assemblages found elsewhere, especially the unclassified protists. However, our results suggest that a fraction of Baikal protists originated evolutionary recently from marine/brackish ancestors. Moreover, our results suggest that rapid radiation may have occurred among some protist taxa, partially mirroring what was already shown for multicellular organisms in Lake Baikal. We found potential species flocks in Stramenopiles, Alveolata, Opisthokonta, Archaeplastida, Rhizaria and Hacrobia. Putative flocks predominated in Chrysophytes, which are highly diverse in Lake Baikal. Some of the species, especially those from these flocks, may be endemic from Lake Baikal, because their 18S rDNA differed > 10% from known DNA. Overall, our study points to novel diversity of planktonic protists in Lake Baikal, some of which may have emerged in situ after evolutionary diversification.

The terrestrial subsurface harbors unique microbial communities that play important biogeochemical roles and allows studying a yet unknown fraction of the Earth’s biodiversity. The Saint-Leonard cave in Montreal city (Canada) is of glaciotectonic origin. Its speleogenesis traces back to the withdrawal of the Laurentide Ice Sheet, 13 000 years ago, during which the moving glacier dislocated the sedimentary rock layers. Our study is the first to investigate the microbial communities of the cave. By using amplicon sequencing, we analyzed the taxonomic diversity and composition of bacterial, archaeal and eukaryotes communities living in the groundwater (0.1µm- and 0.2µm-filtered water), in the sediments and in surface soils. We identified a microbial biodiversity typical of cave ecosystems. Communities were mainly shaped by habitat type and harbored taxa associated with a wide variety of lifestyles and of metabolic capacities. Although we found evidence of a geochemical connection between the above soils and the cave’s galleries, our results suggest that the community assembly dynamics are driven by habitat selection rather than dispersal. Furthermore, we found that the cave’s groundwater, in addition to being generally richer in microbial taxa than sediments, contained a considerable diversity of ultra-small bacteria and archaea.

We report here a giant microfossil resembling the conidium of an ascomycete fungus (cf. Alternaria alternata). The specimen is preserved in stromatolitic black chert of the Gunflint Iron Formation (Paleoproterozoic Eon, Orosirian Period, ca. 1.9-2.0 Ga) of southern Ontario, Canada, and the rock that provided the thin section may have been collected by Elso Barghoorn as part of the original discovery of the Gunflint microbiota. The large size of the fossil sets it apart from other, tiny by comparison, Gunflint microfossils. The fossil is 200 microns in length and has cross walls. Individual cells are 30-46 microns in greatest dimension. The apical ‘spore’ is cap-shaped, and has partly separated from the rest of the structure. Cloulicaria gunflintensis gen. nov. sp. nov. may provide early evidence for eukaryotes (fungi) in the fossil record, and may also represent the earliest evidence for asexual reproduction in a eukaryote by means of mitospores.

Biofilm formation by unicellular eukaryotes presents major challenges in healthcare, agriculture, and food industries, primarily due to enhanced resistance to environmental stressors and antimicrobial agents. Understanding the regulatory mechanisms of biofilm formation, such as quorum sensing (QS) and cyclic di-GMP signaling, has led to the discovery of novel compounds that can inhibit biofilm development. In 2024, significant advancements were made in identifying compounds like betulinic acid, methyl anthranilate, and pulmonarin B analogues that target these pathways. This review explores the potential applications of these compounds, especially in Vietnam's agriculture and food industries, where biofilm formation contributes to contamination and antimicrobial resistance. The findings underscore the global relevance of biofilm-disrupting technologies and their role in combating biofilm-associated infections and resistance.