Computational protocol: Genotyping and comparative pathology of Spirocerca in black-backed jackals (Canis mesomelas) in South Africa

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Protocol publication

[…] Larvae that were collected from the subintimal surface of the thoracic aorta as well as from peri-aortic nodules were submitted in 95% ethanol to the Department of Genetics, University of Pretoria, for genotyping. Previously published protocols were used for the deoxyribonucleic acid (DNA) extraction, polymerase chain reaction (PCR) amplification and sequencing []. Polymorphic forward primers of nine microsatellite loci for S. lupi from domestic dogs were labeled fluorescently. After combining the nine primer sets into a single multiplex reaction, the Quantitect Multiplex PCR kit (Qiagen) was used according to the manufacturer’s protocol. An ABI3500xl Genetic Analyser (Applied Biosystems), using GeneScan LIZ500 Internal Size Standard (Applied Biosystems) was used to separate and measure all allele sizes. By evaluating chromatograms in GeneMarker™ version 2.4.0. (SoftGenetics LLC), the genotype of each individual larva was established. Following published protocols, using the program Arlequin version 3.5.1, pairwise FST values were calculated from larvae collected from jackals and from dogs from three different provinces in South Africa []. […]

Pipeline specifications

Software tools GeneMarker, Arlequin
Application Population genetic analysis
Organisms Caenorhabditis elegans, Spirocerca lupi, Canis lupus familiaris, Canis latrans
Diseases Aortic Aneurysm, Aortic Diseases, Infection, Spondylitis