Genome resources for three modern cotton lines guide future breeding efforts.

Cotton (Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars ('UGA230', 'UA48' and 'CSX8308') and updating the 'TM-1' cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from 'Pima' cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.

Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders.

Variant detection from long-read genome sequencing (lrGS) has proven to be considerably more accurate and comprehensive than variant detection from short-read genome sequencing (srGS). However, the rate at which lrGS can increase molecular diagnostic yield for rare disease is not yet precisely characterized. We performed lrGS using Pacific Biosciences "HiFi" technology on 96 short-read-negative probands with rare disease that were suspected to be genetic. We generated hg38-aligned variants and de novo phased genome assemblies, and subsequently annotated, filtered, and curated variants using clinical standards. New disease-relevant or potentially relevant genetic findings were identified in 16/96 (16.7%) probands, eight of which (8/96, 8.33%) harbored pathogenic or likely pathogenic variants. Newly identified variants were visible in both srGS and lrGS in nine probands (~9.4%) and resulted from changes to interpretation mostly from recent gene-disease association discoveries. Seven cases included variants that were only interpretable in lrGS, including copy-number variants, an inversion, a mobile element insertion, two low-complexity repeat expansions, and a 1 bp deletion. While evidence for each of these variants is, in retrospect, visible in srGS, they were either: not called within srGS data, were represented by calls with incorrect sizes or structures, or failed quality-control and filtration. Thus, while reanalysis of older data clearly increases diagnostic yield, we find that lrGS allows for substantial additional yield (7/96, 7.3%) beyond srGS. We anticipate that as lrGS analysis improves, and as lrGS datasets grow allowing for better variant frequency annotation, the additional lrGS-only rare disease yield will grow over time.

A multi-institutional pediatric dataset of clinical radiology MRIs by the Children's Brain Tumor Network.

Pediatric brain and spinal cancers remain the leading cause of cancer-related death in children. Advancements in clinical decision-support in pediatric neuro-oncology utilizing the wealth of radiology imaging data collected through standard care, however, has significantly lagged other domains. Such data is ripe for use with predictive analytics such as artificial intelligence (AI) methods, which require large datasets. To address this unmet need, we provide a multi-institutional, large-scale pediatric dataset of 23,101 multi-parametric MRI exams acquired through routine care for 1,526 brain tumor patients, as part of the Children's Brain Tumor Network. This includes longitudinal MRIs across various cancer diagnoses, with associated patient-level clinical information, digital pathology slides, as well as tissue genotype and omics data. To facilitate downstream analysis, treatment-naïve images for 370 subjects were processed and released through the NCI Childhood Cancer Data Initiative via the Cancer Data Service. Through ongoing efforts to continuously build these imaging repositories, our aim is to accelerate discovery and translational AI models with real-world data, to ultimately empower precision medicine for children.

Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA.

Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy and bioproducts. Hybrid aspen Populus tremula × P. alba INRA 717-1B4 is a widely used transformation model in tree functional genomics and biotechnology research. As an outcrossing interspecific hybrid, its genome is riddled with sequence polymorphisms which present a challenge for sequence-sensitive analyses. Here we report a telomere-to-telomere genome for this hybrid aspen with two chromosome-scale, haplotype-resolved assemblies. We performed a comprehensive analysis of the repetitive landscape and identified both tandem repeat array-based and array-less centromeres. Unexpectedly, the most abundant satellite repeats in both haplotypes lie outside of the centromeres, consist of a 147 bp monomer PtaM147, frequently span >1 megabases, and form heterochromatic knobs. PtaM147 repeats are detected exclusively in aspens (section Populus) but PtaM147-like sequences occur in LTR-retrotransposons of closely related species, suggesting their origin from the retrotransposons. The genomic resource generated for this transformation model genotype has greatly improved the design and analysis of genome editing experiments that are highly sensitive to sequence polymorphisms. The work should motivate future hypothesis-driven research to probe into the function of the abundant and aspen-specific PtaM147 satellite DNA.

Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii.

The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the 2 major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and Ka/Ks ratio results characterized the evolutionary features of DMR-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology.

Direct Fabrication of Functional Shapes on 3D Surfaces Using Electrospinning.

In this work, we demonstrate the ability to simultaneously pattern fibers and fabricate functional 2D and 3D shapes (e.g., letters, mask-like structures with nose bridges and ear loops, aprons, hoods) using a single step electrospinning process. Using 2D and 3D mesh templates, electrospun fibers were preferentially attracted to the metal protrusions relative to the voids so that the pattern of the electrospun mat mimicked the woven mesh macroscopically. On a microscopic scale, the electrostatic lensing effect decreased fiber diameter and narrowed the fiber size distribution, e.g., the coefficient of variation of the fiber diameter for sample collected on a 0.6 mm mesh was 14% compared to 55% for the sample collected on foil). Functionally, the mesh did not affect the wettability of the fiber mats. Notably, the fiber patterning increased the rigidity of the fiber mat. There was a 2-fold increase in flexural rigidity using the 0.6 mm mesh compared to the sample collected on foil. Overall, we anticipate this approach will be a versatile tool for design and fabrication of 2D and 3D patterns with potential applications in personalized wound care and surgical meshes.

A novel role for trithorax in the gene regulatory network for a rapidly evolving fruit fly pigmentation trait.

Animal traits develop through the expression and action of numerous regulatory and realizator genes that comprise a gene regulatory network (GRN). For each GRN, its underlying patterns of gene expression are controlled by cis-regulatory elements (CREs) that bind activating and repressing transcription factors. These interactions drive cell-type and developmental stage-specific transcriptional activation or repression. Most GRNs remain incompletely mapped, and a major barrier to this daunting task is CRE identification. Here, we used an in silico method to identify predicted CREs (pCREs) that comprise the GRN which governs sex-specific pigmentation of Drosophila melanogaster. Through in vivo assays, we demonstrate that many pCREs activate expression in the correct cell-type and developmental stage. We employed genome editing to demonstrate that two CREs control the pupal abdomen expression of trithorax, whose function is required for the dimorphic phenotype. Surprisingly, trithorax had no detectable effect on this GRN's key trans-regulators, but shapes the sex-specific expression of two realizator genes. Comparison of sequences orthologous to these CREs supports an evolutionary scenario where these trithorax CREs predated the origin of the dimorphic trait. Collectively, this study demonstrates how in silico approaches can shed novel insights on the GRN basis for a trait's development and evolution.

The effects of feeding benzoic acid and/or active dry yeast (Saccharomyces cerevisiae) on fatty acid composition, sensory attributes, and retail shelf-life of beef longissimus thoracis.

Fifty-nine Angus-cross steers (492 ± SD 36 kg) were arranged in a randomized complete block design and assigned to the following dietary treatments for the final 106 days of the finishing phase: no supplementation (CON), 0.5% benzoic acid (ACD), 3 g/steer/d active dry Saccharomyces cerevisiae (YST), or both [0.5% benzoic acid and 3 g/steer/d S. cerevisiae (AY)]. Steers were slaughtered at a commercial facility where longissimus thoracis (IMPS #107 Beef Rib) samples were retrieved and evaluated for fatty acid composition, sensory attributes, and shelf-life during a simulated retail display period. Data (N = 57) were analyzed using dietary treatment as a fixed effect, blocking weight at the beginning of the study as a random effect, and steer as the experimental unit. Muscle pH and proximate composition (moisture and intramuscular lipid) for longissimus samples were not different (P ≥ 0.39) among dietary treatments. Most fatty acid profile values and calculations were not different among dietary treatments (P ≥ 0.10); however, the n-6:n-3 ratio differed (P = 0.01), with ACD samples having lower n-6:n-3 compared with CON and YST samples while AY samples were intermediate and not different from other dietary treatments. The trained sensory panel did not detect differences among dietary treatments (P ≥ 0.23) for juiciness, beef flavor intensity, or off-flavor intensity; however, they did score AY samples as chewier than ACD samples with CON and YST samples intermediate and not different from other dietary treatments. Yet, tenderness was not different when scored by trained panelists (P = 0.10) or measured instrumentally (P = 0.21). Total color change tended to differ (P = 0.09) during the 12-d simulated retail display period with AY samples experiencing less color change compared with YST samples, while CON and ACD samples were intermediate and not different from other dietary treatments. Lipid oxidation (as measured with TBARS) tended to differ (P = 0.08) following the 12-d simulated retail display period with ACD and AY samples experiencing lower levels of oxidation compared with CON, while YST samples were intermediate and not different from other dietary treatments. Overall, these results suggest there were no negative impacts on meat quality when finishing steers were supplemented with either benzoic acid or S. cerevisiae, and there may even be advantages for fatty acid composition and oxidative stability when steers were supplemented with benzoic acid.

Widespread cis- and trans-regulatory evolution underlies the origin, diversification, and loss of a sexually dimorphic fruit fly pigmentation trait.

Changes in gene expression are a prominent feature of morphological evolution. These changes occur to hierarchical gene regulatory networks (GRNs) of transcription factor genes that regulate the expression of trait-building differentiation genes. While changes in the expression of differentiation genes are essential to phenotypic evolution, they can be caused by mutations within cis-regulatory elements (CREs) that drive their expression (cis-evolution) or within genes for CRE-interacting transcription factors (trans-evolution). Locating these mutations remains a challenge, especially when experiments are limited to one species that possesses the ancestral or derived phenotype. We investigated CREs that control the expression of the differentiation genes tan and yellow, the expression of which evolved during the gain, modification, and loss of dimorphic pigmentation among Sophophora fruit flies. We show these CREs to be necessary components of a pigmentation GRN, as deletion from Drosophila melanogaster (derived dimorphic phenotype) resulted in lost expression and lost male-specific pigmentation. We evaluated the ability of orthologous CRE sequences to drive reporter gene expression in species with modified (Drosophila auraria), secondarily lost (Drosophila ananassae), and ancestrally absent (Drosophila willistoni) pigmentation. We show that the transgene host frequently determines CRE activity, implicating trans-evolution as a significant factor for this trait's diversity. We validated the gain of dimorphic Bab transcription factor expression as a trans-change contributing to the dimorphic trait. Our findings suggest an amenability to change for the landscape of trans-regulators and begs for an explanation as to why this is so common compared to the evolution of differentiation gene CREs.

Gender Gap: A Qualitative Study of Women and Leadership Acquisition in Anesthesiology.

BACKGROUND: The representation of women among leaders in the field of anesthesia continues to trail that of their male counterparts. This qualitative study was conducted to understand the pathway of leadership acquisition among women in the field of anesthesiology. METHODS: Using constructivist grounded theory, we sought to determine whether there were specific internal or external factors that were common to women in leadership in the specialty field of anesthesiology, and specifically, how they obtained leadership positions. Semistructured interviews were conducted for data collection. A total of 26 women in leadership positions in anesthesiology participated in this study. RESULTS: The analysis of these interviews resulted in the development of 4 common themes related to career pathways for these women in leadership. Each theme was examined in depth to determine the qualities necessary for individuals to advance in the field and the pathway to obtaining leadership positions. The findings of this study showed that early-career, high-value mentorship and sponsorship were important factors in leadership acquisition. Most participants (n = 20; 76%) had early mentors. Of those with early mentorship, 13 (65%) had high-value mentors, who we define as someone with power or authority. Sponsorship was the leading factor contributing to leadership acquisition. CONCLUSIONS: The results of this qualitative study may serve as a guide for encouraging female anesthesiologists with leadership aspirations. We suggest that the specialty field of anesthesiology institute targeted measures to help increase the percentage of women leadership with formal sponsorship programs at the local and national levels.

Looking the Part: Stereotypicality in Appearance Among White Professionals Predicts Leadership Attainment and Perceived Leadership Suitability.

This project explores the effects of racial phenotypic stereotypicality, or the degree to which a person's appearance is perceived as typical of their racial group, on leadership outcomes. Building on research showing that people hold an image of the ideal leader as a White person, we propose that looking more typically White may facilitate leadership attainment. In Study 1, which used a sample of American college football coaches (N = 1,106), White (vs. Black) coaches were more likely to occupy leadership roles. Furthermore, within race, stereotypicality positively predicted occupying a leadership or head-coach role among White professionals (and negatively predicted occupying a head-coach role among Black professionals). Study 2 elucidated a possible mechanism by showing a causal effect of stereotypicality on perceived suitability for leadership among Whites. These findings advance theorizing on the White-leader link and have implications for the ability of people of color to access lucrative professional roles.

Dynamic genome evolution in a model fern.

The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.

Implementation of the 'Kimberley Mum's Mood Scale' across primary health care services in the Kimberley region of Western Australia: A mixed methods assessment.

The Kimberley Mum's Mood Scale (KMMS) was co-designed with Aboriginal women and healthcare professionals to improve culturally appropriate screening practices for perinatal depression and anxiety. This paper describes the implementation of the KMMS across the remote Kimberley region of Western Australia from January 2018 to December 2021. We used the Dynamic Sustainability Framework to progress the implementation and assess at the intervention, practice setting and ecological system level using a mixed methods approach to analyse implementation. Rates of administration and results of screening were described using a retrospective audit of electronic medical records. Analyses of KMMS training registry, stakeholder engagement and sustainability initiatives were descriptive. KMMS acceptability was assessed using qualitative descriptive approaches to analyse patient feedback forms (n = 39), healthcare professional surveys (n = 15) and qualitative interviews with healthcare professionals (n = 6). We found a significant increase in overall recorded perinatal screening (pre-implementation: 30.4% v Year 3: 46.5%, P < 0.001) and use of the KMMS (pre-implementation: 16.4% v Year 3: 46.4%, P < 0.001). There was improved fidelity in completing the KMMS (from 2.3% to 61.8%, P < 0.001), with 23.6% of women screened recorded as being at increased risk of depression and anxiety. Most healthcare professionals noted the high levels of perinatal mental health concerns, stress, and trauma that their patients experienced, and identified the KMMS as the most appropriate perinatal screening tool. Aboriginal women reported that it was important for clinics to ask about mood and feelings during the perinatal period, and that the KMMS was appropriate. Aboriginal women consistently reported that it was good to have someone to talk to. This study demonstrates that innovation in perinatal depression and anxiety screening for Aboriginal women is possible and can be implemented into routine clinical care with the support of a sustained multi-year investment and strong partnerships.

The effects of feeding benzoic acid and/or live active yeast (Saccharomyces cerevisiae) on beef cattle performance, feeding behavior, and carcass characteristics.

Fifty-nine Angus-cross finishing steers were used to evaluate benzoic acid, active dry yeast (Saccharomyces cerevisiae), or a combination of benzoic acid and active dry yeast when supplemented in a high-grain finishing diet on live animal performance, feeding behavior, and carcass characteristics. Steers were fed a high-grain diet for the final 106 d of finishing. Treatments were as follows: no additional supplementation (CON), 0.5% benzoic acid (ACD), 3 g per head per day active dry S. cerevisiae (YST), or both 0.5% benzoic acid and 3 g/head per day S. cerevisiae (AY). Steers were weighed every 14 d, and ultrasound was performed for rib and rump fat thickness at the beginning (day 1), middle (day 57), and end (day 99) of the experiment. Insert feeding stations were used to collect individual feeding behavior data and DMI daily throughout. Blood samples were collected on days 21 and 22 and days 99-101 to assess plane of nutrition and metabolism. Ruminal fluid samples were collected by oral gavage 4 wk prior to slaughter. Carcass characteristics were examined at a federally inspected slaughter facility. Data were analyzed using PROC GLIMMIX of SAS with initial body weight (BW) as a covariate. Benzoic acid supplementation increased (P = 0.002) overall dry matter intake (DMI) compared to YST and CON steers, which may be due to a faster eating rate (P ≤ 0.008). Animal performance parameters (BW, average daily gain, feed conversion, and ultrasound fat depth) were not different (P ≥ 0.11) among treatment groups. Aspartate aminotransferase concentration was greatest (P ≤ 0.01) for YST steers, which may have been reflected in numerically greater liver abscesses. Carcass traits did not differ (P ≥ 0.33) among treatment groups. Ruminal pH was greater (P = 0.006) for ACD steers than AY steers (pH of 6.16 vs. 5.66, respectively), which indicated that there may be an interactive effect between benzoic acid and active dry yeast. To summarize, steers fed a high-grain finishing diet supplemented with benzoic acid, active dry yeast, or both benzoic acid and active dry yeast had similar growth performance and carcass characteristics compared to those without supplementation. However, the addition of benzoic acid alone increased DMI, variation in DMI, eating rate, and ruminal pH. Future studies are warranted to further investigate the impacts of benzoic acid on the ruminal environment of feedlot cattle.

Concurrent Improvement Observed in Patient-Reported Burden and Sensor-Collected Medication Use Among Patients Enrolled in a COPD Digital Health Program.

Background: The COPD assessment test (CAT) is an 8-item questionnaire widely used in clinical practice to assess patient burden of disease. Digital health platforms that leverage electronic medication monitors (EMMs) are used to track the time and date of maintenance and short-acting beta-agonist (SABA) inhaler medication use and record patient-reported outcomes. The study examined changes in CAT and SABA inhaler use in COPD to determine whether passively collected SABA and CAT scores changed in a parallel manner. Methods: Patients with self-reported COPD enrolled in a digital health program, which provided EMMs to track SABA and maintenance inhaler use, and a companion smartphone application ("app") to provide medication feedback and reminders. Patients completing the CAT questionnaire in the app at enrollment and at 6 months were included in the analysis. Changes in CAT burden category [by the minimally important difference (MID)] and changes in EMM-recorded mean SABA inhaler use per day were quantified at baseline and 6 months. Results: The analysis included 611 patients. At 6 months, mean CAT improved by -0.9 (95% CI: -1.4, -0.4; p < 0.001) points, and mean SABA use decreased by -0.6 (-0.8, -0.4; p < 0.001) puffs/day. Among patients with higher burden (CAT ≥ 21) at enrollment, CAT improved by -2.0 (-2.6, -1.4; p < 0.001) points, and SABA use decreased by -0.8 (-1.1, -0.6; p < 0.001) puffs/day. Conclusion: Significant and parallel improvement in CAT scores and SABA use at 6 months were noted among patients enrolled in a digital health program, with greater improvement for patients with higher disease burden.

Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass).

Background: Seagrasses (Alismatales) are the only fully marine angiosperms.  Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass  Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings.   Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding.  Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins.  Conclusions: As an important marine angiosperm, the improved  Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.

Long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders.

Exome and genome sequencing have proven to be effective tools for the diagnosis of neurodevelopmental disorders (NDDs), but large fractions of NDDs cannot be attributed to currently detectable genetic variation. This is likely, at least in part, a result of the fact that many genetic variants are difficult or impossible to detect through typical short-read sequencing approaches. Here, we describe a genomic analysis using Pacific Biosciences circular consensus sequencing (CCS) reads, which are both long (>10 kb) and accurate (>99% bp accuracy). We used CCS on six proband-parent trios with NDDs that were unexplained despite extensive testing, including genome sequencing with short reads. We identified variants and created de novo assemblies in each trio, with global metrics indicating these datasets are more accurate and comprehensive than those provided by short-read data. In one proband, we identified a likely pathogenic (LP), de novo L1-mediated insertion in CDKL5 that results in duplication of exon 3, leading to a frameshift. In a second proband, we identified multiple large de novo structural variants, including insertion-translocations affecting DGKB and MLLT3, which we show disrupt MLLT3 transcript levels. We consider this extensive structural variation likely pathogenic. The breadth and quality of variant detection, coupled to finding variants of clinical and research interest in two of six probands with unexplained NDDs, support the hypothesis that long-read genome sequencing can substantially improve rare disease genetic discovery rates.

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.

Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2-4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6-knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate-gene-biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene-trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.

A workflow for visualizing human cancer biopsies using large-format electron microscopy.

Recent developments in large format electron microscopy have enabled generation of images that provide detailed ultrastructural information on normal and diseased cells and tissues. Analyses of these images increase our understanding of cellular organization and interactions and disease-related changes therein. In this manuscript, we describe a workflow for two-dimensional (2D) and three-dimensional (3D) imaging, including both optical and scanning electron microscopy (SEM) methods, that allow pathologists and cancer biology researchers to identify areas of interest from human cancer biopsies. The protocols and mounting strategies described in this workflow are compatible with 2D large format EM mapping, 3D focused ion beam-SEM and serial block face-SEM. The flexibility to use diverse imaging technologies available at most academic institutions makes this workflow useful and applicable for most life science samples. Volumetric analysis of the biopsies studied here revealed morphological, organizational and ultrastructural aspects of the tumor cells and surrounding environment that cannot be revealed by conventional 2D EM imaging. Our results indicate that although 2D EM is still an important tool in many areas of diagnostic pathology, 3D images of ultrastructural relationships between both normal and cancerous cells, in combination with their extracellular matrix, enables cancer researchers and pathologists to better understand the progression of the disease and identify potential therapeutic targets.

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement.

Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N6-methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement.