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The raw bulk metagenomic data were trimmed and de-novo assembled. The assemblies were screened for viral contigs (by virsorter2, Deepvirfinder, VIBRANT, checkV) and binned to generate MAGs that were further refined by Hi-C read links.
Quercus variabilis (Fagaceae) is an ecologically and economically important deciduous broadleaved tree species native to and widespread in East Asia. It is a valuable woody species and an indicator of local forest health, and occupies a dominant position in forest ecosystems in East Asia. However, genomic resources from Q. variabilis are still lacking. Here, we present a high-quality Q. variabilis genome generated by PacBio HiFi and Hi-C sequencing. The assembled genome size is 787 Mb, with a contig N50 of 26.04 Mb and scaffold N50 of 64.86 Mb, comprising 12 pseudo-chromosomes. The repetitive sequences constitute 67.6% of the genome, of which the majority are long terminal repeats, accounting for 46.62% of the genome. We used ab initio , RNA sequence-based and homology-based predictions to identify protein-coding genes. A total of 32,466 protein-coding genes were identified, of which 95.11% could be functionally annotated. Evolutionary analysis showed that Q. variabilis was more closely related to Q. suber than to Q. lobata or Q. robur. We found no evidence for species-specific whole genome duplications in Quercus after the species had diverged. This study provides the first genome assembly and the first gene annotation data for Q. variabilis. These resources will inform the design of further breeding strategies, and will be valuable in the study of genome editing and comparative genomics in oak species.
In 0.5 arcsec/pixel TRACE coronal EUV images, the corona rooted in active regions that are at the limb and are not flaring is seen to consist of (1) a complex array of discrete loops and plumes embedded in (2) a diffuse ambient component that shows no fine structure and gradually fades with height. For each of two not-flaring active regions, found that the diffuse component is (1) approximately isothermal and hydrostatic and (2) emits well over half of the total EUV luminosity of the active-region corona. Here, from a TRACE Fe XII coronal image of another not-flaring active region, the large sunspot active region AR 10652 when it was at the west limb on 30 July 2004, we separate the diffuse component from the discrete loop component by spatial filtering, and find that the diffuse component has about 60% of the total luminosity. If under much higher spatial resolution than that of TRACE (e. g., the 0.1 arcsec/pixel resolution of the Hi-C sounding-rocket experiment proposed by J. W. Cirtain et al), most of the diffuse component remains diffuse rather being resolved into very narrow loops and plumes, this will raise the possibility that the EUV corona in active regions consists of two basically different but comparably luminous components: one being the set of discrete bright loops and plumes and the other being a truly diffuse component filling the space between the discrete loops and plumes. This dichotomy would imply that there are two different but comparably powerful coronal heating mechanisms operating in active regions, one for the distinct loops and plumes and another for the diffuse component. We present a scenario in which (1) each discrete bright loop or plume is a flux tube that was recently reconnected in a burst of reconnection, and (2) the diffuse component is heated by MHD waves that are generated by these reconnection events and by other fine-scale explosive reconnection events, most of which occur in and below the base of the corona where they are seen as UV explosive events, EUV blinkers, and type II spicules. These MHD waves propagate across field lines and dissipate, heating the plasma in the field between the bright loops and plumes.
The recently-launched High-resolution Coronal imager (Hi-C) sounding rocket provided the highest resolution images of coronal loops and other small-scale structures in the 193 Angstrom passband to date. With just 5 minutes of observations, the instrument recorded a variety of dynamic coronal events -- including even a small B-class flare. We will present our results comparing these extreme-ultraviolet (EUV) observations with X-ray imaging from Hinode/XRT as well as EUV AIA data to identify sources of hot plasma rooted in the photosphere and track their affect on the overall topology and dynamics of the active region.
We present an overview of solar sounding rocket instruments developed jointly by NASA Marshall Space Flight Center and the University of Alabama in Huntsville. The High Resolution Coronal Imager (Hi-C) is an EUV (19.3 nm) imaging telescope which was flown successfully in July 2012. The Chromospheric Lyman-Alpha SpectroPolarimeter (CLASP) is a Lyman Alpha (121.6 nm) spectropolarimeter developed jointly with the National Astronomical Observatory of Japan and scheduled for launch in 2015. The Marshall Grazing Incidence X-ray Spectrograph is a soft X-ray (0.5-1.2 keV) stigmatic spectrograph designed to achieve 5 arcsecond spatial resolution along the slit.
The recently-launched High-resolution Coronal imager (Hi-C) sounding rocket provided the highest resolution images of coronal loops and other small-scale structures in the 193 Angstrom passband to date. With just 5 minutes of observations, the instrument recorded a variety of dynamic coronal events -- including even a small B-class flare. We will present our results comparing these extreme-ultraviolet (EUV) observations with X-ray imaging from Hinode/XRT as well as EUV AIA data to identify sources of hot plasma rooted in the photosphere and track their affect on the overall topology and dynamics of the active region.
The coronal heating problem remains unsolved today, 80 years after its discovery, despite 50 years of suborbital and orbital coronal observatories. Tens of theoretical coronal heating mechanisms have been suggested, but only a few have been able to be ruled out. In this talk, we will explore the reasons for the slow progress and discuss the measurements that will be needed for potential breakthrough, including imaging the solar corona at small spatial scales, measuring the chromospheric magnetic fields, and detecting the presence of high temperature, low emission measure plasma. We will discuss three sounding rocket instruments developed to make these measurements: the High resolution Resolution Coronal Imager (Hi-C), the Chromospheric Lyman-Alpha Spectropolarimeter (CLASP), and the Marshall Grazing Incidence X-ray Spectrometer (MaGIXS).
We present high resolution (0.2”) high cadence (5s) extreme ultraviolet (EUV) observations of small-scale jetlet-like features and spicule-like features observed with NASA’s High-resolution Coronal Imager2.1 (Hi-C) during its 5‐min observing span. We investigate the magnetic setting of 4 on-disk jetlets and 2 on-disk spicules by using high resolution 172A images from Hi-‐C and EUV images from Solar Dynamics Observatory (SDO)/Atmospheric Imaging Assembly (AIA) and line-of-sight magnetograms from SDO/Helioseismic and Magnetic Imager (HMI). The jetlets and spicules are at edges of magnetic network lanes. From magnetograms co-aligned with the Hi-C and AIA images, we find that the jetlets stem from sites of likely flux cancelation between merging majority-polarity and weaker minority-polarity flux, but in contrast to larger jetlets observed by IRIS some do not show obvious enhanced brightenings at their base. Based on the similarity of these observations of approx. 4 obvious Hi-C small jetlets with our previous observations of 10 IRIS larger jetlets and approx. 30 coronal jets in quiet regions and coronal holes, we infer that flux cancelation is probably the essential process in the buildup and triggering of jetlets. Our observations suggest that network jetlet eruptions, large and small, are small-scale analogs of both larger-scale coronal jet eruptions and the still-larger-scale eruptions that makemajor CMEs. For simplicitywe will use termjetlets for jetlet-like features and spicules for spicule-like features.