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Eukaryot Cell DOI:10.1128/EC.00312-12

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

Publication TypeJournal Article
Year of Publication2013
AuthorsPombert, J-F, Xu, J, Smith, DR, Heiman, D, Young, S, Cuomo, CA, Weiss, LM, Keeling, PJ
JournalEukaryot Cell
Date Published2013 Apr
KeywordsAmino Acid Sequence, Chromosome Mapping, DNA, Intergenic, Encephalitozoon cuniculi, Genetic Markers, Genome, Fungal, Genotype, Genotyping Techniques, Molecular Sequence Data, Mutagenesis, Insertional, Phylogeny, Polymorphism, Single Nucleotide, Sequence Alignment, Sequence Analysis, DNA, Sequence Deletion

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.


Alternate JournalEukaryotic Cell
PubMed ID23291622
PubMed Central IDPMC3623445
Grant ListHHSN272200900018C / 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