Identifying Structural Variation in Haploid Microbial Genomes from Short-Read Resequencing Data Using Breseq

Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. Results: We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for similar to 25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation with modest read-depth coverage of the reference genome (>40-fold). Conclusions: Using breseq to predict structural variation should be useful for studies of microbial epidemiology, experimental evolution, synthetic biology, and genetics when a reference genome for a closely related strain is available. In these cases, breseq can discover mutations that may be responsible for important or unintended changes in genomes that might otherwise go undetected.U.S. National Institutes of Health R00-GM087550U.S. National Science Foundation (NSF) DEB-0515729NSF BEACON Center for the Study of Evolution in Action DBI-0939454Cancer Prevention & Research Institute of Texas (CPRIT) RP130124University of Texas at Austin startup fundsUniversity of Texas at AustinCPRIT Cancer Research TraineeshipMolecular Bioscience

Dendroclimatology of arctic shrubs

Thesis focuses on the influence of climate on microscopic structure of anatomic features in juniper wood. Dendrochronology as a method reaches its limits in the Arctic regions. Insufficient network of meteorological stations providing sufficiently long series of climatical data is the reason of increasing interest in studying Arctic shrubs, which can occur even beyond the latitudal forrest line. Thirty-three discs from juniper shrubs were collected in Gangasdalen valley on the banks of Jarfjord fjord in the August 2014. The master chronology was developed from 26 cross-dated samples. Eight carefully chosen samples were used for microscopic measurement of wood anatomic features during the reliable period of the main chronology using WinCell Wood Cell Anatomy software. Lumen area, wall thickness, number of cells and tree ring (its part) width were measured for both whole ring, and for earlywod and latewood. It was found that ring width does not necessarily have the highest dependency on climate and therefore may not always be the best climatic proxy. The highest dependency reached the number of cells, which was generally positively correlated with summer temperatures. On the other hand, lumen area shows the lowest dependency on climate

Data from: Genome-wide association study of Arabidopsis thaliana identifies determinants of natural variation in seed oil composition

The renewable source of highly reduced carbon provided by plant triacylglycerols (TAGs) fills an ever increasing demand for food, biodiesel, and industrial chemicals. Each of these uses requires different compositions of fatty acid proportions in seed oils. Identifying the genes responsible for variation in seed oil composition in nature provides targets for bioengineering fatty acid proportions optimized for various industrial and nutrition goals. Here, we characterized the seed oil composition of 391 world-wide, wild accessions of Arabidopsis thaliana, and performed a genome-wide association study (GWAS) of the 9 major fatty acids in the seed oil and 4 composite measures of the fatty acids. Four to 19 regions of interest were associated with the seed oil composition traits. Thirty-four of the genes in these regions are involved in lipid metabolism or transport, with 14 specific to fatty acid synthesis or breakdown. Eight of the genes encode transcription factors. We have identified genes significantly associated with variation in fatty acid proportions that can be used as a resource across the Brassicaceae. Two-thirds of the regions identified contain candidate genes that have never been implicated in lipid metabolism and represent potential new targets for bioengineering

TableS3

List of the regions of interest and the genes within them for each of the traits. Lipid genes are in bold and transcription factors are italicized

Active control of noise from hot, supersonic turbulent jets

We report on an experimental and reduced-order modeling study aimed at reducing mixing noise in hot supersonic jets relevant to military aircraft. A spinning valve is used to modulate four injection nozzles near the main jet nozzle lip over a range of frequencies and mass flow rates. Diagnostics include near-, mid-, and far-field microphone arrays aimed at measuring the effect of actuation on the near-field turbulent wavepacket structures and their correlation with mixing noise. The actuators provide more than 4 dB noise reduction at peak frequencies in the aft arc, and up to 2 dB reduction in OASPL. Experiments are performed to contrast the performance of steady and unsteady blowing with different amplitudes. The results to date suggest that the noise reduction is primarily associated with attenuated wave packet activity associated with the rapidly thickened shear layers that occur with both steady and unsteady blowing. Mean flow surveys are also preformed and serve as inputs to reduced-order models for the wave packets based on parabolized stability equations. These models are in turn used to corroborate the experimental evidence suggesting mechanisms of noise suppression in the actuated flow

TableS3

P-values and FDR-corrected values for the a priori candidate gene analysis

Data from: Genome-wide association study in Arabidopsis thaliana of natural variation in seed oil melting point, a widespread adaptive trait in plants

Seed oil melting point is an adaptive, quantitative trait determined by the relative proportions of the fatty acids that compose the oil. Micro- and macro-evolutionary evidence suggests selection has changed the melting point of seed oils to covary with germination temperatures because of a trade-off between total energy stores and the rate of energy acquisition during germination under competition. The seed oil compositions of 391 natural accessions of Arabidopsis thaliana, grown under common-garden conditions, were used to assess whether seed oil melting point within a species varied with germination temperature. In support of the adaptive explanation, long-term monthly spring and fall field temperatures of the accession collection sites significantly predicted their seed oil melting points. In addition, a genome-wide association study (GWAS) was performed to determine which genes were most likely responsible for the natural variation in seed oil melting point. The GWAS found a single highly significant association within the coding region of FAD2, which encodes a fatty acid desaturase central to the oil biosynthesis pathway. In a separate analysis of fifteen a priori oil synthesis candidate genes, two (FAD2 and FATB) were located near significant SNPs associated with seed oil melting point. These results comport with others’ molecular work showing that lines with alterations in these genes affect seed oil melting point as expected. Our results suggest natural selection has acted on a small number of loci to alter a quantitative trait in response to local environmental conditions

Box-Cox transformed fatty acid proportions for 391 Arabidopsis thaliana accessions.

Box-Cox transformed fatty acid proportions for 391 Arabidopsis thaliana accessions