13 research outputs found
Antimicrobial resistance profiles after conjugative events with an escherichia coli isolate from hospital effluent
info:eu-repo/semantics/publishedVersio
Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster
Wolbachia are maternally-inherited symbiotic bacteria commonly found in
arthropods, which are able to manipulate the reproduction of their host in
order to maximise their transmission. Here we use whole genome resequencing
data from 290 lines of Drosophila melanogaster from North America, Europe and
Africa to predict Wolbachia infection status, estimate cytoplasmic genome copy
number, and reconstruct Wolbachia and mtDNA genome sequences. Complete
Wolbachia and mitochondrial genomes show congruent phylogenies, consistent with
strict vertical transmission through the maternal cytoplasm and imperfect
transmission of Wolbachia. Bayesian phylogenetic analysis reveals that the most
recent common ancestor of all Wolbachia and mitochondrial genomes in D.
melanogaster dates to around 8,000 years ago. We find evidence for a recent
incomplete global replacement of ancestral Wolbachia and mtDNA lineages, which
is likely to be one of several similar incomplete replacement events that have
occurred since the out-of-Africa migration that allowed D. melanogaster to
colonize worldwide habitats.Comment: 41 pages, 5 figure
TE-Tracker: systematic identification of transposition events through whole-genome resequencing
Recommended from our members
The Drosophila melanogaster Genetic Reference Panel
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 melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype–phenotype mapping using the power of Drosophila genetics
LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences
A unique cluster of roo insertions in the promoter region of a stress response gene in Drosophila melanogaster
Transposable elements (TEs) are not randomly distributed in the genome. A genome-wide analysis of the D. melanogaster genome found that differences in TE density across 50 kb genomic regions was due both to transposition and duplication. At smaller genomic scales, promoter regions of hsp genes and the promoter region of CG18446 have been shown to accumulate TE insertions. In this work, we have further analyzed the promoter region of CG18446. We screened 218 strains collected in 15 natural populations, and we found that the CG18446 promoter region contains 20 independent roo insertions. Based on phylogenetic analysis, we suggest that the presence of multiple roo insertions in this region is likely to be the result of several bursts of transposition. Moreover, we found that the roo insertional cluster in the CG18446 promoter region is unique: no other promoter region in the genome contains a similar number of roo insertions. We found that, similar to hsp gene promoters, chromatin accessibility could be one of the factors explaining the recurrent insertions of roo elements in CG18446 promoter region.This work was funded by the European Commission (H2020-ERC-2014-CoG-647900). C.I. was funded by an ERASMUS+ fellowship. We acknowledge the support of the Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de laGeneralitat de Catalunya (GRC 2017 SGR 880). We also acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI)
Genome-Wide Sequencing and an Open Reading Frame Analysis of Dichlorodiphenyltrichloroethane (DDT) Susceptible (91-C) and Resistant (91-R) Drosophila melanogaster Laboratory Populations
Recommended from our members
The Drosophila melanogaster Genetic Reference Panel.
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 melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics