Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi.

Eukaryot Cell
Authors
Keywords
Abstract

Microsporidia from the Encephalitozoonidae are obligate intracellular parasites with highly conserved and compacted nuclear genomes: they have few introns, short intergenic regions, and almost identical gene complements and chromosome arrangements. Comparative genomics of Encephalitozoon and microsporidia in general have focused largely on the genomic diversity between different species, and we know very little about the levels of genetic diversity within species. Polymorphism studies with Encephalitozoon are so far restricted to a small number of genes, and a few genetically distinct strains have been identified; most notably, three genotypes (ECI, ECII, and ECIII) of the model species E. cuniculi have been identified based on variable repeats in the rRNA internal transcribed spacer (ITS). To determine if E. cuniculi genotypes are genetically distinct lineages across the entire genome and at the same time to examine the question of intraspecies genetic diversity in microsporidia in general, we sequenced de novo genomes from each of the three genotypes and analyzed patterns of single nucleotide polymorphisms (SNPs) and insertions/deletions across the genomes. Although the strains have almost identical gene contents, they harbor large numbers of SNPs, including numerous nonsynonymous changes, indicating massive intraspecies variation within the Encephalitozoonidae. Based on this diversity, we conclude that the recognized genotypes are genetically distinct and propose new molecular markers for microsporidian genotyping.

Year of Publication
2013
Journal
Eukaryot Cell
Volume
12
Issue
4
Pages
503-11
Date Published
2013 Apr
ISSN
1535-9786
URL
DOI
10.1128/EC.00312-12
PubMed ID
23291622
PubMed Central ID
PMC3623445
Links
Grant list
HHSN272200900018C / AI / NIAID NIH HHS / United States
HHSN272200900018C / PHS HHS / United States
MOP-42517 / Canadian Institutes of Health Research / Canada
R01 AI031788 / AI / NIAID NIH HHS / United States
NIAID AI31788 / PHS HHS / United States