DOI: 10.5061/dryad.h44j0zpt3
title: Development of twenty-four microsatellite markers for Afrotropical Ornithodoros ticks

description: Background: Soft ticks of the genus Ornithodoros are responsible for the
 maintenance and transmission of the African swine fever (ASF) virus in the
 sylvatic and domestic viral cycles in Southern Africa. They are also the
 main vectors of Borrelia species causing relapsing fevers. Currently, no
 genetic markers are available for Afrotropical Ornithodoros ticks. As ASF
 spreads globally, such markers are needed to assess the role of ticks in
 the emergence of new outbreaks. The aim of this study was to design
 microsatellite markers that could be used for ticks of the Ornithodoros
 moubata complex, particularly Ornithodoros phacochoerus, to assess
 population structure and tick movements in ASF endemic areas. Methods: One
 hundred and fifty-one markers were designed using the O. moubata
 and O. porcinus genomes after elimination of repeated sequences
 in the genomes. All designed markers were tested on
 O. phacochoerus and O. porcinus DNA to select the best
 markers. Results: Twenty-four microsatellite markers were genotyped on two
 populations of O. phacochoerus and on few individuals from four
 other Ornithodoros species. Nineteen markers were selected to be as robust
 as possible for population genetic studies on O. phacochoerus.
 Conclusions: The microsatellite markers developed here represent the first
 genetic tool to study nidicolous populations of Afrotropical Ornithodoros.
 This dataset contains the genotyping results obtained for all twenty-four
 markers tested.
description: This dataset results from genotyping of twenty-four
 microsatellite loci on <em>Ornithodoros phacochoerus</em>
 ticks and on four other <em>Ornithodoros</em>
 species. Fluorescent-labeled forward primers (FAM, VIC,
 NED or PET) were used for the 24 microsatellite loci. Touchdown PCRs were
 performed in six multiplexes of four microsatellite loci each.
 The amplification mix consisted in 2 μL of DNA template, 10 μL of
 2x Type-it Microsatellite PCR Kit (Qiagen, Courtaboeuf, France), adjusted
 volume of fluorescence-labeled forward primer, and reverse primer for
 microsatellite loci, in a final volume of 20 μL. The touchdown PCR program
 was set as follows: 95°C for 3 min, then 10 cycles of 95°C for 20 sec,
 60°C -0.5°C/cycle, for 30 sec, and 72°C for 1 min, then 30 cycles of 95°C
 for 20 sec, 55°C for 30 sec, and 72°C for 1 min, followed by a final
 extension step at 72°C for 7 min. Formamide for
 denaturation and GeneScan-600 (LIZ) Size Standard Kit for ladder were
 added to the PCR products before genotyping by capillary electrophoresis
 at the GPTR laboratory (Great Regional Technical Platform of genotyping,
 AGAP Institut/CIRAD, Montpellier, France) with an ABI 3500xL Genetic
 Analyzer (Applied Biosystems, Foster City, CA, USA).
 Genotypes were read using GeneMapper® v.6 software (Applied
 Biosystems, Waltham, MA, USA). Allele bins were set manually after a
 review of all samples. Allele scoring was performed automatically
 according to the bin set designed for the marker, then manually checked by
 two different experimenters. Alleles were named according to their length
 in base pairs.
description: # Development of twenty-four microsatellite markers for Afrotropical
 Ornithodoros ticks ### Summary The three datasheets made available here
 result from the genotyping of twenty-four microsatellite loci on five
 *Ornithodoros* species.\ These datasheets can be transformed (using CREATE
 for instance) to be used in any population genetics software (Fstat,
 Genepop, Micro-Checker...). This dataset was used to test the robustness
 of twenty-four microsatellite loci for the species *Ornithodoros
 phacochoerus*. The microsatellite loci were also tested on four other
 *Ornithodoros* species (*O. moubata*, *O. porcinus*, *O. maritimus*, and
 *O. erraticus*) to assess specificity. ## Description of the data and file
 structure This dataset contains three different datasheets of genotyping
 results. Two of the datasheets present genotyping data from the species
 *O. phacochoerus*. *Ornithodoros phacochoerus* ticks came from two
 different sites: Coutada9 Game Reserve (pop 69) and Gorongosa National
 Park (pop G3) in Mozambique. The file names indicate which data are
 contained in the datasheet: * "Plex1-2-3_pop69etG3_19markers"
 contains the genotyping results for *O. phacochoerus* species (pop69etG3)
 from the 19 microsatellite loci that were selected to be as robust as
 possible. (Number of ticks tested n=58, 29 individuals *per* site) *
 "Plex1-2-3_pop69etG3_5markersDiscarded" contains the genotyping
 results for *O. phacochoerus* species (pop69etG3) from the 5
 microsatellite loci that were discarded due to lack of robustness in this
 species. (Number of ticks tested n=58, 29 individuals *per* site) *
 "Plex1-2-3_FourOtherSpecies\_ 24markers" contains the genotyping
 results for *O. moubata*, *O. porcinus*, *O. maritimus*, and *O.
 erraticus* species from all the 24 microsatellite loci. (Number of ticks
 tested n=8, 2 individual *per* species tested) Here is the detail of how
 the information were collected/registered/transformed for each variable:
 “Pop“: Site number for *O. phacochoerus* ticks (69 or G3). Was replaced by
 the species name for the four other species. “SampleName“: Individual
 unique identifier for each of the ticks. “NumPop“: Number associated with
 the "Pop" column for easier use in population genetics
 softwares. “Parc“: Name of the game reserve or national park from which
 *O. phacochoerus* ticks were collected. Was replaced by
 "AutreEspece" (OtherSpecies) for the four other species. “ms35“,
 "ms48", "ms59" etc...: Names of microsatellite loci
 that were tested. For each microsatellite locus, there is two columns, one
 for each allele detected in the tick. Alleles are named according to their
 size in base pair (for instance, individual 69_1 presents two alleles for
 microsatellite locus ms35, one allele which is 67 base pair long and one
 which is 71 base pair long) Empty cells: Empty cells were not filled with
 "null," or "n/a," due to interference with population
 genetics software. Empty cells occur either after no data was obtained for
 the genotyping of a tick at a microsatellite locus, or if the data were of
 low quality and did not allow correct reading of the peaks. Data files are
 in .txt format with tabulations as separators, they can be visualized
 using any software capable of handling .txt files (Excel, LibreOffice
 Calc, TextPad etc…). ## Sharing/Access information This dataset is
 associated with a paper entitled "**Development of microsatellite
 markers for Afrotropical Ornithodoros ticks"** submitted for
 peer-reviewing (no DOI available yet, DOI will be provided as soon as
 possible). ## Software The authors used this dataset by converting it to
 Fstat and Micro-Checker format using CREATE (Coombs, Letcher, and Nislow
 2008). Fstat v 2.9.4. was used to calculate Linkage disequilibrium
 p-values, observed heterozygosity, expected heterozygosity, Fis, and Fst.
 Micro-Checker (Van Oosterhout, Hutchinson, Wills, and Shipley 2004) was
 used to test for presence of null alleles, stuttering and short allele
 dominance.