Metchnikovellids (Microsporidia: Metchnikovellida) are poorly studied hyperparasitic micro-sporidia that live in gregarines inhabiting the intestines of marine invertebrates, mostly poly-chaetes. Our recent studies showed that the diversity of the metchnikovellids might be signifi-cantly higher than previously thought, even within a single host. Four species of metchnikovellids were found in the gregarines inhabiting the gut of the polychaete Pygospio elegans from littoral populations of the White and Barents Seas: the eugregarine Polyrhabdina pygospionis is the host for Metchnikovella incurvata and M. spiralis, while the archigregarine Selenidium pygospionis is the host for M. dogieli and M. dobrovolskiji. The most common species in the White Sea is M. in-curvata, while M. dobrovolskiji prevails in the Barents Sea. The gregarines within a single worm could be infected with different metchnikovellid species. However, co-infection of one and the same gregarine with several species of metchnikovellids has never been observed. The difference in prevalence and intensity of metchnikovellid invasion apparently depends on the features of the life cycle and on the development strategies of individual species.

The microsporidium Nosema ceranae is a high prevalent parasite of the European honey bee (Apis mellifera). This parasite is spreading across the world into its novel host. The developmental process and some mechanisms of N. ceranae infected honey bees has been studied thoroughly, however, few studies have been carried out in the mechanism of gene expression in N. ceranae during infection process. We therefore performed suppressive subtractive hybridization (SSH) approach to investigate the candidate genes of N. ceranae during its infection process. Each 96 clones of infected (forward) and non-infected (reverse) library were dipped onto the membrane for hybridization. A total of 118 differentially expressed sequence tags (ESTs) had been sequenced. For the host responses, 20% of ESTs (13 ESTs, 10 genes and 1 non-coding RNA) from forward library and 83% of ESTs (44 ESTs, 28 genes) from reverse library were identified as differentially expressed genes (DEGs) of the hosts. High percentage of DEGs involved in catalytic activity and metabolic processes, revealed the host gene expression change after N. ceranae infection might lead to the unbalance of physiological mechanism. Among the ESTs from forward library, 75.4% ESTs (49 ESTs belonged to 24 genes) were identified as N. ceranae genes. Of 24 N. ceranae genes, nine DEGs were subjected to real-time quantitative reverse transcription PCR (real-time qRT-PCR) for validation. The results indicated that these genes showed highly up-regulated during N. ceranae infection. Among nine N. ceranae genes, one N. ceranae gene (AAJ76_1600052943) showed the highest expression level after infection. These identified differentially expressed genes from this SSH could provide information about the pathological effects of N. ceranae. Validation of nine up-regulated N. ceranae genes revealed highly potential for the detection of early nosemosis in the field and provide insight for further applications.

With nearly 1,700 species, Microsporidia represent a group of obligate intracellular eukaryotes with veterinary, economic and medical impacts. To help in understanding the biological functions of these microorganisms, complete genome sequencing is used routinely. Nevertheless, the proper prediction of their gene catalogue is challenging due to taxon-specific evolutionary features. As innovative genome annotation strategies are needed to obtain a representative snapshot of the overall lifestyle of these parasites, the MicroAnnot tool, a dedicated workflow for microsporidian sequence annotation using data from curated databases of accurately annotated microsporidian genes, has been developed. Furthermore, specific modules have been implemented to perform small genes (< 300bp) and transposable element identification. Finally, functional annotation was performed using the signature-based InterProScan software. MicroAnnot’s accuracy has been verified by the re-annotation of four microsporidian genomes for which structural annotation had previously been validated. With its comparative approach and transcriptional signal identification method, MicroAnnot provides accurate prediction of translation initiation sites, efficient identification of transposable elements, as well as high specificity and sensitivity for microsporidian genes including those under 300 bp. Thanks to its web interface (https://microannot.org), MicroAnnot is available to the community to ensure high quality annotation of microsporidian genomes.