From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (Pinus lambertiana).

We investigate the utility and scalability of new read cloud technologies to improve the draft genome assemblies of the colossal, and largely repetitive, genomes of conifers. Synthetic long read technologies have existed in various forms as a means of reducing complexity and resolving repeats since the outset of genome assembly. Recently, technologies that combine subhaploid pools of high molecular weight DNA with barcoding on a massive scale have brought new efficiencies to sample preparation and data generation. When combined with inexpensive light shotgun sequencing, the resulting data can be used to scaffold large genomes. The protocol is efficient enough to consider routinely for even the largest genomes. Conifers represent the largest reference genome projects executed to date. The largest of these is that of the conifer Pinus lambertiana (sugar pine), with a genome size of 31 billion bp. In this paper, we report on the molecular and computational protocols for scaffolding the P. lambertiana genome using the library technology from 10× Genomics. At 247,000 bp, the NG50 of the existing reference sequence is the highest scaffold contiguity among the currently published conifer assemblies; this new assembly's NG50 is 1.94 million bp, an eightfold increase

The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.

Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets

Circumventing Heterozygosity: Sequencing the Amplified Genome of a Single Haploid Drosophila melanogaster Embryo

Heterozygosity is a major challenge to efficient, high-quality genomic assembly and to the full genomic survey of polymorphism and divergence. In Drosophila melanogaster lines derived from equatorial populations are particularly resistant to inbreeding, thus imposing a major barrier to the determination and analyses of genomic variation in natural populations of this model organism. Here we present a simple genome sequencing protocol based on the whole-genome amplification of the gynogenetically derived haploid genome of a progeny of females mated to males homozygous for the recessive male sterile mutation, ms(3)K81. A single “lane” of paired-end sequences (2 × 76 bp) provides a good syntenic assembly with >95% high-quality coverage (more than five reads). The amplification of the genomic DNA moderately inflates the variation in coverage across the euchromatic portion of the genome. It also increases the frequency of chimeric clones. But the low frequency and random genomic distribution of the chimeric clones limits their impact on the final assemblies. This method provides a solid path forward for population genomic sequencing and offers applications to many other systems in which small amounts of genomic DNA have unique experimental relevance

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).

Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq have been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly. A technology comparison is provided here to contribute to the otherwise scarce comparisons of second and third generation transcriptome sequencing approaches in plant species. In addition, the transcriptome reference was essential for gene model identification and quality assessment in the parallel project responsible for sequencing and assembly of the entire genome. In this study, the transcriptomic data were also used to address questions surrounding lineage-specific Dicer-like proteins in conifers. These proteins play a role in the control of transposable element proliferation and the related genome expansion in conifers

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco (Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp). Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms

Janus: Launch of a NASA SmallSat Mission to Near-Earth Binary Asteroids

Janus is a two-spacecraft SmallSat mission to fly by two different pairs of binary near Earth asteroids, (175706) 1996 FG3 and (35107) 1991 VH. The two identical Janus spacecraft are scheduled to launch during a launch period opening 1 August 2022 as secondary payloads with the NASA Psyche mission, on a SpaceX Falcon Heavy launch vehicle. Janus is led by principal investigator Dr. Dan Scheeres at the University of Colorado Boulder and managed, built, and operated by Lockheed Martin. These planetary SmallSats share many deep space challenges similar to larger missions: Janus must execute deep space maneuvers to achieve hundreds of meters per second ΔV to reach its destinations, close a telecommunication link at ranges up to 2.4 AU, autonomously manage a several-month-long telecommunications blackout during solar conjunction, operate at a maximum Sun range of 1.62 AU, and survive for approximately four years in interplanetary space before encountering their target asteroids. During the encounters, the spacecraft will return high resolution visible and infra-red images of the asteroids. In getting Janus to the pad, the implementation team successfully managed an aggressive mission schedule despite COVID-19 related supply chain impacts and work environments, all while remaining on target for the SIMPLEx-2 cost cap. Janus is a pathfinder for achievable and affordable SmallSat science missions and demonstrates the valuable partnership between an experienced deep space mission engineering team, the SmallSat commercial component industry, and a forward- looking NASA model for Class-D science missions

Apremilast, an oral phosphodiesterase 4 (PDE4) inhibitor, in patients with moderate to severe plaque psoriasis: Results of a phase III, randomized, controlled trial (Efficacy and Safety Trial Evaluating the Effects of Apremilast in Psoriasis [ESTEEM] 1)

BackgroundApremilast works intracellularly to regulate inflammatory mediators.ObjectiveESTEEM 1 evaluated efficacy/safety of apremilast at 30 mg twice a day for moderate to severe plaque psoriasis.MethodsThis phase III, multicenter, double-blind, placebo-controlled study randomized adults (2:1) to apremilast or placebo. At week 16, the placebo group switched to apremilast through week 32, followed by a randomized treatment withdrawal phase to week 52. Binary end points were analyzed using χ2 test; continuous end points used analysis of covariance.ResultsIn all, 844 patients were randomized (n = 282, placebo; n = 562, apremilast). At week 16, significantly more patients taking apremilast achieved 75% or greater reduction from baseline Psoriasis Area and Severity Index score (PASI-75) (33.1%) versus placebo (5.3%, P < .0001; primary end point). Most (61.0%) patients rerandomized to apremilast at week 32 achieved PASI-75 at week 52 versus 11.7% rerandomized to placebo. Of patients rerandomized to apremilast at week 32, mean percentage change from baseline PASI score was −88% to −81% (weeks 32-52). During the placebo-controlled period, 55.7% and 69.3% of patients randomized to placebo and apremilast, respectively, had 1 or more adverse events. Most adverse events were mild/moderate in severity. No new significant adverse events emerged with continued apremilast exposure versus the placebo-controlled period.LimitationsData were limited to 52 weeks and may not generalize to nonplaque psoriasis.ConclusionsApremilast was effective in moderate to severe plaque psoriasis

Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans

The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. Here we present a population genetic analysis of Drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba. We discovered previously unknown, large-scale fluctuations of polymorphism and divergence along chromosome arms, and significantly less polymorphism and faster divergence on the X chromosome. We generated a comprehensive list of functional elements in the D. simulans genome influenced by adaptive evolution. Finally, we characterized genomic patterns of base composition for coding and noncoding sequence. These results suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophila genome, and provide a rich resource for the investigation of adaptive evolution and functional variation in D. simulans

Estimation of composition of quinoa (Chenopodium quinoa Willd.) grains by Near-Infrared Transmission spectroscopy

The aim of this study was to develop robust chemometric models for the routine determination of dietary constituents of quinoa (Chenopodium quinoa Willd.) using Near-Infrared Transmission (NIT) spectroscopy. Spectra of quinoa grains of 77 cultivars were acquired while dietary constituents were determined by reference methods. Spectra were subjected to multiplicative scatter correction (MSC) or extended multiplicative signal correction (EMSC), and were (or not) treated by Savitzky-Golay (SG) filters. Latent variables were extracted by partial least squares regression (PLSR) or canonical powered partial least squares (CPPLS) algorithms, and the accuracy and predictability of all modelling strategies were compared. Smoothing the spectra improved the accuracy of the models for fat (root mean square error of cross-validation, RMSECV: 0.3190.327%), ashes (RMSECV: 0.2240.230%), and particularly for protein (RMSECV: 0.5180.564%) and carbohydrates (RMSECV: 0.5420.559%), while enhancing the prediction performance, particularly, for fat (root mean square error of prediction, RMSEP: 0.2480.335%) and ashes (RMSEP: 0.1370.191%). Although the highest predictability was achieved for ashes (SG-filtered EMSC/PLSR: bootstrapped 90% confidence interval for RMSEP: [0.3760.512]) and carbohydrates (SG-filtered MSC/CPPLS: 90% CI RMSEP: [0.6510.901]), precision was acceptable for protein (SG-filtered MSC/CPPLS: 90% CI RMSEP: [0.6500.852]), fat (SG-filtered EMSC/CPPLS: 90% CI RMSEP: [0.4780.654]) and moisture (non-filtered EMSC/PLSR: 90% CI RMSEP: [0.6580.833]).Mr. Encina-Zelada acknowledges the financial aid provided by the Peruvian National Programme of Scholarships and Student Loans (PRONABEC) in the mode of PhD grants (Presidente de La República Grant Number 183308). Dr. Gonzales-Barron wishes to acknowledge the financial support provided by the Portuguese Foundation for Science and Technology (FCT) through the award of a five-year Investigator Fellowship (IF) in the mode of Development Grants (IF/00570)