| Summary: | Microsporidia are unicellular eukaryotes that are closely related to fungi. They are obligate intracellular parasites of diverse animals. Microsporidia possess some of the smallest eukaryotic primary nuclear genomes in existence. The human pathogen Encephalitozoon cuniculi has a fully sequenced genome, and at 2.9 Mbp, is at the smaller end of the 2.3 to 19.5 Mbp microsporidian range. E. cuniculi’s genome has undergone a process of reduction, and is characterized by short intergenic spaces, few introns and shorter genes compared to homologues in yeast.
A combined eight-gene dataset was employed in order to identify the closest fungal relative of microsporidia. All phylogenetic methods recovered microsporidia as a sister to a combined ascomycete and basidiomycete clade, but other options could not be rejected based on approximately unbiased (AU) tests. The effects of genome reduction on E. cuniculi’s DNA repair systems were examined by determining the presence or absence of the components of five evolutionarily conserved single and double strand repair pathways. While some individual proteins that participate in the single strand repair pathways were absent in E. cuniculi, the essential functional machinery of each pathway remained intact. However, integral proteins were absent from both double strand repair pathways, suggesting that E. cuniculi does not repair its double stranded DNA lesions by previously characterized mechanisms. E. cuniculi meront and spore transcripts were compared to examine differences in life cycle regulation of 5’ untranslated region (5’UTR) length and mRNA splicing. Spore transcripts are never spliced and have longer 5’UTRs that frequently overlap with upstream genes, meront transcripts are often spliced with shorter 5’UTRs that overlap less frequently with upstream genes. Large differences in transcriptional regulation exist between the spore and the meront, and the odd spore transcripts may be a byproduct sporulation. Transcription was examined in Edhazardia aedis, a microsporidian with a larger, non-compact genome. A large degree of similarity was found when clusters of orthologous groups of gene (COG) categories of unique transcripts of Ed. aedis and another distantly related species, Antonospora locustae were compared. In addition, we documented the first known case of transcription of a transposable element in a microsporidian.
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