Typical structure of rRNA coding genes in diplonemids points to two independent origins of the bizarre rDNA structures of euglenozoans

Co-infection of Liburna oophaga sp. nov. and Ikanecator primus on cuttlefish (Sepia pharaonis) eggs and the effectiveness of peracetic acid as a treatment

The cuttlefish Sepia pharaonis species complex is emerging as a promising set of organisms for research in neuroscience, the behavioral sciences, and commercial aquaculture. At the same time, information about pathogens and diseases that could affect cuttlefish cultivation in intensive aquaculture settings remains limited. Our study has identified two species of parasite, the protozoan Liburna oophaga sp. nov. and the metazoan Ikanecator primus, that co-infect cuttlefish eggs, increasing mortality and reducing hatching rates. L. oophaga sp. nov. is reported here for the first time to enhance mortality during the incubation period by inducing deformity in cuttlefish eggs. We investigated the application of peracetic acid to parasite elimination during cuttlefish egg incubation. When cuttlefish eggs were treated with a peracetic acid containing product (PAA-product); 35 mg/L PAA + 15 mg/L H2O2, L. oophaga on the surfaces of the eggs were eliminated within 10 min. PAA-product; 70 mg/L PAA + 30 mg/L H2O2 was required to achieve the same effect for I. primus. Immersion treatment with PAA-product at 70 mg/L PAA + 30 mg/L H2O2 reduced parasitic load and improved survival of cuttlefish embryos and hatchling size, demonstrating that PAA product can inhibit and control parasitic co-infections in cephalopod culture.

Circular extrachromosomal DNA in Euglena gracilis under normal and stress conditions

Extrachromosomal circular DNA (eccDNA) enhances genomic plasticity, augmenting its coding and regulatory potential. Advances in high-throughput sequencing have enabled the investigation of these structural variants. Although eccDNAs have been investigated in numerous taxa, they remained understudied in euglenids. Therefore, we examined eccDNAs predicted from Illumina sequencing data of Euglena gracilis Z SAG 1224-5/25, grown under optimal photoperiod and exposed to UV irradiation. We identified approximately 1000 unique eccDNA candidates, about 20% of which were shared across conditions. We also observed a significant enrichment of mitochondrially encoded eccDNA in the UV-irradiated sample. Furthermore, we found that the heterogeneity of eccDNA was reduced in UV-exposed samples compared to cells that were grown in optimal conditions. Hence, eccDNA appears to play a role in the response to oxidative stress in Euglena, as it does in other studied organisms. In addition to contributing to the understanding of Euglena genomes, our results contribute to the validation of bioinformatics pipelines on a large, non-model genome.

Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes

BACKGROUND

Diplonemid flagellates are among the most abundant and species-rich of known marine microeukaryotes, colonizing all habitats, depths, and geographic regions of the world ocean. However, little is known about their genomes, biology, and ecological role.

RESULTS

We present the first nuclear genome sequence from a diplonemid, the type species Diplonema papillatum. The ~ 280-Mb genome assembly contains about 32,000 protein-coding genes, likely co-transcribed in groups of up to 100. Gene clusters are separated by long repetitive regions that include numerous transposable elements, which also reside within introns. Analysis of gene-family evolution reveals that the last common diplonemid ancestor underwent considerable metabolic expansion. D. papillatum-specific gains of carbohydrate-degradation capability were apparently acquired via horizontal gene transfer. The predicted breakdown of polysaccharides including pectin and xylan is at odds with reports of peptides being the predominant carbon source of this organism. Secretome analysis together with feeding experiments suggest that D. papillatum is predatory, able to degrade cell walls of live microeukaryotes, macroalgae, and water plants, not only for protoplast feeding but also for metabolizing cell-wall carbohydrates as an energy source. The analysis of environmental barcode samples shows that D. papillatum is confined to temperate coastal waters, presumably acting in bioremediation of eutrophication.

CONCLUSIONS

Nuclear genome information will allow systematic functional and cell-biology studies in D. papillatum. It will also serve as a reference for the highly diverse diplonemids and provide a point of comparison for studying gene complement evolution in the sister group of Kinetoplastida, including human-pathogenic taxa.