Selective Sweep of a cis-Regulatory Sequence in a Non-African Population of Drosophila melanogaster

Abstract

Although it is thought that changes in gene expression play an important role in adaptation, the identification of gene-regulatory sequences that have been targets of positive selection has proved difficult. Here, we identify a cis-regulatory element of the Drosophila melanogaster CG9509 gene that is associated with a selective sweep in a derived non-African population of the species. Expression analyses indicate that CG9509 consistently shows greater expression in non-African than in African strains of D. melanogaster. We find that a 1.8 kb region located just upstream of the CG9509 coding region is devoid of DNA sequence polymorphism in a European population sample and that this is best explained by the recent action of positive selection (within the past 4,000-10,000 years). Using a reporter gene construct and phiC31-mediated site-specific integration, we show that the European version of the CG9509 upstream region drives 2-3 times greater expression than the African version in an otherwise identical genetic background. This expression difference corresponds well to that of the native gene and indicates that sequence variation within the CG9509 upstream region can completely account for its high expression in the European population. Selection appears to have favored a quantitative increase in gene expression in the Malphigian tubule, the tissue where CG9509 is predominantly expressed.

A cis-regulatory sequence driving metabolic insecticide resistance in mosquitoes: Functional characterisation and signatures of selection

“…(Catania et al, 2004;Karasov et al, 2010;Lynd et al, 2010;Saminadin-Peter et al, 2012). Through cloning and sequencing of the region upstream of CYP9M10 in field populations we have shown that sequence identical to that found in the ISOP450 strain can be found in Ghana, Malawi, Zambia and Uganda.…”

Adaptive divergence of a transcriptional enhancer between populations ofDrosophila melanogaster

“…One gene that shows a large and consistent expression difference between African and non-African flies of both sexes is CG9509 [9,41,44]. The specific function of this gene in D. melanogaster is unknown, although sequence homology has led to it being annotated as a choline dehydrogenase [45].…”

“…We find that sequence polymorphism is very low in all . The Zimbabwe and The Netherlands populations were used in a previous study of sequence and expression variation associated with the CG9509 enhancer region [44], as well as in previous genome-wide studies [29,35,36,47]. The Malaysian population also was used in previous genome-wide demographic studies [31,48].…”

“…For each line, DNA was extracted from a single male fly using the MasterPure DNA Purification Kit (Epicentre). PCR was performed under standard conditions using four primer pairs published in Saminadin-Peter et al [44] and one additional reverse primer (5 0 -AGCTGCAAGCAGA ACCGTAT-3 0 ). The amplified region consisted of 1.2 kb of intergenic sequence, ranging from the stop codon of CG14406 to the start codon of CG9509.…”

“…Experiments using a transgenic reporter gene have shown that the twofold to threefold CG9509 expression difference observed between flies from The Netherlands and Zimbabwe is caused by sequence variation in a 1.2-kb enhancer located just upstream of the CG9509 coding region (figure 1) [44]. Within this region, there are nine sites that show a fixed or nearly fixed difference between the cosmopolitan and the sub-Saharan African populations (figure 4 figure 4).…”