Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems

Abstract

Fungal species play extremely important roles in ecosystems. Clustered at the base of the fungal kingdom are Microsporidia, a group of obligate intracellular eukaryotes infecting multiple animal lineages. Because of their large host spectrum and their implications in host population regulation, they influence food webs, and accordingly, ecosystem structure and function. Unfortunately, their ecological role is not well understood. Present also as highly resistant spores in the environment, their characterisation requires special attention. Different techniques based on direct isolation and/or molecular approaches can be considered to elucidate their role in the ecosystems, but integrating environmental and genomic data (for example, genome architecture, core genome, transcriptional and translational signals) is crucial to better understand the diversity and adaptive capacities of Microsporidia. Here, we review the current status of Microsporidia in trophic networks; the various genomics tools that could be used to ensure identification and evaluate diversity and abundance of these organisms; and how these tools could be used to explore the microsporidian life cycle in different environments. Our understanding of the evolution of these widespread parasites is currently impaired by limited sampling, and we have no doubt witnessed but a small subset of their diversity.

The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites

“…G. muris appears to fall into this category as it encodes no known classes of mobile elements and repetitive elements are mostly confined to telomeric contexts. The shortness of intergenic regions in G. muris ranks among the most extreme recorded for any eukaryote, even shorter than Microsporidia, which are known as the most compact and reduced eukaryotic genomes [67]. The global synteny map of G. muris to G. intestinalis indicates many frequent small-scale genome rearrangements that often favours a more efficient gene packing in G. muris, thus allowing shorter intergenic regions.…”

Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes

“…Microsporidia are spore-forming, single-celled fungal pathogens best known for their unique infection apparatus called the polar tube and for harboring species with the smallest reported nuclear genomes. Microsporidia as a group are highly diverse, with more than 1,500 distinct species infecting vertebrate and invertebrate hosts widely spread across the Tree of Life, and cause growing concerns due to their medical, environmental and economic relevance [ 1 ]. Their diversity is reflected at the genetic level, as the extreme levels of reduction encountered in the Encephalitozoon lineage [ 2 – 5 ] are not characteristic of the group.…”

Microsporidia: Eukaryotic Intracellular Parasites Shaped by Gene Loss and Horizontal Gene Transfers

“…have also lost noncoding regions (introns and intergenic regions), resulting in genomes that are ultracompressed and have a median intergenic length of approximately 80 bp (65). Investigators have proposed that this compression affected RNA transcription in these parasites, given that microsporidian RNA molecules are sometimes found to overlap several genes on different strands (10,11,67,96).…”