Spraguea lophii (Microsporidia) parasite of the teleost fish, Lophius piscatorius from Tunisian coasts: evidence for an extensive chromosome length polymorphism

Polyploidy is widespread in Microsporidia

Microsporidia are obligate intracellular eukaryotic parasites with an extremely broad host range. They have both economic and public health importance. Ploidy in microsporidia is variable, with a few species formally identified as diploid and one as polyploid. Given the increase in the number of studies sequencing microsporidian genomes, it is now possible to assess ploidy levels across all currently explored microsporidian diversity. We estimate ploidy for all microsporidian data sets available on the Sequence Read Archive using k-mer-based analyses, indicating that polyploidy is widespread in Microsporidia and that ploidy change is dynamic in the group. Using genome-wide heterozygosity estimates, we also show that polyploid microsporidian genomes are relatively homozygous, and we discuss the implications of these findings on the timing of polyploidization events and their origin.IMPORTANCEMicrosporidia are single-celled intracellular parasites, distantly related to fungi, that can infect a broad range of hosts, from humans all the way to protozoans. Exploiting the wealth of microsporidian genomic data available, we use k-mer-based analyses to assess ploidy status across the group. Understanding a genome's ploidy is crucial in order to assemble it effectively and may also be relevant for better understanding a parasite's behavior and life cycle. We show that tetraploidy is present in at least six species in Microsporidia and that these polyploidization events are likely to have occurred independently. We discuss why these findings may be paradoxical, given that Microsporidia, like other intracellular parasites, have extremely small, reduced genomes.

G lugea sp. infecting Sardinella aurita in Algeria

Parasitological examination of the commercially important pelagic fish Sardinella aurita Valenciennes, 1847 (Clupeidae) from the Eastern coast of Algeria revealed xenomas in the peritoneal cavity, suggesting a microsporidian infection. The prevalence of the disease was approximately 30% on average, higher in smaller individuals and showing significant seasonal variation. The xenomas contained numerous ellipsoidal spores, surrounded by a dense layer of connective tissue. Spore sizes were 6.10 ± 0.38 µm length and 3.54 ± 0.43 µm width. Ultrastructural examination by transmission electron microscopy showed various development stages of the parasite, including meronts, sporonts, sporoblasts and mature spores. The internal organization of the mature spores, with a single nucleus, prominent posterior vacuole, a lamellar polaroplast and an isofilar polar tube arranged in a single row, was typical of the genus Glugea. The DNA sequence of the small subunit ribosomal RNA gene confirmed that this parasite belongs to the genus Glugea. Genetic and morphologic comparison with G. sardinellensis, a species previously described in the same host from Tunisia shows many similarities, although some molecular and morphometric inconsistencies precluded the unambiguous assignment of our samples to G. sardinellensis. At the same time, we do not find sufficient grounds to erect a new taxon for our parasite. We discuss the implications of our findings for the current state of the systematics of Glugea.

Microsporidians xenomas of anglerfish from NE Atlantic waters

The presence of emergent visible parasites at commercial valuable fish species is increasingly causing problems at fisheries and seafood industries. Microsporidians have been previously reported to appear forming apparent xenomas complexes in anglerfish species, but no effort has been carried out to simultaneously integrate epidemiological data, phenotypic, genotypic and fine structural characterizations in the same parasite sample. In this work, specimens of Lophius budegassa and Lophius piscatorius from NE Atlantic waters were sampled and examined to provide information about specific site of infection and demographic data of two groups of different sizes of xenomas present at both fish species. Histological descriptions and scanning and transmission electron microscopy were carried out on fresh spores of Lophius budegassa for ultrastructural studies. In both types of xenomas, it was observed simultaneously the microsporidian genus Spraguea in the form of two different types of spores. Molecular analyses of both xenomas from the two fish species, based on the small subunit ribosomal DNA gene, were also performed to genetically support the morphological diagnostic provided.

Ultrastructural characterization of Pleistophora macrozoarcidis Nigerelli 1946 (Microsporidia) infecting the ocean pout Macrozoarces americanus (Perciformes, Zoarcidae) from the gulf of Maine, MA, USA

Pleistophora macrozoarcidis a microsporidian parasite infecting the muscle tissue of the ocean pout Macrozoarces americanus collected from the Gulf of Maine of the Atlantic Ocean, MA, USA, was morphologically described on the basis of ultrastructural features. Infection was detected as opaque white or rusty brown lesions scattered throughout the musculature of the fish mainly in the region anterior to anus. Transmission electron microscopy showed that in individual parasitized muscle cells, the infection progresses within parasite formed vesicles which are in direct contact with muscle cell elements. The earliest observed parasitic stages are the globular multinucleated proliferative cells or plasmodia limited by a highly tortuous plasmalemma with intervesicular finger-like digitations projecting into the parasite cytoplasm. These cells divided through the invagination of the plasmalemma and the amorphous coat producing daughter-cells. Fine electron-dense secretion is deposited on the plasmalemma that causes its thickening which is a sign of commencement of the sporogonic phase. This phase is carried out by cytokinesis of the sporonts and results in the formation of sporoblasts and finally spores. Mature spore has a thin electron-dense exospore, a thick electron-lucent endospore, and the plasma membrane which encloses the spore contents. A single nucleus is centrally located with the posterior region containing a posterior vacuole. The majority of spores have 7-13 coils in 1-2 rows, and a small group of spores had about 23 coils forming two rows. Events of polar filament extrusion for penetration of uninfected cells were studied. The polaroplast membranes were expanded and occupy most of the length of the spore. The coils are dislocated from the sides of the spore to throughout the entire sporoplasm. The polar filament everts and extrudes through the polar cap with a sufficient force to pierce adjacent sporophorous vesicle walls. After eversion, the polar filament is referred to as a polar tubule, as it forms a tube through which the sporoplasm travels. It pierces anything in its path and deposits the sporoplasm at a new location to begin another infective cycle.

A Recent Whole-Genome Duplication Divides Populations of a Globally Distributed Microsporidian

The Microsporidia are a major group of intracellular fungi and important parasites of animals including insects, fish, and immunocompromised humans. Microsporidian genomes have undergone extreme reductive evolution but there are major differences in genome size and structure within the group: some are prokaryote-like in size and organisation (<3 Mb of gene-dense sequence) while others have more typically eukaryotic genome architectures. To gain fine-scale, population-level insight into the evolutionary dynamics of these tiny eukaryotic genomes, we performed the broadest microsporidian population genomic study to date, sequencing geographically isolated strains of Spraguea, a marine microsporidian infecting goosefish worldwide. Our analysis revealed that population structure across the Atlantic Ocean is associated with a conserved difference in ploidy, with American and Canadian isolates sharing an ancestral whole genome duplication that was followed by widespread pseudogenisation and sorting-out of paralogue pairs. While past analyses have suggested de novo gene formation of microsporidian-specific genes, we found evidence for the origin of new genes from noncoding sequence since the divergence of these populations. Some of these genes experience selective constraint, suggesting the evolution of new functions and local host adaptation. Combining our data with published microsporidian genomes, we show that nucleotide composition across the phylum is shaped by a mutational bias favoring A and T nucleotides, which is opposed by an evolutionary force favoring an increase in genomic GC content. This study reveals ongoing dramatic reorganization of genome structure and the evolution of new gene functions in modern microsporidians despite extensive genomic streamlining in their common ancestor.

The genome of Spraguea lophii and the basis of host-microsporidian interactions

Microsporidia are obligate intracellular parasites with the smallest known eukaryotic genomes. Although they are increasingly recognized as economically and medically important parasites, the molecular basis of microsporidian pathogenicity is almost completely unknown and no genetic manipulation system is currently available. The fish-infecting microsporidian Spraguea lophii shows one of the most striking host cell manipulations known for these parasites, converting host nervous tissue into swollen spore factories known as xenomas. In order to investigate the basis of these interactions between microsporidian and host, we sequenced and analyzed the S. lophii genome. Although, like other microsporidia, S. lophii has lost many of the protein families typical of model eukaryotes, we identified a number of gene family expansions including a family of leucine-rich repeat proteins that may represent pathogenicity factors. Building on our comparative genomic analyses, we exploited the large numbers of spores that can be obtained from xenomas to identify potential effector proteins experimentally. We used complex-mix proteomics to identify proteins released by the parasite upon germination, resulting in the first experimental isolation of putative secreted effector proteins in a microsporidian. Many of these proteins are not related to characterized pathogenicity factors or indeed any other sequences from outside the Microsporidia. However, two of the secreted proteins are members of a family of RICIN B-lectin-like proteins broadly conserved across the phylum. These proteins form syntenic clusters arising from tandem duplications in several microsporidian genomes and may represent a novel family of conserved effector proteins. These computational and experimental analyses establish S. lophii as an attractive model system for understanding the evolution of host-parasite interactions in microsporidia and suggest an important role for lineage-specific innovations and fast evolving proteins in the evolution of the parasitic microsporidian lifecycle.

Microsporidia are unusual intracellular parasites that infect a broad range of animal cells. In comparison to their fungal relatives, microsporidian genomes have shrunk during evolution, encoding as few as 2000 proteins. This minimal molecular repertoire makes them a reduced model system for understanding host-parasite interactions. A number of microsporidian genomes have now been sequenced, but the lack of a system for genetic manipulation makes it difficult to translate these data into a better understanding of microsporidian biology. Here we present a deep sequencing project of Spraguea lophii, a fish-infecting microsporidian that is abundantly available from environmental samples. We use our sequence data combined with germination protocols and complex-mix proteomics to identify proteins released by the cell at the earliest stage of germination, representing potential pathogenicity factors. We profile the RNA expression pattern of germinating cells and identify a set of highly transcribed hypothetical genes. Our study provides new insight into the importance of uncharacterized, lineage-specific and/or fast evolving proteins in microsporidia and provides new leads for the investigation of virulence factors in these enigmatic parasites.