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Genomic diversity of the human intestinal parasite Entamoeba histolytica

Gareth D Weedall1, C Graham Clark2, Pia Koldkjaer1, Suzanne Kay1, Iris Bruchhaus3, Egbert Tannich3, Steve Paterson1 and Neil Hall1*

Author Affiliations

1 Institute of Integrative Biology, University of Liverpool, Biosciences building, Crown Street, Liverpool L69 7AH, UK

2 Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK

3 Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Str. 74, 20359 Hamburg, Germany

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Genome Biology 2012, 13:R38  doi:10.1186/gb-2012-13-5-r38

Published: 25 May 2012



Entamoeba histolytica is a significant cause of disease worldwide. However, little is known about the genetic diversity of the parasite. We re-sequenced the genomes of ten laboratory cultured lines of the eukaryotic pathogen Entamoeba histolytica in order to develop a picture of genetic diversity across the genome.


The extreme nucleotide composition bias and repetitiveness of the E. histolytica genome provide a challenge for short-read mapping, yet we were able to define putative single nucleotide polymorphisms in a large portion of the genome. The results suggest a rather low level of single nucleotide diversity, although genes and gene families with putative roles in virulence are among the more polymorphic genes. We did observe large differences in coverage depth among genes, indicating differences in gene copy number between genomes. We found evidence indicating that recombination has occurred in the history of the sequenced genomes, suggesting that E. histolytica may reproduce sexually.


E. histolytica displays a relatively low level of nucleotide diversity across its genome. However, large differences in gene family content and gene copy number are seen among the sequenced genomes. The pattern of polymorphism indicates that E. histolytica reproduces sexually, or has done so in the past, which has previously been suggested but not proven.