Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley

Qingke, the local name of hulless barley in the Tibetan Plateau, is a staple food for Tibetans. The availability of its reference genome sequences could be useful for studies on breeding and molecular evolution. Taking advantage of the third-generation sequencer (PacBio), we de novo assembled a 4.84-Gb genome sequence of qingke, cv. Zangqing320 and anchored a 4.59-Gb sequence to seven chromosomes. Of the 46,787 annotated 'high-confidence' genes, 31 564 were validated by RNA-sequencing data of 39 wild and cultivated barley genotypes with wide genetic diversity, and the results were also confirmed by nonredundant protein database from NCBI. As some gaps in the reference genome of Morex were covered in the reference genome of Zangqing320 by PacBio reads, we believe that the Zangqing320 genome provides the useful supplements for the Morex genome. Using the qingke genome as a reference, we conducted a genome comparison, revealing a close genetic relationship between a hulled barley (cv. Morex) and a hulless barley (cv. Zangqing320), which is strongly supported by the low-diversity regions in the two genomes. Considering the origin of Morex from its breeding pedigree, we then demonstrated a close genomic relationship between modern cultivated barley and qingke. Given this genomic relationship and the large genetic diversity between qingke and modern cultivated barley, we propose that qingke could provide elite genes for barley improvement

Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism

The evolution of parasitism is a recurrent event in the history of life and a core problem in evolutionary biology. Trypanosomatids are important parasites and include the human pathogens Trypanosoma brucei, Trypanosoma cruzi, and Leishmania spp., which in humans cause African trypanosomiasis, Chagas disease, and leishmaniasis, respectively. Genome comparison between trypanosomatids reveals that these parasites have evolved specialized cell-surface protein families, overlaid on a well-conserved cell template. Understanding how these features evolved and which ones are specifically associated with parasitism requires comparison with related non-parasites. We have produced genome sequences for Bodo saltans, the closest known non-parasitic relative of trypanosomatids, and a second bodonid, Trypanoplasma borreli. Here we show how genomic reduction and innovation contributed to the character of trypanosomatid genomes. We show that gene loss has “streamlined” trypanosomatid genomes, particularly with respect to macromolecular degradation and ion transport, but consistent with a widespread loss of functional redundancy, while adaptive radiations of gene families involved in membrane function provide the principal innovations in trypanosomatid evolution. Gene gain and loss continued during trypanosomatid diversification, resulting in the asymmetric assortment of ancestral characters such as peptidases between Trypanosoma and Leishmania, genomic differences that were subsequently amplified by lineage-specific innovations after divergence. Finally, we show how species-specific, cell-surface gene families (DGF-1 and PSA) with no apparent structural similarity are independent derivations of a common ancestral form, which we call “bodonin.” This new evidence defines the parasitic innovations of trypanosomatid genomes, revealing how a free-living phagotroph became adapted to exploiting hostile host environments

Primitive Duplicate Hox Clusters in the European Eel's Genome

The enigmatic life cycle and elongated body of the European eel (Anguilla anguilla L., 1758) have long motivated scientific enquiry. Recently, eel research has gained in urgency, as the population has dwindled to the point of critical endangerment. We have assembled a draft genome in order to facilitate advances in all provinces of eel biology. Here, we use the genome to investigate the eel's complement of the Hox developmental transcription factors. We show that unlike any other teleost fish, the eel retains fully populated, duplicate Hox clusters, which originated at the teleost-specific genome duplication. Using mRNA-sequencing and in situ hybridizations, we demonstrate that all copies are expressed in early embryos. Theories of vertebrate evolution predict that the retention of functional, duplicate Hox genes can give rise to additional developmental complexity, which is not immediately apparent in the adult. However, the key morphological innovation elsewhere in the eel's life history coincides with the evolutionary origin of its Hox repertoire

Forschungsverbund LeanTurb Förderkennzeichen 20T1108B Auslegung einer an Magerverbrennung angepassten 2-stufigen Turbine Schlussbericht

Bisherige Optimierungen des Wirkungsgrades von Turbinen verwendeten einfache radiale Profile der Eintrittsbedingungen. Der Einfluss von auch in Umfangsrichtung variierenden Strömungsfeldern auf den Wirkungsgrad wurde bislang nicht betrachtet, sondern nur der Einfluss auf einzelne Strömungsphänomene. Daher war es Ziel dieser Untersuchung zu bestimmen, inwieweit eine 2D-Turbineneintrittsverteilung (Variation der Strömungsgrößen über Radius und Umfang) den Wirkungsgrad verändert, wie der Unterschied im Wirkungsgrad im Vergleich zur 1D-Verteilung ist, wie die Wirkungsgradänderungen bei Geometrievariation mit den verschiedenen Verteilung (1D und 2D) sind und wie sich Heißgassträhnen in der Turbine ausbreiten. Die Arbeiten wurden mit Austrittsverteilungen einer Magerbrennkammer durchgeführt, wodurch zusätzlich noch ein Vergleich mit der Verteilung aus dem Vorhaben InterTurb (FKZ 20T0905B), welches einer konventionellen Brennkammer entspricht, ermöglicht wurde. Die Untersuchungen wurden mit dem speziell für Turbomaschinen entwickelten Strömungslöser TRACE des DLR durchgeführt. Es wurden zwei Optimierungen zur Erhöhung des Wirkungsgrades durchgeführt. Eine mit 1D-Verteilung sowie stationärer RANS-Simulation und die zweite mit 2D-Verteilung sowie instationärer RANS-Simulation. Ein Vorteil von 2D-Verteilungen oder der instationären Simulationsmethode für eine aerodynamische Optimierung hinsichtlich des Wirkungsgrades ist nicht erkennbar. Für die gezielte Untersuchung von Heißgassträhnen, Oberflächentemperaturen und der damit einhergehenden Kühlluftverteilung sind zweidimensionale Verteilungen, instationäre Simulationen und die Betrachtung der Positionierung von Brennkammer zur Hochdruckturbine unbedingt erforderlich. Auf Grundlage dieser Ergebnisse lassen sich Ressourcen bei der aerodynamischen Optimierung einsparen. Des Weiteren wurde der Bedarf für eine interdisziplinäre Optimierung (Simulation der Strömung und Simulation der Festkörperphysik) herausgearbeitet, um den Wirkungsgrad des Triebwerks weiter zu verbessern

Experimentelle Untersuchung des Strömungsfeldes einer HDT-Stufe zum Einfluss von beschädigten Statorschaufeln auf den Stufenwirkungsgrad

Im vorliegenden Bericht wird die aerodynamische Bewertung einer beschädigten HD-Turbinenstufe dargelegt. Die stationären Druckmessungen wurden im Windkanal für rotierenden Gitter, Göttingen durchgeführt. Für die Beurteilung des Schadens auf die Strömungsgrößen und Leistungsdaten wurden Sonden in die Stator- und Rotorabströmung verbaut

Experimental and CFD analysis of stator vanes with trailing edge damage

In this paper we will give an overview on the results of a research project dedicated to the analysis of rotor forcing due to in-service trailing edge damage of high pressure turbine nozzle guide vanes (HPT NGVs). Due to the extremely high temperatures in this region of the engine, which on average exceed the melting temperature of the employed vane material by several hundred degrees during takeoff, any unintended decrease of the vane cooling mass flow can lead to a loss of trailing edge material. The structure of the NGV can withstand a significant amount of trailing edge material loss, but the damage changes the flow through the affected passage, causing a so-called low engine order excitation of the rotor blades downstream. This can lead –in extreme cases– to high cycle fatigue failure of the rotor blade caused by resonances in the operating range. Thus it is very important to be able to quantify the damage-induced rotor forcing in case a trailing edge damage is detected during routine engine inspection. This quantification can be obtained by solving the unsteady fluid flow, typically modeled using the Reynolds-averaged Navier-Stokes equations together with a suitable turbulence model. In order to gain confidence in the CFD analysis results for those configurations, a dedicated measurement campaign with different representative trailing edge damage shapes has been set up at the DLR Göttingen, including both steady, unsteady and pressure-sensitive paint measurements and on both stationary and rotating components. The results of those measurements together with post-test CFD simulations will be presented in this paper

Vermessung eines generischen Kühlkanals unter Verwendung von Temperature-Sensitive Paint (TSP)

In einer ersten Machbarkeitsstudie soll ein generischer Kühlkanal mit Hilfe von TSP vermessen werden, der die interne konvektive Kühlung einer Gasturbinenschaufel simuliert. Eine Validierung der TSP-Messung erfolgt mit Hilfe einer bereits zuvor durchgeführten Infrarotmessung sowie einer CFD-Simulation des Kühlkanals. Erstmals kommt es bei dieser Untersuchung neben der qualitativen Analyse der TSP-Ergebnisse auch zu einer quantitativen Beurteilung, bei der nicht nur Temperaturgradienten sondern die Absoluttemperaturen gemessen werden können. Als Sensor wird bei den TSP-Messungen eine auf Europium basierende TSP-Farbe verwendet

Chromera velia, Endosymbioses and the Rhodoplex Hypothesis - Plastid Evolution in Cryptophytes, Alveolates, Stramenopiles and Haptophytes (CASH Lineages)

The discovery of Chromera velia, a free-living photosynthetic relative of apicomplexan pathogens, has provided an unexpected opportunity to study the algal ancestry of malaria parasites. In this work we compared the molecular footprints of a eukaryote-to-eukaryote endosymbiosis in C. velia to their equivalents in peridinin-containing dinoflagellates (PCD) to re- evaluate recent claims in favor of a common ancestry of their plastids. To this end, we established the draft genome and a set of full-length cDNA sequences from C. velia via next- generation sequencing. We documented the presence of a single coxI gene in the mitochondrial genome, which thus represents the genetically most reduced aerobic organelle identified so far, but focused our analyses on five “lucky genes” of the Calvin cycle. These were selected because of their known support for a common origin of complex plastids from cryptophytes, alveolates (represented by PCDs), stramenopiles and haptophytes (CASH) via a single secondary endosymbiosis with a red alga. As expected, our broadly sampled phylogenies of the nuclear- encoded Calvin cycle markers support a rhodophycean origin for the complex plastid of Chromera. However, they also suggest an independent origin of apicomplexan and dinophycean (PCD) plastids via two eukaryote-to-eukaryote endosymbioses. Although at odds with the current view of a common photosynthetic ancestry for alveolates, this conclusion is nonetheless in line with the deviant plastome architecture in dinoflagellates and the morphological paradox of four versus three plastid membranes in the respective lineages. Further support for independent endosymbioses is provided by analysis of five additional markers, four of them involved in the plastid protein import machinery. Finally, we introduce the “rhodoplex hypothesis” as a convenient way to designate evolutionary scenarios where CASH plastids are ultimately the product of a single secondary endosymbiosis with a red alga, but were subsequently horizontally spread via higher-order eukaryote-to-eukaryote endosymbioses