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Highlights d Long-read sequencing of 100 tomato genomes uncovered 238,490 structural variants d Transposons underlie many SVs, and SV hotspots revealed large introgressions d SVs associated with genes are predictive of population-scale changes in expression d New genome assemblies resolved complex breeding QTLs caused by SVs

We present RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes. After the pseudomolecules are constructed, RaGOO identifies structural variants, including those spanning sequencing gaps. We show that RaGOO accurately orders and orients 3 de novo tomato genome assemblies, including the widely used M82 reference cultivar. We then demonstrate the scalability and utility of RaGOO with a pan-genome analysis of 103 Arabidopsis thaliana accessions by examining the structural variants detected in the newly assembled pseudomolecules. RaGOO is available open source at https://github.com/malonge/RaGOO.

The National Spherical Torus Experiment (NSTX) is being built at PPPL to test the fusion physics principles for the ST concept at the MA level. The NSTX nominal plasma parameters are R 0 = 85 cm, a = 67 cm, R/a ³ 1.26, B T = 3 kG, I p = 1 MA, q 95 = 14, elongation k £ 2.2, triangularity d £ 0.5, and plasma pulse length of up to 5 sec. The plasma heating / current drive (CD) tools are High Harmonic Fast Wave (HHFW) (6 MW, 5 sec), Neutral Beam Injection (NBI) (5 MW, 80 keV, 5 sec), and Coaxial Helicity Injection (CHI). Theoretical calculations predict that NSTX should provide exciting possibilities for exploring a number of important new physics regimes including very high plasma beta, naturally high plasma elongation, high bootstrap current fraction, absolute magnetic well, and high pressure driven sheared flow. In addition, the NSTX program plans to explore fully noninductive plasma start-up as well as a dispersive scrape-off layer for heat and particle flux handling. MotivationA broad range of encouraging advances has been made in the exploration of the Spherical Torus (ST) concept. 1 Such advances include promising experimental data from pioneering experiments, theoretical predictions, near-term fusion energy development projections such as the Volume Neutron Source 2 , and future applications such as power plant studies 3 . Recently, the START device has achieved a very high toroidal beta b T » 40% regime with b N » 5.0 at low q 95 » 3. 4 The National Spherical Torus Experiment (NSTX) is being built at PPPL to test the fusion physics principles for the ST concept at the MA level. 5 The NSTX device/plasma configuration allows the plasma shaping factor, I p q 95 / a B , to reach as high as 80 an order of magnitude greater than that achieved in conventional high aspect ratio tokamaks. The key physics objective of NSTX is to attain an advanced ST regime; i.e., simultaneous ultra high beta (b), high confinement, and high bootstrap current fraction (f bs ). 6 This regime is considered to be essential for the development of an economical ST power-plant because it minimizes the recirculating power and power plant core size. Other NSTX mission elements crucial for ST power plant development are the demonstration at the MA level of fully noninductive operation and the development of acceptable power and particle handling concepts. NSTX Facility Design Capability and Technology ChallengesThe NSTX facility is designed to achieve the NSTX mission with the following capabilities: ¥ I p = 1 MA for low collisionality at relevant densities, ¥ R/a ³ 1.26, including OH solenoid and coaxial helicity injection 7 (CHI) for startup,

Background Repeat COVID-19 molecular testing can lead to positive test results after negative tests and to multiple positive test results over time. The association between positive tests and infectious virus is important to quantify. Methods A two months cohort of retrospective data and consecutively collected specimens from COVID-19 patients or patients under investigation were used to understand the correlation between prolonged viral RNA positive test results, cycle threshold (Ct) values and growth of SARS-CoV-2 in cell culture. Whole genome sequencing was used to confirm virus genotype in patients with prolonged viral RNA detection. Droplet digital PCR (ddPCR) was used to assess the rate of false negative COVID-19 diagnostic tests. Results In two months, 29,686 specimens were tested and 2,194 patients received repeated testing. Virus recovery in cell culture was noted in specimens with SARS-CoV-2 target genes’ Ct value average of 18.8 ± 3.4. Prolonged viral RNA shedding was associated with positive virus growth in culture in specimens collected up to 20 days after the first positive result but mostly in individuals symptomatic at time of sample collection. Whole genome sequencing provided evidence the same virus was carried over time. Positive tests following negative tests had Ct values higher than 29.5 and were not associated with virus culture. ddPCR was positive in 5.6% of negative specimens collected from COVID-19 confirmed or clinically suspected patients. Conclusions Low Ct values in SARS-CoV-2 diagnostic tests were associated with virus growth in cell culture. Symptomatic patients with prolonged viral RNA shedding can also be infectious.

After many years of fusion research, the conditions needed for a D–T fusion reactor have been approached on the Tokamak Fusion Test Reactor (TFTR) [Fusion Technol. 21, 1324 (1992)]. For the first time the unique phenomena present in a D–T plasma are now being studied in a laboratory plasma. The first magnetic fusion experiments to study plasmas using nearly equal concentrations of deuterium and tritium have been carried out on TFTR. At present the maximum fusion power of 10.7 MW, using 39.5 MW of neutral-beam heating, in a supershot discharge and 6.7 MW in a high-βp discharge following a current rampdown. The fusion power density in a core of the plasma is ≊2.8 MW m−3, exceeding that expected in the International Thermonuclear Experimental Reactor (ITER) [Plasma Physics and Controlled Nuclear Fusion Research (International Atomic Energy Agency, Vienna, 1991), Vol. 3, p. 239] at 1500 MW total fusion power. The energy confinement time, τE, is observed to increase in D–T, relative to D plasmas, by 20% and the ni(0) Ti(0) τE product by 55%. The improvement in thermal confinement is caused primarily by a decrease in ion heat conductivity in both supershot and limiter-H-mode discharges. Extensive lithium pellet injection increased the confinement time to 0.27 s and enabled higher current operation in both supershot and high-βp discharges. Ion cyclotron range of frequencies (ICRF) heating of a D–T plasma, using the second harmonic of tritium, has been demonstrated. First measurements of the confined alpha particles have been performed and found to be in good agreement with TRANSP [Nucl. Fusion 34, 1247 (1994)] simulations. Initial measurements of the alpha ash profile have been compared with simulations using particle transport coefficients from He gas puffing experiments. The loss of alpha particles to a detector at the bottom of the vessel is well described by the first-orbit loss mechanism. No loss due to alpha-particle-driven instabilities has yet been observed. D–T experiments on TFTR will continue to explore the assumptions of the ITER design and to examine some of the physics issues associated with an advanced tokamak reactor.

Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes, however, the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5-gigabase (Gb) diploid pepper (Capsicum annuum) genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus. With a phased assembly approach, we targeted a heterozygous F1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/deletion. The Supernova software generated a highly ordered, more contiguous sequence assembly than all currently available C. annuum reference genomes. Over 83% of the final assembly was anchored and oriented using four publicly available de novo linkage maps. A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly. The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F1 sample that represents pungent and nonpungent peppers, as well as nearly full recovery of the BUSCO2 gene set within each of the two haplotypes. The most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant genomes. This technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.

Merr.) is a fruit crop originated and domesticated in South America. According to Bertoni 2 , the genus name Ananas means 'excellent fruit' in the Guaraní language of Paraguay. Pineapple was domesticated >6,000 years ago with archaeobotanical remains dated 3,500 years ago in South America and distributed to Mesoamerica >2,500 years ago 3-5. Pineapple is clonally propagated using the leafy fruit crown, slips or suckers. Red pineapple (Ananas comosus var. bracteatus) was anciently cultivated for fiber, fruit juice and as a living hedge, and is now a pantropical ornamental 6,7. The bracteatus plant is conspicuous for its bright pink-to-red colored fruit. The name 'bracteatus' refers to its long bracts. The plant is vigorous with long leaves, coarse spines and abundant suckers. Plant fibers have been used in numerous applications that are beneficial to agriculture and the environment, partly