Genomic DNA was extracted with various standard procedures, and specimens were identified to species and molecular forms by PCR-RFLP [38 (
link),39 (
link)].
SINE200 elements were located
in silico by BLASTN searches on the genome sequence of the
A. gambiae PEST genome using the obtained
SINE200 consensus sequence as a query. Thirteen
SINE200 insertions lying within the
A. gambiae molecular form speciation islands (
sensu Turner [11 (
link)]) on X, 2L and 2R chromosomes, and characterized by the presence of 500 bp flanking regions showing a single hit in the genome, were selected. Primers were designed to amplify across the element using Primer 3 software [40 (
link)]. The selected loci were named '
S200' followed by the abbreviation of the chromosomal arm (2L, 2R, X), by a number/letter corresponding to the chromosomal location on the cytogenetic map [4 (
link)] and by an additional number aimed to distinguish primer sets positioned on the same chromosome division. Genes annotated within a 20 Kb genome sequence including
SINE200 insertions for each locus were retrieved from the PEST genome ver. Agam P3 Feb. 2006 (Table
2).
PCR reactions were carried out in a 25 μl reaction which contained 1 pmol of each primer, 0.2 mM of each dNTP, 1.5 mM MgCl2, 2.5 U Taq polymerase, and 0.5 μl of template DNA extracted from a single mosquito. Thermocycler conditions were 94°C for 10 min followed by thirty-five cycles of 94°C for 30 s, 54°C for 30 s and 72°C for 1 min., with a final elongation at 72°C for 10 min, and a 4°C hold. The resulting products were analysed on 1.5% agarose gels stained with ethidium bromide, with low and high molecular weight bands corresponding to fragments containing or lacking the targeted
SINE200, respectively.
PCR products representing 'filled' and 'empty' sites of
S200 X6.1 locus on X chromosome were sequenced on both strands using ABI Big Dye Terminator v.2 chemistry and an ABI Prism 3700 DNA Analyser. Multiple alignments were performed using ClustalX [37 (
link)]. All sequences were deposited in GenBank under accession numbers
EU881868–
EU881887.
Indices of polymorphism (i.e.
SINE200 insertion frequency and heterozygosity) and differentiation (
Fst) at polymorphic loci were computed using
Fstat 2.9.3.2 [41 ]. Significance was tested with Bonferroni-adjusted
P-values, using the randomization approach implemented in
Fstat.
Santolamazza F., Mancini E., Simard F., Qi Y., Tu Z, & della Torre A. (2008). Insertion polymorphisms of SINE200 retrotransposons within speciation islands of Anopheles gambiae molecular forms. Malaria Journal, 7, 163.