Reference Genome Assembly for Australian Ascochyta rabiei Isolate ArME14

Copyright © 2020 Mohd Shah et al. Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. Division of the genome by OcculterCut into GC-balanced and AT-dominant segments reveals 21% of the genome contains gene-sparse, AT-rich isochores. Transposable elements and repetitive DNA sequences in the ArME14 assembly made up 15% of the genome. A total of 11,257 protein-coding genes were predicted compared with 10,596 for ArD2. Many of the predicted genes missing from the ArD2 assembly were in genomic regions adjacent to AT-rich sequence. We compared the complement of predicted transcription factors and secreted proteins for the two A. rabiei genome assemblies and found that the isolates contain almost the same set of proteins. The small number of differences could represent real differences in the gene complement between isolates or possibly result from the different sequencing methods used. Prediction pipelines were applied for carbohydrate-active enzymes, secondary metabolite clusters and putative protein effectors. We predict that ArME14 contains between 450 and 650 CAZymes, 39 putative protein effectors and 26 secondary metabolite clusters

Reference genome assembly for Australian Ascochyta rabiei Isolate ArME14

Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. Division of the genome by OcculterCut into GC-balanced and AT-dominant segments reveals 21% of the genome contains gene-sparse, AT-rich isochores. Transposable elements and repetitive DNA sequences in the ArME14 assembly made up 15% of the genome. A total of 11,257 protein-coding genes were predicted compared with 10,596 for ArD2. Many of the predicted genes missing from the ArD2 assembly were in genomic regions adjacent to AT-rich sequence. We compared the complement of predicted transcription factors and secreted proteins for the two A. rabiei genome assemblies and found that the isolates contain almost the same set of proteins. The small number of differences could represent real differences in the gene complement between isolates or possibly result from the different sequencing methods used. Prediction pipelines were applied for carbohydrate-active enzymes, secondary metabolite clusters and putative protein effectors. We predict that ArME14 contains between 450 and 650 CAZymes, 39 putative protein effectors and 26 secondary metabolite clusters

Missense-depleted regions in population exomes implicate ras superfamily nucleotide-binding protein alteration in patients with brain malformation.

Genomic sequence interpretation can miss clinically relevant missense variants for several reasons. Rare missense variants are numerous in the exome and difficult to prioritise. Affected genes may also not have existing disease association. To improve variant prioritisation, we leverage population exome data to identify intragenic missense-depleted regions (MDRs) genome-wide that may be important in disease. We then use missense depletion analyses to help prioritise undiagnosed disease exome variants. We demonstrate application of this strategy to identify a novel gene association for human brain malformation. We identified de novo missense variants that affect the GDP/GTP-binding site of ARF1 in three unrelated patients. Corresponding functional analysis suggests ARF1 GDP/GTP-activation is affected by the specific missense mutations associated with heterotopia. These findings expand the genetic pathway underpinning neurologic disease that classically includes FLNA. ARF1 along with ARFGEF2 add further evidence implicating ARF/GEFs in the brain. Using functional ontology, top MDR-containing genes were highly enriched for nucleotide-binding function, suggesting these may be candidates for human disease. Routine consideration of MDR in the interpretation of exome data for rare diseases may help identify strong genetic factors for many severe conditions, infertility/reduction in reproductive capability, and embryonic conditions contributing to preterm loss

Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing

<p>Abstract</p> <p>Background</p> <p>The emergence of next-generation sequencing technology presents tremendous opportunities to accelerate the discovery of rare variants or mutations that underlie human genetic disorders. Although the complete sequencing of the affected individuals' genomes would be the most powerful approach to finding such variants, the cost of such efforts make it impractical for routine use in disease gene research. In cases where candidate genes or loci can be defined by linkage, association, or phenotypic studies, the practical sequencing target can be made much smaller than the whole genome, and it becomes critical to have capture methods that can be used to purify the desired portion of the genome for shotgun short-read sequencing without biasing allelic representation or coverage. One major approach is array-based capture which relies on the ability to create a custom in-situ synthesized oligonucleotide microarray for use as a collection of hybridization capture probes. This approach is being used by our group and others routinely and we are continuing to improve its performance.</p> <p>Results</p> <p>Here, we provide a complete protocol optimized for large aggregate sequence intervals and demonstrate its utility with the capture of all predicted amino acid coding sequence from 3,038 human genes using 241,700 60-mer oligonucleotides. Further, we demonstrate two techniques by which the efficiency of the capture can be increased: by introducing a step to block cross hybridization mediated by common adapter sequences used in sequencing library construction, and by repeating the hybridization capture step. These improvements can boost the targeting efficiency to the point where over 85% of the mapped sequence reads fall within 100 bases of the targeted regions.</p> <p>Conclusions</p> <p>The complete protocol introduced in this paper enables researchers to perform practical capture experiments, and includes two novel methods for increasing the targeting efficiency. Coupled with the new massively parallel sequencing technologies, this provides a powerful approach to identifying disease-causing genetic variants that can be localized within the genome by traditional methods.</p

Multi-Element Abundance Measurements from Medium-Resolution Spectra. IV. Alpha Element Distributions in Milky Way Dwarf Satellite Galaxies

We derive the star formation histories of eight dwarf spheroidal (dSph) Milky Way satellite galaxies from their alpha element abundance patterns. Nearly 3000 stars from our previously published catalog (Paper II) comprise our data set. The average [alpha/Fe] ratios for all dSphs follow roughly the same path with increasing [Fe/H]. We do not observe the predicted knees in the [alpha/Fe] vs. [Fe/H] diagram, corresponding to the metallicity at which Type Ia supernovae begin to explode. Instead, we find that Type Ia supernova ejecta contribute to the abundances of all but the most metal-poor ([Fe/H] < -2.5) stars. We have also developed a chemical evolution model that tracks the star formation rate, Types II and Ia supernova explosions, and supernova feedback. Without metal enhancement in the supernova blowout, massive amounts of gas loss define the history of all dSphs except Fornax, the most luminous in our sample. All six of the best-fit model parameters correlate with dSph luminosity but not with velocity dispersion, half-light radius, or Galactocentric distance.Comment: 28 pages, 14 figures; accepted for publication in ApJ; very minor editorial corrections in v

Production Across the Nordics

In the uncertain and volatile market that companies are currently facing worldwide, researchers and engineers\ua0become a key link to\ua0strengthen the industry and universities\ua0in order to\ua0understand, communicate, and tackle\ua0current challenges. In the PhD course, International Production, the goal is to investigate what makes Sweden and Iceland booming industrial hubs\ua0driven by technology. Through the\ua0visits to different types of industries, such as fintech, medical, or automotive industry,\ua0we as researchers have gained a better understanding of the challenges they are currently facing. This report is a summary of our findings and observations.\ua0\ua0The participants have focused on the\ua0six challenge areas highlighted within the Produktion2030 graduate school and summarize their findings as:\ua0\ua0•Resource-efficient production:\ua0Data as a resource is becoming increasingly important for the majority of companies in the Nordics and the application of traditional resource management tools on data is a suggested area for future research. \ua0•Flexible production:To strengthen organizations by\ua0enabling\ua0production systems to be flexible to address\ua0market variations is a key\ua0challenge to consider in the manufacturing industry•Virtual production development:Digitalization level is distinct in each Nodic country with the reason that each country has its own digitalization transformation policy and different measures on digitalization level.\ua0•Humans in the production system:Humans are central in the production systems of the visited companies. Use of automation technology and AI to support humans in their work may become more common in the future.•Circular production systems and maintenance:Circular production systems require a complex approach through the whole value chain. Industry in the Nordics has started the adoption of a circularity approach.\ua0•Integrated product and production development:\ua0Integration of product and production development is a key business factor for the Nordic countries, and geographical proximity between the two departments can have a beneficial effect. \ua0We hope that this report provides more\ua0details\ua0regarding\ua0the success and current challenges of the Swedish and Icelandic enterprises

Spectroscopic versus Photometric Metallicities: Milky Way Dwarf Spheroidal Companions as a Test Case

Aims. The method of deriving photometric metallicities using red giant branch stars is applied to resolved stellar populations under the common assumption that they mainly consist of single-age old stellar populations. We explore the effect of the presence of mixed-age stellar populations on deriving photometric metallicities. Methods. We use photometric data sets for the five Galactic dwarf spheroidals Sculptor, Sextans, Carina, Fornax, and Leo II in order to derive their photometric metallicity distribution functions from their resolved red giant branches using isochrones of the Dartmouth Stellar Evolutionary Database. We compare the photometric metallicities with published spectroscopic metallicities based on the analysis of the near-infrared Ca triplet (Ca T), both on the metallicity scale of Carretta & Gratton and on the scale defined by the Dartmouth isochrones. In addition, we compare the photometric metallicities with published spectroscopic metallicities based on spectral synthesis and medium-resolution spectroscopy, and on high resolution spectra where available. Results. The mean properties of the spectroscopic and photometric metallicity samples are comparable within the intrinsic scatter of each method although the mean metallicities of dSphs with pronounced intermediate-age population fractions may be underestimated by the photometric method by up to a few tenths of dex in [Fe/H]. The star-by-star differences of the spectroscopic minus the photometric metallicities show a wide range of values along the fiducial spectroscopic metallicity range, with the tendency to have systematically lower photometric metallicities for those dwarf spheroidals with a higher fraction of intermediate-age populations. Such discrepancies persist even in the case of the purely old Sculptor dSph, where one would na\"ively expect a very good match when comparing with medium or low resolution metallicity measurements. Overall, the agreement between Ca T metallicities and photometric metallicities is very good in the metallicity range from ~ -2 dex to ~ -1.5 dex. We find that the photometric method is reliable in galaxies that contain small (less than 15%) intermediate-age stellar fractions. Therefore, in the presence of mixed-age stellar populations, one needs to quantify the fraction of the intermediate-age stars in order to assess their effect on determining metallicities from photometry alone. Finally, we note that the comparison of spectroscopic metallicities of the same stars obtained with different methods reveals similarly large discrepancies as the comparison with photometric metallicities.Comment: 17 pages, 12 figures; A&A accepte

A close look at the Centaurus A group of galaxies III. Recent star formation histories of late-type dwarfs around M83

We study the resolved stellar populations of dwarf galaxies in the nearby Centaurus A/M83 group of galaxies. Our goal is to characterize their evolutionary history and to investigate eventual similarities or differences with the dwarf population in other group environments. This work presents the analysis of five late-type (irregular) dwarfs found in the vicinity of the giant spiral M83. Using archival HST/ACS data, we perform synthetic color-magnitude diagram modeling to derive the star formation histories of these late-type dwarfs. The target objects show heterogeneous star formation histories, with average star formation rates of 0.08 to 0.70x10^{-2} M_odot/yr. Some of them present prolonged, global bursts of star formation (~300-500 Myr). The studied galaxies are all metal-poor ([Fe/H] ~-1.4). We further investigate the spatial extent of different stellar populations, finding that the young stars show a clumpy distribution, as opposed to the smooth, broad extent of the old ones. The actively star forming regions have sizes of ~100 pc and lifetimes of >~100 Myr, thus suggesting a stochastic star formation mode for the target dwarf irregular galaxies. The galaxies formed ~20% to 70% of their stars more than ~7 Gyr ago. The studied dwarfs have average star formation rates slightly higher than their analogues in the Local Group, but comparable to those in the M81 group. Our preliminary sample indicates that the neutral gas content of the target dwarfs does seem to be affected by the group environment: galaxies within a denser region have a much lower M_HI/ than the isolated ones, meaning that they will exhaust their gas reservoir more quickly.Comment: 20 pages, 12 figures; accepted for publication in A&

Infall Times for Milky Way Satellites From Their Present-Day Kinematics

We analyze subhalos in the Via Lactea II (VL2) cosmological simulation to look for correlations among their infall times and z = 0 dynamical properties. We find that the present day orbital energy is tightly correlated with the time at which subhalos last crossed into the virial radius. This energy-infall correlation provides a means to infer infall times for Milky Way satellite galaxies. Assuming that the Milky Way's assembly can be modeled by VL2, we show that the infall times of some satellites are well constrained given only their Galactocentric positions and line-of-sight velocities. The constraints sharpen for satellites with proper motion measurements. We find that Carina, Ursa Minor, and Sculptor were all accreted early, more than 8 Gyr ago. Five other dwarfs, including Sextans and Segue 1, are also probable early accreters, though with larger uncertainties. On the other extreme, Leo T is just falling into the Milky Way for the first time while Leo I fell in \sim 2 Gyr ago and is now climbing out of the Milky Way's potential after its first perigalacticon. The energies of several other dwarfs, including Fornax and Hercules, point to intermediate infall times, 2 - 8 Gyr ago. We compare our infall time estimates to published star formation histories and find hints of a dichotomy between ultrafaint and classical dwarfs. The classical dwarfs appear to have quenched star formation after infall but the ultrafaint dwarfs tend to be quenched long before infall, at least for the cases in which our uncertainties allow us to discern differences. Our analysis suggests that the Large Magellanic Cloud crossed inside the Milky Way virial radius recently, within the last \sim 4 billion years.Comment: 15 pages, 7 figures, all figures include colors, submitted for publication in MNRA

Multi-Element Abundance Measurements from Medium-Resolution Spectra. III. Metallicity Distributions of Milky Way Dwarf Satellite Galaxies

We present metallicity distribution functions (MDFs) for the central regions of eight dwarf satellite galaxies of the Milky Way: Fornax, Leo I and II, Sculptor, Sextans, Draco, Canes Venatici I, and Ursa Minor. We use the published catalog of abundance measurements from the previous paper in this series. The measurements are based on spectral synthesis of iron absorption lines. For each MDF, we determine maximum likelihood fits for Leaky Box, Pre-Enriched, and Extra Gas (wherein the gas supply available for star formation increases before it decreases to zero) analytic models of chemical evolution. Although the models are too simplistic to describe any MDF in detail, a Leaky Box starting from zero metallicity gas fits none of the galaxies except Canes Venatici I well. The MDFs of some galaxies, particularly the more luminous ones, strongly prefer the Extra Gas Model to the other models. Only for Canes Venatici I does the Pre-Enriched Model fit significantly better than the Extra Gas Model. The best-fit effective yields of the less luminous half of our galaxy sample do not exceed 0.02 Z_sun, indicating that gas outflow is important in the chemical evolution of the less luminous galaxies. We surmise that the ratio of the importance of gas infall to gas outflow increases with galaxy luminosity. Strong correlations of average [Fe/H] and metallicity spread with luminosity support this hypothesis.Comment: 17 pages, 5 figures; accepted for publication in ApJ; minor corrections in v3; corrected typographical errors in Tables 1 and 3 in v