Chromosome-level assembly of Lemnamoeba sinaloensis gen. nov. et sp. nov. (Apofilosa) reveals dynamic genome evolution in Rhizaria

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.