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    Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity.

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    Author
    Palmateer, Nicholas C
    Tretina, Kyle
    Orvis, Joshua
    Ifeonu, Olukemi O
    Crabtree, Jonathan
    Drabék, Elliott
    Pelle, Roger
    Awino, Elias
    Gotia, Hanzel T
    Munro, James B
    Tallon, Luke
    Morrison, W Ivan
    Daubenberger, Claudia A
    Nene, Vish
    Knowles, Donald P
    Bishop, Richard P
    Silva, Joana C
    Show allShow less

    Date
    2020-10-29
    Journal
    PLoS Neglected Tropical Diseases
    Publisher
    Public Library of Science
    Type
    Article
    
    Metadata
    Show full item record
    See at
    https://doi.org/10.1371/journal.pntd.0008781
    Abstract
    Theileria parva is an economically important, intracellular, tick-transmitted parasite of cattle. A live vaccine against the parasite is effective against challenge from cattle-transmissible T. parva but not against genotypes originating from the African Cape buffalo, a major wildlife reservoir, prompting the need to characterize genome-wide variation within and between cattle-and buffalo-associated T. parva populations. Here, we describe a capture-based tar-get enrichment approach that enables, for the first time, de novo assembly of nearly com-plete T. parva genomes derived from infected host cell lines. This approach has exceptionally high specificity and sensitivity and is successful for both cattle-and buffalo-derived T. parva parasites. De novo genome assemblies generated for cattle genotypes differ from the reference by ~54K single nucleotide polymorphisms (SNPs) throughout the 8.31 Mb genome, an average of 6.5 SNPs/kb. We report the first buffalo-derived T. parva genome, which is ~20 kb larger than the genome from the reference, cattle-derived, Muguga strain, and contains 25 new potential genes. The average non-synonymous nucleotide diversity (πN) per gene, between buffalo-derived T. parva and the Muguga strain, was 1.3%. This remarkably high level of genetic divergence is supported by an average Wright’s fixa-tion index (FST), genome-wide, of 0.44, reflecting a degree of genetic differentiation between cattle-and buffalo-derived T. parva parasites more commonly seen between, rather than within, species. These findings present clear implications for vaccine development, further demonstrated by the ability to assemble nearly all known antigens in the buffalo-derived strain, which will be critical in design of next generation vaccines. The DNA capture approach used provides a clear advantage in specificity over alternative T. parva DNA enrichment methods used previously, such as those that utilize schizont purification, is less labor intensive, and enables in-depth comparative genomics in this apicomplexan parasite. © 2020 Palmateer et al.
    Keyword
    Cattle
    Buffaloes
    Theileria parva
    Parasites
    Ticks
    DNA
    Genomics
    Vaccines
    Identifier to cite or link to this item
    http://hdl.handle.net/10713/14066
    ae974a485f413a2113503eed53cd6c53
    10.1371/journal.pntd.0008781
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