Genome Analysis of Pseudoloma neurophilia: A Microsporidian Parasite of Zebrafish (Danio rerio)

Abstract

Microsporidia are highly successful parasites that infect virtually all known animal lineages, including the model Danio rerio (zebrafish). The widespread use of this aquatic model for biomedical research has resulted in an unexpected increase in infections from the microsporidium Pseudoloma neurophilia, which can lead to significant physical, behavioral and immunological modifications resulting in non-protocol variation during experimental procedures. Here, we seek to obtain insights into the biology of P. neurophilia by investigating its genome content, which was obtained from only 29 nanograms of DNA using the Miseq technology and paired-end Illumina sequencing. We found that the genome of P. neurophilia is phylogenetically and genetically related to other fish-microsporidians, but features unique to this intracellular parasite are also found. The small 5.25-Mb genome assembly includes 1,139 unique open reading frames and an unusually high number of transposable elements for such a small genome. Investigations of intragenomic diversity also provided strong indications that the mononucleate nucleus of this species is diploid. Overall, our study provides insights into the dynamics of microsporidian genomes, and represents a solid sequence reference to be used in future studies of host-parasite interactions using the zebrafish Danio rerio and P. neurophilia as a model.

Error-prone protein synthesis in parasites with the smallest eukaryotic genome

“…To compare microsporidian synthetases with their homologs from other eukaryotes, we analyzed available genome sequences from 19 microsporidian species (SI Appendix, Table S1). Each of these genomes was shown to harbor a full set of 20 different aminoacyl-tRNA synthetases corresponding to the 20 proteinogenic amino acids, but to lack the genes coding for mitochondrial aminoacyl-tRNA synthetases due to degeneration of mitochondria in microsporidian cells (9,16,(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36). Moreover, microsporidian genomes lack duplicated synthetase genes or genes coding for synthetase fragments that are present in other eukaryotes (9,16,(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38).…”

Evolution of microsporidia: An extremely successful group of eukaryotic intracellular parasites

“…The sporoplasm then proliferates, eventually producing spores that then exit the host to cause subsequent infections. Microsporidia are thought to reproduce mostly asexually, although most are likely diploid based on genomic heterozygosity and conservation of meiotic genes [2][3][4][5].…”

Microsporidia: Obligate Intracellular Pathogens Within the Fungal Kingdom

“…This divergence of ssRNA sequence structure while once thought to be evidence of microsporidia being an early branch in evolution instead is due to the specialization and extremely reduced genome size reduction of these obligate intracellular pathogens (11). The genome size of the microsporidia varies from 2.3 to 51.3 Mb (89, 90). The genome size of microsporidia in the family Encephalitizoonidae (all of which are human pathogens) are all under 3.0 Mb, making these genomes among the smallest eukaryotic nuclear genomes (91–96).…”