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DNA Barcoding of Apicomplexa: Mitochondrial Evolution across the Phylum

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Title: DNA Barcoding of Apicomplexa: Mitochondrial Evolution across the Phylum
Author: Ogedengbe, Mosunmola Elina
Department: Department of Pathobiology
Program: Pathobiology
Advisor: Barta, R. John
Abstract: The parasitic phylum Apicomplexa contains thousands of species identified historically using morphology, morphometrics and host/tissue associations. Diagnostic stages of apicomplexan parasites are difficult to identify morphologically; thus, classical methods were supplemented with molecular techniques. Broadly applicable molecular markers that could support species identification and phylogenetic studies were sorely needed. “DNA barcoding” utilizes short, standardized DNA sequence obtained from the mitochondrial (mt) cytochrome c oxidase subunit I (COI) gene. Lack of PCR primers suitable for apicomplexan parasites limited mt COI use. Research reported herein tested utility of mt COI sequences for identification and phylogenetics of tissue (i.e. Sarcocystidae), eimeriid (e.g. Eimeriidae, Lankesterellidae) and adeleid coccidia (i.e. Hepatozoon and other haemogregarines). Degenerate primers of broad specificities generated mt COI DNA barcodes that, with few exceptions (notably Cystoisospora spp.), identified any enteric (e.g. Isospora, Cyclospora, Eimeria) or tissue (e.g. Toxoplasma, Hammondia, Sarcocystis) coccidium. The mt COI locus is recommended as a suitable DNA barcoding target for coccidian parasites of veterinary and zoonotic importance. Complete mt genomes of >20 eimeriid and adeleid coccidia were sequenced. More 17 species representing 6 genera of eimeriid (Eimeria, Isospora, Caryospora, Cyclospora, Lankesterella) and adeleid coccidia (Hepatozoon catesbianae) were sequenced. Eimeriid mt genomes (~ 6,000 bases) are predominantly circular-mapping possessing 3 protein-coding genes (CDS) and rDNA fragments in conserved order; only Cyclospora cayetanensis, a human pathogen, had a linear mt genome possessing a 5´-terminal hairpin and 3´-terminus with telomere-like repetitive elements. Gene orders and directions were largely conserved within, but divergent between, major groups of apicomplexan parasites. Phylogenetic analyses using mt CDS sequences (i.e. partial mt COI or concatenated CDS sequences) with or without nuclear 18S rDNA sequences suggest combined nu 18S rDNA and mt COI sequences (analysed using partitioned data with suitable nucleotide substitution models for each partition) provide robust evolutionary hypotheses for these parasites. Taxonomic solutions addressing paraphylies identified in phylogenetic analyses were proposed. The mt genomes of Apicomplexa possess divergent structures and gene arrangements. Mitochondrial COI sequences were concluded to be better species-level markers than the widely used nu 18S rDNA locus; mt COI sequences had utility in both diagnostic and phylogenetic studies.
URI: http://hdl.handle.net/10214/9097
Date: 2015-08
Rights: Attribution-NonCommercial-NoDerivs 2.5 Canada
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Attribution-NonCommercial-NoDerivs 2.5 Canada Except where otherwise noted, this item's license is described as Attribution-NonCommercial-NoDerivs 2.5 Canada