Hana Pecková

Background: Rhizaria is a eukaryotic supergroup including many amoeboid protists. Despite harboring a large diversity and many ecologically important species, the genomes belonging to this supergroup remain poorly explored. With only a handful available genome sequences, most of low contiguity, little is known about overall architecture, characteristics, and evolution of rhizarian genomes. Results: We provide a highly contiguous genome assembly of an undescribed marine rhizarian amoeba formerly known as M6MM. The assembly revealed a small (27 Mb; 8704 genes) and compact genome (84% genes, 10% repeats, 6% intergenic regions), and was almost fully captured in six contigs confirmed cytologically to represent chromosomes. The genome contains a very large amount of simple-sequence repeats (SSRs), particularly of the AC:GT dinucleotide class (206 loci/Mb), in total covering almost 2% of the assembly. We also obtained the complete mitochondrial genome, which is reduced and devoid of ribosomal protein genes similarly to some other rhizarians. Some of these “missing” mitochondrial-encoded genes are found in the nuclear genome and are predicted to be targeted to the mitochondrion. In our 18S rDNA phylogenetic analysis, M6MM loosely groups with environmental sequences and the amoeboflagellate Viscidocauda repens . However, this amoeba is phylogenetically distant from any described species and expresses a unique pseudopodial morphology, prompting us to erect the novel genus and species Lemnamoeba sinaloensis gen. nov. et. sp. nov. Environmental data show that L. sinaloensis has a wide marine distribution and can mostly be found between the surface and 100 m depths. Conclusion: This study adds another genus to the hitherto taxonomically poor Apofilosa, provides one of the highest-quality rhizarian genome assemblies to date, and reveals an abundance of SSRs in the genome, highlighting the complexity of eukaryotic genomes in underexplored parts of the tree of life.

Microsporidians are highly specialised intracellular parasites adapted to an obligate parasitic lifestyle. Although more than 1,500 species have been described to date, their true diversity is likely much higher, particularly in poorly-studied aquatic environments. Here, we applied an optimised tissue-based metabarcoding approach to investigate the diversity and distribution of microsporidians in aquatic invertebrates from three nearby fish ponds in South Bohemia in the Czech Republic. We analysed more than two thousand individuals of chironomids and oligochaetes, which represent important aquatic invertebrate hosts of microsporidians, and compared microsporidian communities across ponds and host morphogroups. In total, 66 microsporidian OTUs were detected across both host groups. Metabarcoding and phylogenetic analyses revealed broad sequence diversity within the studied localities, with parasite sequences clustering into four main clades. The high proportion of OTUs without close matches to described taxa (more than 95%) highlights substantial undocumented diversity of microsporidians in freshwater ecosystems. The occurrence of shared OTUs amongst different invertebrate taxa is consistent with multi-host strategies and/or complex life cycles. Overall, our findings emphasise the ecological complexity of microsporidians in aquatic habitats. Further experimental work, including parasite localisation and transmission studies, is needed to determine whether the observed host associations represent active infections or incidental detection.