Genetic and Genome Analyses Reveal Genetically Distinct Populations of the Bee Pathogen Nosema ceranae from Thailand

Development of a ptp2-LAMP assay for the specific and sensitive detection of Nosema apis and its comparison with ptp3-LAMP for the detection of Nosema ceranae, in a region endemic for both microsporidium pathogens of the Western honey bee

The Western honey bee plays a pivotal role in global food security as the primary commercial pollinator. The microsporidian pathogens Nosema apis and Nosema ceranae infect the bee midgut, causing nosemosis, a debilitating infectious disease that results in considerable economic losses in apiculture. Traditionally, Nosema spp. infection is diagnosed by microscopic detection and quantification of spores. However, only molecular diagnostics allow differentiation between N. apis and N. ceranae. Loop-mediated isothermal amplification (LAMP) is a rapid, highly specific, and sensitive DNA detection method. The present study aimed to develop a LAMP protocol for N. apis based on the species-specific single copy polar tube protein 2 (ptp2) gene, and to analyze and compare its diagnostic performance with the previously developed polar tube protein 3 (ptp3) gene-based LAMP protocol for N. ceranae. The ptp2- and ptp3-LAMP assays specifically identified N. apis and N. ceranae, respectively. Their analytical sensitivity was tested using serial dilutions of plasmid and genomic DNA, demonstrating that ptp2- and ptp3-LAMP consistently detected down to 103ptp2 and 104ptp3-gene copies, respectively. Amplification was verified by agarose gel electrophoresis (conventional format), and by a change from pink to yellow color after addition of a suitable dye (colorimetric format). The ptp2- and ptp3-LAMP assays and a reference duplex PCR were applied to a panel of field samples (n = 55) from a region endemic for both Nosema spp. Conventional and colorimetric ptp2-LAMP showed an almost perfect test agreement (kappa value > 0.81) compared with duplex PCR. Conventional and colorimetric ptp3-LAMP assays showed a substantial (kappa value > 0.60) and almost perfect test agreement (kappa value > 0.81), respectively. The ptp2- and ptp3-LAMP assays provide excellent performance, ease of implementation, cost savings, and rapid execution, making them ideal choices for molecular detection and differentiation of N. apis and N. ceranae.

Bioinformatics analysis of the Microsporidia sp. MB genome: a malaria transmission-blocking symbiont of the Anopheles arabiensis mosquito

BACKGROUND

The use of microsporidia as a disease-transmission-blocking tool has garnered significant attention. Microsporidia sp. MB, known for its ability to block malaria development in mosquitoes, is an optimal candidate for supplementing malaria vector control methods. This symbiont, found in Anopheles mosquitoes, can be transmitted both vertically and horizontally with minimal effects on its mosquito host. Its genome, recently sequenced from An. arabiensis, comprises a compact 5.9 Mbp.

RESULTS

Here, we analyze the Microsporidia sp. MB genome, highlighting its major genomic features, gene content, and protein function. The genome contains 2247 genes, predominantly encoding enzymes. Unlike other members of the Enterocytozoonida group, Microsporidia sp. MB has retained most of the genes in the glycolytic pathway. Genes involved in RNA interference (RNAi) were also identified, suggesting a mechanism for host immune suppression. Importantly, meiosis-related genes (MRG) were detected, indicating potential for sexual reproduction in this organism. Comparative analyses revealed similarities with its closest relative, Vittaforma corneae, despite key differences in host interactions.

CONCLUSION

This study provides an in-depth analysis of the newly sequenced Microsporidia sp. MB genome, uncovering its unique adaptations for intracellular parasitism, including retention of essential metabolic pathways and RNAi machinery. The identification of MRGs suggests the possibility of sexual reproduction, offering insights into the symbiont's evolutionary strategies. Establishing a reference genome for Microsporidia sp. MB sets the foundation for future studies on its role in malaria transmission dynamics and host-parasite interactions.

Geographic population structure of the honeybee microsporidian parasite Vairimorpha (Nosema) ceranae in the South West Indian Ocean

The microsporidian Vairimorpha (Nosema) ceranae is one of the most common parasites of the honeybee. A single honeybee carries many parasites and therefore multiple alleles of V. ceranae genes that seem to be ubiquitous. As a consequence, nucleotide diversity analyses have not allowed discriminating genetic structure of parasite populations. We performed deep loci-targeted sequencing to monitor the haplotype frequencies of genome markers in isolates from discontinuous territories, namely the tropical islands of the South West Indian Ocean. The haplotype frequency distribution corroborated the suspected tetraploidy of the parasite. Most major haplotypes were ubiquitous in the area but with variable frequency. While oceanic isolates differed from European and Asian outgroups, parasite populations from distinct archipelagoes also differed in their haplotype distribution. Interestingly an original and very divergent Malagasy isolate was detected. The observed population structure allowed formulating hypotheses upon the natural history of V. ceranae in this oceanic area. We also discussed the usefulness of allelic distribution assessment, using multiple informative loci or genome-wide analyses, when parasite population is not clonal within a single host.

Honey Bee Habitat Sharing Enhances Gene Flow of the Parasite Nosema ceranae

Host-parasite co-evolution is a process of reciprocal, adaptive genetic change. In natural conditions, parasites can shift to other host species, given both host and parasite genotypes allow this. Even though host-parasite co-evolution has been extensively studied both theoretically and empirically, few studies have focused on parasite gene flow between native and novel hosts. Nosema ceranae is a native parasite of the Asian honey bee Apis cerana, which infects epithelial cells of mid-guts. This parasite successfully switched to the European honey bee Apis mellifera, where high virulence has been reported. In this study, we used the parasite N. ceranae and both honey bee species as model organisms to study the impacts of two-host habitat sharing on parasite diversity and virulence. SNVs (Single Nucleotide Variants) were identified from parasites isolated from native and novel hosts from sympatric populations, as well as novel hosts from a parapatric population. Parasites isolated from native hosts showed the highest levels of polymorphism. By comparing the parasites isolated from novel hosts between sympatric and parapatric populations, habitat sharing with the native host significantly enhanced parasite diversity, suggesting there is continuing gene flow of parasites between the two host species in sympatric populations.

Comparative Genomics of Microsporidia

The microsporidia are a phylum of intracellular parasites that represent the eukaryotic cell in a state of extreme reduction, with genomes and metabolic capabilities embodying eukaryotic cells in arguably their most streamlined state. Over the past 20 years, microsporidian genomics has become a rapidly expanding field starting with sequencing of the genome of Encephalitozoon cuniculi, one of the first ever sequenced eukaryotes, to the current situation where we have access to the data from over 30 genomes across 20+ genera. Reaching back further in evolutionary history, to the point where microsporidia diverged from other eukaryotic lineages, we now also have genomic data for some of the closest known relatives of the microsporidia such as Rozella allomycis, Metchnikovella spp. and Amphiamblys sp. Data for these organisms allow us to better understand the genomic processes that shaped the emergence of the microsporidia as a group. These intensive genomic efforts have revealed some of the processes that have shaped microsporidian cells and genomes including patterns of genome expansions and contractions through gene gain and loss, whole genome duplication, differential patterns of invasion and purging of transposable elements. All these processes have been shown to occur across short and longer time scales to give rise to a phylum of parasites with dynamic genomes with a diversity of sizes and organisations.

MicroRNA-6498-5p Inhibits Nosema bombycis Proliferation by Downregulating BmPLPP2 in Bombyx mori

As microRNAs (miRNAs) are important expression regulators of coding RNA, it is important to characterize their role in the interaction between hosts and pathogens. To obtain a comprehensive understanding of the miRNA alternation in Bombyx mori (B. mori) infected with Nosema bombycis (N. bombycis), RNA sequencing and stem-loop qPCR were conducted to screen and identify the significantly differentially expressed miRNAs (DEmiRNAs). A total of 17 such miRNAs were identified in response to N. bombycis infection, among which miR6498-5p efficiently inhibited the proliferation of N. bombycis in BmE-SWU1 (BmE) cells by downregulating pyridoxal phosphate phosphatase 2 (BmPLPP2). In addition, a fluorescence in situ hybridization (FISH) assay showed that miR6498-5p was located in the cytoplasm of BmE cells, while it was not found in the schizonts of N. bombycis. Further investigation of the effect of BmPLPP2 on the proliferation of schizonts found that the positive factor BmPLPP2 could facilitate N. bombycis completing its life cycle in cells by overexpression and RNAi of BmPLPP2. Our findings offer multiple new insights into the role of miRNAs in the interaction between hosts and microsporidia.

Polyploidy: an evolutionary and ecological force in stressful times

Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.