Draft genome of Brasenia schreberi, a worldwide distributed and endangered aquatic plant

OBJECTIVES

Brasenia is a monotypic genus in the family of Cabombaceae. The only species, B. schreberi, is a macrophyte distributed worldwide. Because it requires good water quality, it is endangered in China and other countries due to the deterioration of aquatic habitats. The young leaves and stems of B. schreberi are covered by thick mucilage, which has high medical value. As an allelopathic aquatic plant, it can also be used in the management of aquatic weeds. Here, we present its assembled and annotated genome to help shed light on medial and allelopathic substrates and facilitate their conservation.

DATA DESCRIPTION

Genomic DNA and RNA extracted from B. schreberi leaf tissues were used for whole genome and RNA sequencing using a Nanopore and/or MGI sequencer. The assembly was 1,055,148,839 bp in length, with 92 contigs and an N50 of 22,379,495 bp. The repetitive elements in the assembly were 555,442,205 bp. A completeness assessment of the assembly with BUSCO and compleasm indicated 88.4 and 90.9% completeness in the Eudicots database and 95.4 and 96.6% completeness in the Embryphyta database. Gene annotation revealed 67,747 genes that coded for 73,344 proteins.

Chromosome-level genome assembly and demographic history of Euryodendron excelsum in monotypic genus endemic to China

Euryodendron excelsum is in a monotypic genus Euryodendron, endemic to China. It has intermediate morphisms in the Pentaphylacaceae or Theaceae families, which make it distinct. Due to anthropogenic disturbance, E. excelsum is currently found in very restricted and fragmented areas with extremely small populations. Although much research and effort has been applied towards its conservation, its long-term survival mechanisms and evolutionary history remain elusive, especially from a genomic aspect. Therefore, using a combination of long/short whole genome sequencing, RNA sequencing reads, and Hi-C data, we assembled and annotated a high-quality genome for E. excelsum. The genome assembly of E. excelsum comprised 1,059,895,887 bp with 99.66% anchored into 23 pseudo-chromosomes and a 99.0% BUSCO completeness. Comparative genomic analysis revealed the expansion of terpenoid and flavonoid secondary metabolite genes, and displayed a tandem and/or proximal duplication framework of these genes. E. excelsum also displayed genes associated with growth, development, and defence adaptation from whole genome duplication. Demographic analysis indicated that its fluctuations in population size and its recent population decline were related to cold climate changes. The E. excelsum genome assembly provides a highly valuable resource for evolutionary and ecological research in the future, aiding its conservation, management, and restoration.

Seeding the Electrothermal Instability through a Three-Dimensional, Nonlinear Perturbation

Electrothermal instability plays an important role in applications of current-driven metal, creating striations (which seed the magneto-Rayleigh-Taylor instability) and filaments (which provide a more rapid path to plasma formation). However, the initial formation of both structures is not well understood. Simulations show for the first time how a commonly occurring isolated defect transforms into the larger striation and filament, through a feedback loop connecting current and electrical conductivity. Simulations have been experimentally validated using defect-driven self-emission patterns.

Three-dimensional feedback processes in current-driven metal

Using three-dimensional (3D) magnetohydrodynamic simulations, we study how a pit on a metal surface evolves when driven by intense electrical current density j. Redistribution of j around the pit initiates a feedback loop: j both reacts to and alters the electrical conductivity σ, through Joule heating and hydrodynamic expansion, so that j and σ are constantly in flux. Thus, the pit transforms into larger striation and filament structures predicted by the electrothermal instability theory. Both structures are important in applications of current-driven metal: The striation constitutes a density perturbation that can seed the magneto-Rayleigh-Taylor instability, while the filament provides a more rapid path to plasma formation, through 3D j redistribution. Simulations predict distinctive self-emission patterns, thus allowing for experimental observation and comparison.

Effects of a Preembedded Axial Magnetic Field on the Current Distribution in a Z-Pinch Implosion

The fundamental physics of the magnetic field distribution in a plasma implosion with a preembedded magnetic field is investigated within a gas-puff Z pinch. Time and space resolved spectroscopy of the polarized Zeeman effect, applied for the first time, reveals the impact of a preembedded axial field on the evolution of the current distribution driven by a pulsed-power generator. The measurements show that the azimuthal magnetic field in the imploding plasma, even in the presence of a weak axial magnetic field, is substantially smaller than expected from the ratio of the driving current to the plasma radius. Much of the current flows at large radii through a slowly imploding, low-density plasma. Previously unpredicted observations in higher-power imploding-magnetized-plasma experiments, including recent, unexplained structures observed in the magnetized liner inertial fusion experiment, may be explained by the present discovery. The development of a force-free current configuration is suggested to explain this phenomenon.

Experimental observation of the stratified electrothermal instability on aluminum with thickness greater than a skin depth

A direct observation of the stratified electrothermal instability on the surface of thick metal is reported. Aluminum rods coated with 70μm Parylene-N were driven to 1 MA in 100ns, with the metal thicker than the skin depth. The dielectric coating suppressed plasma formation, enabling persistent observation of discrete azimuthally correlated stratified thermal perturbations perpendicular to the current whose wave numbers, k, grew exponentially with rate γ(k)=0.06ns^{-1}-(0.4ns^{-1}μm^{2}rad^{-2})k^{2} in ∼1g/cm^{3}, ∼7000K aluminum.

Experimental Demonstration of the Stabilizing Effect of Dielectric Coatings on Magnetically Accelerated Imploding Metallic Liners

Enhanced implosion stability has been experimentally demonstrated for magnetically accelerated liners that are coated with 70  μm of dielectric. The dielectric tamps liner-mass redistribution from electrothermal instabilities and also buffers coupling of the drive magnetic field to the magneto-Rayleigh-Taylor instability. A dielectric-coated and axially premagnetized beryllium liner was radiographed at a convergence ratio [CR=Rin,0/Rin(z,t)] of 20, which is the highest CR ever directly observed for a strengthless magnetically driven liner. The inner-wall radius Rin(z,t) displayed unprecedented uniformity, varying from 95 to 130  μm over the 4.0 mm axial height captured by the radiograph.

Pressure and energy balance of stagnating plasmas in z-pinch experiments: implications to current flow at stagnation

Detailed spectroscopic diagnostics of the stagnating plasma in two disparate z pinches allow, for the first time, the examination of the plasma properties within a 1D shock wave picture, demonstrating a good agreement with this picture. The conclusion is that for a wide range of imploding-plasma masses and current amplitudes, in experiments optimizing non-Planckian hard radiation yields, contrary to previous descriptions the stagnating plasma pressure is balanced by the implosion pressure, and the radiation energy is provided by the imploding-plasma kinetic energy, rather than by the magnetic-field pressure and magnetic-field-energy dissipation, respectively.

Investigation of high-temperature bright plasma X-ray sources produced in 5-MA X-pinch experiments

Using solid, machined X-pinch targets driven by currents rising from 0 to 5-6 MA in 60 ns, we observed bright spots of 5-9-keV continuum radiation from 5±2-μm diameter regions. The >6-keV radiation is emitted in about 0.4 ns, and the bright spots are roughly 75 times brighter than the bright spots measured at 1 MA. A total x-ray power of 10 TW peak and yields of 165±20 kJ were emitted from a 3-mm height. The 3-5-keV continuum radiation had a 50-90-GW peak power and 0.15-0.35-kJ yield. The continuum is plausibly from a 1275±75-eV blackbody or alternatively from a 3500±500-eV bremsstrahlung source.

Doppler measurement of implosion velocity in fast Z-pinch x-ray sources

The observation of Doppler splitting in K-shell x-ray lines emitted from optically thin dopants is used to infer implosion velocities of up to 70 cm/μs in wire-array and gas-puff Z pinches at drive currents of 15-20 MA. These data can benchmark numerical implosion models, which produce reasonable agreement with the measured velocity in the emitting region. Doppler splitting is obscured in lines with strong opacity, but red-shifted absorption produced by the cooler halo of material backlit by the hot core assembling on axis can be used to diagnose velocity in the trailing mass.

Effects of mass ablation on the scaling of X-ray power with current in wire-array Z pinches

X-ray production by imploding wire-array Z pinches is studied using radiation magnetohydrodynamics simulation. It is found that the density distribution created by ablating wire material influences both x-ray power production, and how the peak power scales with applied current. For a given array there is an optimum ablation rate that maximizes the peak x-ray power, and produces the strongest scaling of peak power with peak current. This work is consistent with trends in wire-array Z pinch x-ray power scaling experiments on the Z accelerator.

Radiation energetics of ICF-relevant wire-array Z pinches

Short-implosion-time 20-mm diameter, 300-wire tungsten arrays maintain high peak x-ray powers despite a reduction in peak current from 19 to 13 MA. The main radiation pulse on tests with a 1-mm on-axis rod may be explained by the observable j x B work done during the implosion, but bare-axis tests require sub-mm convergence of the magnetic field not seen except perhaps in >1 keV emission. The data include the first measurement of the imploding mass density profile of a wire-array Z pinch that further constrains simulation models.

Characteristics and scaling of tungsten-wire-array z -pinch implosion dynamics at 20 MA

We present observations for 20-MA wire-array z pinches of an extended wire ablation period of 57%+/-3% of the stagnation time of the array and non-thin-shell implosion trajectories. These experiments were performed with 20-mm-diam wire arrays used for the double- z -pinch inertial confinement fusion experiments [M. E. Cuneo, Phys. Rev. Lett. 88, 215004 (2002)] on the Z accelerator [R. B. Spielman, Phys. Plasmas 5, 2105 (1998)]. This array has the smallest wire-wire gaps typically used at 20 MA (209 microm ). The extended ablation period for this array indicates that two-dimensional (r-z) thin-shell implosion models that implicitly assume wire ablation and wire-to-wire merger into a shell on a rapid time scale compared to wire acceleration are fundamentally incorrect or incomplete for high-wire-number, massive (>2 mg/cm) , single, tungsten wire arrays. In contrast to earlier work where the wire array accelerated from its initial position at approximately 80% of the stagnation time, our results show that very late acceleration is not a universal aspect of wire array implosions. We also varied the ablation period between 46%+/-2% and 71%+/-3% of the stagnation time, for the first time, by scaling the array diameter between 40 mm (at a wire-wire gap of 524 mum ) and 12 mm (at a wire-wire gap of 209 microm ), at a constant stagnation time of 100+/-6 ns . The deviation of the wire-array trajectory from that of a thin shell scales inversely with the ablation rate per unit mass: f(m) proportional[dm(ablate)/dt]/m(array). The convergence ratio of the effective position of the current at peak x-ray power is approximately 3.6+/-0.6:1 , much less than the > or = 10:1 typically inferred from x-ray pinhole camera measurements of the brightest emitting regions on axis, at peak x-ray power. The trailing mass at the array edge early in the implosion appears to produce wings on the pinch mass profile at stagnation that reduces the rate of compression of the pinch. The observation of precursor pinch formation, trailing mass, and trailing current indicates that all the mass and current do not assemble simultaneously on axis. Precursor and trailing implosions appear to impact the efficiency of the conversion of current (driver energy) to x rays. An instability with the character of an m = 0 sausage grows rapidly on axis at stagnation, during the rise time of pinch power. Just after peak power, a mild m = 1 kink instability of the pinch occurs which is correlated with the higher compression ratio of the pinch after peak power and the decrease of the power pulse. Understanding these three-dimensional, discrete-wire implosion characteristics is critical in order to efficiently scale wire arrays to higher currents and powers for fusion applications.

Mass-profile and instability-growth measurements for 300-wire Z-pinch implosions driven by 14-18 MA

We present the first comprehensive study of high wire-number, wire-array Z-pinch dynamics at 14-18 MA using x-ray backlighting and optical shadowgraphy diagnostics. The cylindrical arrays retain slowly expanding, dense wire cores at the initial position up to 60% of the total implosion time. Azimuthally correlated instabilities at the array edge appear during this stage which continue to grow in amplitude and wavelength after the start of bulk motion, resulting in measurable trailing mass that does not arrive on axis before peak x-ray emission.