Comparative genomic analyses of Entamoeba species


Wilson, Ian ORCID: 0000-0001-7303-164X Comparative genomic analyses of Entamoeba species. PhD thesis, University of Liverpool.

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Abstract

Amoebiasis is the third-most common cause of mortality worldwide from a disease borne of a parasitic infection. It affects up to 50 million people annually, of which 40,000 to 100,000 cases are fatal. Entamoeba histolytica is an obligate protozoon parasite of humans and is the aetiological agent of the disease. Recent suggestions that other members of the Entamoeba genus are human-infective, and potentially pathogenic, have been investigated here. A draft assembly and annotation of the 25 Mb genome of E. moshkovskii strain Laredo is presented, to which multiple E. moshkovskii strains were mapped. The E. moshkovskii genome was found to be approximately 200 times more variable than that of E. histolytica. Performance of the four-haplotype test revealed that genetic recombination does not seem to occur in E. moshkovskii. As such, it is suggested that it be referred to as a ‘species complex’, rather than an individual species. A comparative genomic analysis of E. histolytica HM-1:IMSS, E. moshkovskii Laredo, E. invadens IP-1 and the avirulent E. dispar SAW760 was performed. Subsequent comparative analyses against members of genera representative of the diversity in the Unikonts clade enabled the identification of orthologous gene families unique to the Entamoeba genus. Analysis of virulence factors within this set revealed that gene families involved in adhesion of amoebic trophozoites to host cells play a key role in the development of invasive amoebiasis. The Gal/GalNAc lectins and members of the BspA family are of particular interest, being present in all analysed species, except for E. dispar. The presence of these key families, plus cysteine proteases, in the E. moshkovskii genome suggests that some sequence types within this species complex may be pathogenic. E. invadens was found to possess larger numbers of more variable genes within many virulence factor families, including the BspA family and the Gal/GalNAc lectins. This suggests that sequence diversity facilitates E. invadens’ polyxenous lifestyle. Finally, a novel species recently isolated from a human faecal sample - E. bangladeshi, strain 8237 – was sequenced. Its genome was assembled using multiple de novo genome assemblers and coding sequences were assembled individually. A combination of all methods tested was found to be beneficial in maximising the number of gene sequences assembled, which is advised as good practice in future similar assemblies. The phylogeny of E. bangladeshi, achieved using the combined assemblies’ outputs suggested that the novel species is human-infective. The work presented here utilised modern comparative genomic techniques to improve understanding of Entamoeba species, their capacity for causing disease and their potential impact upon the epidemiology of amoebiasis.

Item Type: Thesis (PhD)
Additional Information: Date: 2014-09 (completed)
Subjects: ?? Q1 ??
Depositing User: Symplectic Admin
Date Deposited: 13 Aug 2015 12:18
Last Modified: 16 Dec 2022 04:43
DOI: 10.17638/02007270
URI: https://livrepository.liverpool.ac.uk/id/eprint/2007270
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