Search

BackgroundTransposable element (TE) insertions are among the most challenging type of variants to detect in genomic data because of their repetitive nature and complex mechanisms of replication. Nevertheless, the recent availability of large resequencing datasets has spurred the development of many new methods to detect TE insertions in whole genome shotgun sequences. These methods generate output in diverse formats and have a large number of software and data dependencies, making their comparative evaluation challenging for potential users.ResultsHere we develop an integrated bioinformatics pipeline for the detection of TE insertions in whole genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), that automatically runs and generates standardized output for multiple TE detection methods. We demonstrate the utility of the McClintock system by performing comparative evaluation of six TE detection methods using simulated and real genome data from the model microbal eukaryote,Saccharomyces cerevisiae. We find substantial variation among McClintock component methods in their ability to detect non-reference insertions in the yeast genome, but show that non-reference TEs at nearly all biologically-realistic locations can be detected in simulated data by combining multiple methods that use split-read and read-pair evidence. In general, our results reveal that split-read methods detect fewer non-reference TE insertions than read-pair methods, but generally have much higher positional accuracy. Analysis of a large sample of real yeast genomes reveals that most, but not all, McClintock component methods can recover known aspects of TE biology in yeast such as the transpositional activity status of families, tRNA gene target preferences, and target site duplication structure, albeit with varying levels of positional accuracy.ConclusionsOur results suggest that no single TE detection method currently provides comprehensive detection of non-reference TEs, even in the context of a simplified model eukaryotic genome likeS. cerevisiae. In spite of these limitations, the McClintock system provides a framework for testing, developing and integrating results from multiple TE detection methods to achieve this ultimate aim, as well as useful guidance for yeast researchers to select appropriate TE detection tools.

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.

Transposable elements are mobile DNA sequences that integrate into host genomes using diverse mechanisms with varying degrees of target site specificity. While the target site preferences of some engineered transposable elements are well studied, the natural target preferences of most transposable elements are poorly characterized. Using population genomic resequencing data from 166 strains of Drosophila melanogaster, we identified over 8,000 new insertion sites not present in the reference genome sequence that we used to decode the natural target preferences of 22 families of transposable element in this species. We found that terminal inverted repeat transposon and long terminal repeat retrotransposon families present clade-specific target site duplications and target site sequence motifs. Additionally, we found that the sequence motifs at transposable element target sites are always palindromes that extend beyond the target site duplication. Our results demonstrate the utility of population genomics data for high-throughput inference of transposable element targeting preferences in the wild and establish general rules for terminal inverted repeat transposon and long terminal repeat retrotransposon target site selection in eukaryotic genomes.

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 figures