Comparative genomics of Ascetosporea gives new insight into the evolutionary basis for animal parasitism in Rhizaria

Abstract

Background: Ascetosporea (Endomyxa, Rhizaria) is a group of unicellular parasites infecting aquatic invertebrates. They are increasingly being recognized as widespread and important in marine environments, causing large annual losses in invertebrate aquaculture. Despite their importance, little molecular data of Ascetosporea exist, with only two genome assemblies published to date. Accordingly, the evolutionary origin of these parasites is unclear, including their phylogenetic position and the genomic adaptations that accompanied the transition from a free-living lifestyle to parasitism. Here, we sequenced and assembled three new ascetosporean genomes, as well as the genome of a closely related amphizoic species, to investigate the phylogeny, origin, and genomic adaptations to parasitism in Ascetosporea.

Results: Using a phylogenomic approach, we confirm the monophyly of Ascetosporea and show that Paramyxida group with Mikrocytida, with Haplosporida being sister to both groups. We report that the genomes of these parasites are relatively small (12-36 Mb) and gene-sparse (~ 2300-5200 genes), while containing surprisingly high amounts of non-coding sequence (~ 70-90% of the genomes). Performing gene-tree aware ancestral reconstruction of gene families, we demonstrate extensive gene losses at the origin of parasitism in Ascetosporea, primarily of metabolic functions, and little gene gain except on terminal branches. Finally, we highlight some functional gene classes that have undergone expansions during evolution of the group.

Conclusions: We present important new genomic information from a lineage of enigmatic but important parasites of invertebrates and illuminate some of the genomic innovations accompanying the evolutionary transition to parasitism in this lineage. Our results and data provide a genetic basis for the development of control measures against these parasites.

Keywords: Bonamia; Marteilia; Mikrocytos; Paramarteilia; Paramikrocytos; Evolutionary transition; Genome reduction; Intracellular parasite; Phylogeny; Protozoa; Reductive evolution.

Fig. 1

Phylogeny of Rhizaria. The tree was built using maximum likelihood from a concatenated supermatrix of 225 single-copy orthologs with the LG + C60 + G + F model in IQ-TREE2. Branch values depict from left to right ultra-fast bootstrap support and posterior probability scores from the consensus of three converged chains of CAT + GTR + GAMMA in PhyloBayes. Branches without values are fully supported by both analyses. The PhyloBayes analysis was performed on a subsampled matrix where the 38% slowest-evolving sites were retained. Branch lengths scaled to substitutions per site, as per the scale bar at the bottom. Within Ascetosporea, branches were collapsed to half their length. For details about the source data of included taxa, see Additional file 6: Dataset S2

Fig. 2

Metabolic genes and gene clusters in Ascetosporea. A Number of genes in major categories of metabolic pathways as classified in comparison to the Kyoto Encyclopedia of Genes and Genomes (KEGG). B Shared and specific gene clusters. “Specific” refers to clusters that are not found outside that group. Numbers in parentheses refer to the number of clusters in that category. Clusters shared between non-sisters not shown. Asc: Ascetosporea; Par: Paramyxida; Mik: Mikrocytida

Fig. 3

Gene family evolution in Ascetosporea. A Gene-tree aware ancestral reconstruction of gene families. Bubble sizes at branches correspond to predicted proteome sizes, and gene evolution events are plotted as bars, where the height of the bar reflects the number of such events (see main text for explanation of the events). The height of the bars in the legend corresponds to 5000 events. The bar for duplications on the branch to Reticulomyxa filosa has for plotting purposes been halved in height. B, C Gene Ontology (GO) enrichment analysis of orthogroups (OGs; i.e., gene clusters) that experienced losses (B) and gains (C; duplications and originations analyzed together) at ancestral branches within the Ascetosporea sub-tree. For plotting, GO terms have been clustered based on semantic similarity, and one representative term per cluster is shown. Only the seven GO terms with lowest p-values are shown, and bars are colored based on top-level GO category (green: Biological Process; red: Cellular Component; blue: Molecular Function). AscCA: Ascetosporea Common Ancestor; PMCA: Paramyxida-Mikrocytida Common Ancestor; MikCA: Mikrocytida Common Ancestor; ParCA: Paramyxida Common Ancestor