Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines (original) (raw)

The Drosophila melanogaster Genetic Reference Panel

Nature, 2012

A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype–phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila

Cinderella of genetics (Drosophila melanogaster): Population genetics to genomics

Journal of entomology and zoology studies, 2021

Drosophila melanogaster is a well-studied and extremely efficacious genetic model organism in order to analyse several genetic processes common to higher organisms including humans. Little more than a few years back, Drosophila emerges as a prototype for the study of genomics and became the third eukaryote to be fully sequenced and used for the application of complete genome sequencing by whole-genome shotgun in eukaryotic genomes. Almost all of coding portion of the Drosophila genome (approximately 120-megabase) has been determined. Fifty years ago, molecular population genetics originated with the first allozyme loci estimation, progressed with the era of nucleotide sequencing, and are now in the age of population genomics. Many regulatory pathways are maintained in Drosophila compared to humans, making it a strong model for the study of epigenetic mechanisms. Many signalling pathways are conserved between humans and fly that's why various studies have been successfully conducted in D. melanogaster such as comparative genomics, disease mechanism, toxicogenomic studies, Immunogenetics studies. Here, we offer a brief description of the genetic history of Drosophila. We hope that an acknowledgement of how we got where we are today and an overview of past studies will help to position the current curiosity about molecular population genetics and genomics.

Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster

PloS one, 2012

The sequencing of pooled non-barcoded individuals is an inexpensive and efficient means of assessing genome-wide population allele frequencies, yet its accuracy has not been thoroughly tested. We assessed the accuracy of this approach on whole, complex eukaryotic genomes by resequencing pools of largely isogenic, individually sequenced Drosophila melanogaster strains. We called SNPs in the pooled data and estimated false positive and false negative rates using the SNPs called in individual strain as a reference. We also estimated allele frequency of the SNPs using ''pooled'' data and compared them with ''true'' frequencies taken from the estimates in the individual strains. We demonstrate that pooled sequencing provides a faithful estimate of population allele frequency with the error well approximated by binomial sampling, and is a reliable means of novel SNP discovery with low false positive rates. However, a sufficient number of strains should be used in the pooling because variation in the amount of DNA derived from individual strains is a substantial source of noise when the number of pooled strains is low. Our results and analysis confirm that pooled sequencing is a very powerful and costeffective technique for assessing of patterns of sequence variation in populations on genome-wide scales, and is applicable to any dataset where sequencing individuals or individual cells is impossible, difficult, time consuming, or expensive.

Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster

Genetics, 2005

Mutation is the underlying force that provides the variation upon which evolutionary forces can act. It is important to understand how mutation rates vary within genomes and how the probabilities of fixation of new mutations vary as well. If substitutional processes across the genome are heterogeneous, then examining patterns of coding sequence evolution without taking these underlying variations into account may be misleading. Here we present the first rigorous test of substitution rate heterogeneity in the Drosophila melanogaster genome using almost 1500 nonfunctional fragments of the transposable element DNAREP1_DM. Not only do our analyses suggest that substitutional patterns in heterochromatic and euchromatic sequences are different, but also they provide support in favor of a recombination-associated substitutional bias toward G and C in this species. The magnitude of this bias is entirely sufficient to explain recombination-associated patterns of codon usage on the autosomes of the D. melanogaster genome. We also document a bias toward lower GC content in the pattern of small insertions and deletions (indels). In addition, the GC content of noncoding DNA in Drosophila is higher than would be predicted on the basis of the pattern of nucleotide substitutions and small indels. However, we argue that the fast turnover of noncoding sequences in Drosophila makes it difficult to assess the importance of the GC biases in nucleotide substitutions and small indels in shaping the base composition of noncoding sequences.

Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans

PLoS Biology, 2007

The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. Here we present a population genetic analysis of Drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba. We discovered previously unknown, large-scale fluctuations of polymorphism and divergence along chromosome arms, and significantly less polymorphism and faster divergence on the X chromosome. We generated a comprehensive list of functional elements in the D. simulans genome influenced by adaptive evolution. Finally, we characterized genomic patterns of base composition for coding and noncoding sequence. These results suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophila genome, and provide a rich resource for the investigation of adaptive evolution and functional variation in D. simulans. Citation: Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, et al. (2007) Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol 5(11): e310.

Genome-Wide Analysis of Long-Term Evolutionary Domestication in Drosophila Melanogaster

Consistent directional selection applied to populations across multiple generations is expected to produce genome-wide reduction in sequence polymorphism. Our goal was to test this hypothesis using five replicate populations of Drosophila melanogaster that have been subjected to over 900 generations of laboratory domestication. To this end, we sampled and sequenced pools of individuals from each of these populations. The resulting sequence data were then aligned to a reference genome, SNPs were identified, and their frequencies were estimated for each population. Measures of sequence polymorphism were then made across the genome, with sequence data from generation zero of another another D. melanogaster domestication experiment serving as a baseline. Several major dips in heterozygosity were found throughout the genome, many of which were consistent across all five replicates. These localized losses of heterozygosity are consistent with patterns associated with adaptation via select...

Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource

Molecular Biology and Evolution

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...

A genome-wide scan for genes under balancing selection in Drosophila melanogaster

BMC evolutionary biology, 2017

In the history of population genetics balancing selection has been considered as an important evolutionary force, yet until today little is known about its abundance and its effect on patterns of genetic diversity. Several well-known examples of balancing selection have been reported from humans, mice, plants, and parasites. However, only very few systematic studies have been carried out to detect genes under balancing selection. We performed a genome scan in Drosophila melanogaster to find signatures of balancing selection in a derived (European) and an ancestral (African) population. We screened a total of 34 genomes searching for regions of high genetic diversity and an excess of SNPs with intermediate frequency. In total, we found 183 candidate genes: 141 in the European population and 45 in the African one, with only three genes shared between both populations. Most differences between both populations were observed on the X chromosome, though this might be partly due to false ...