Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in > 20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.
Vinculin is thought to be an important cytoskeletal protein in the linkage between actin cytoskeleton and integrin transmembrane receptors. We identified Vinculin (Vine) gene in the X chromosome of D. melanogaster. Drosophila vinculin is highly homologous in its N-and C-terminal domains both to mammalian and nematode vinculins, and contains internal repeats and proline-rich region typical for vinculins. The X chromosome rearrangement In(lLR)pn2a was found to disrupt Vine so that the coding sequence is interrupted by the (AAGAG)" satellite DNA. Northern analysis revealed that the Vine transcript is completely absent in the In(lLR)pn2a homozygous flies. Surprisingly, these Vine flies are viable and fertile. This finding highlights plasticity and adaptive capacity of cellular cytoskeletal and anchorage system. © 1997 Federation of European Biochemical Societies.
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