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Abstract Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define pangenes, which summarize a species coding potential and link back to original annotations. The protocol get_pangenes performs whole genome alignments (WGA) to call syntenic gene models based on coordinate overlaps. A benchmark with small and large plant genomes shows that pangenes recapitulate phylogeny-based orthologies and produce complete soft-core gene sets. Moreover, WGAs support lift-over and help confirm gene presence-absence variation. Source code and documentation: https://github.com/Ensembl/plant-scripts .

This ‘project proceedings’ article comprises eight reflections from students involved in the Pilot Year of the Literature across Borders project, facilitated by The Green Literature Festival (India) between Ashoka University (India) and Bath Spa University (UK). This article pairs with a partner piece (see this issue) outlining the concept, planning, and delivery of the pilot year, and exploring staff reflections.

When researching and writing my first MA Writing for Young People essay, I made two observations: my peers and I were overwhelmed with how to go about it and, through the process, I learned more specific and applicable techniques for the craft of children’s writing than I had from craft manuals. To write my essay, I utilised my knowledge of teaching essay structure to teens. I share the process I took to create my Writing for Young People essay in order to illustrate how a scholar can apply the same steps to their own interests. Steps that I discuss include developing a focus question, reading and researching, collating observations and making conclusions, and outlining, drafting, and polishing. Though some of the steps I offer seem obvious, I collect them to support new scholars in efficiently writing an essay and to support them in unlocking a way to learn from children’s authors. Throughout I model from my own essay, sharing the strategies I learned about using animal companions to develop the protagonist in Middle Grade novels. I end with one example of how I have applied what I learned to my current manuscript.

Abstract Vietnam harnesses a rich diversity of rice landraces adapted to a range of conditions, which constitute a largely untapped source of diversity for the continuous improvement of cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five Indica and four Japonica subpopulations, including an outlying Indica‐5 group. Here, we leveraged that strong differentiation and 672 native rice genomes to identify genomic regions and genes putatively selected during the breeding of rice in Vietnam. We identified significant distorted patterns in allele frequency (XP‐CLR) and population differentiation scores (FST) resulting from differential selective pressures between native subpopulations, and later annotated them with QTLs previously identified by GWAS in the same panel. We particularly focussed on the outlying Indica‐5 subpopulation because of its likely novelty and differential evolution, where we annotated 52 selected regions, which represented 8.1% of the rice genome. We annotated the 4576 genes in these regions and selected 65 candidate genes as promising breeding targets, several of which harboured alleles with nonsynonymous substitutions. Our results highlight genomic differences between traditional Vietnamese landraces, which are likely the product of adaption to multiple environmental conditions and regional culinary preferences in a very diverse country. We also verified the applicability of this genome scanning approach to identify potential regions harbouring novel loci and alleles to breed a new generation of sustainable and resilient rice.

Abstract Background Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns. Results We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. Conclusions We showed how the rice diversity within Vietnam relates to the wider Asian rice diversity by using a number of approaches to provide a clear picture of the novel diversity present within Vietnam, mainly around the Indica-5 subpopulation. Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of low input sustainable and climate resilient rice.

Abstract Background Miscanthus is a commercial lignocellulosic biomass crop owing to its high biomass productivity and low chemical input requirements. Within an interspecific Miscanthus cross, progeny with high biomass yield were shown to have low concentrations of starch and sucrose but high concentrations of fructose. We performed a transcriptional RNA-seq analysis between selected Miscanthus hybrids with contrasting values for these phenotypes to clarify how these phenotypes are genetically controlled. Results We observed that genes directly involved in the synthesis and degradation of starch and sucrose were down-regulated in high-yielding Miscanthus hybrids. At the same time, glycolysis and export of triose phosphates were up-regulated in high-yielding Miscanthus hybrids. These differentially expressed genes and biological functions were regulated by a well-connected network of less than 25 co-regulated transcription factors. Conclusions Our results evidence a direct relationship between high expression of essential enzymatic genes in the starch and sucrose pathways and co-expression with their transcriptional regulators, with high starch concentrations and lower biomass production. The strong interconnectivity between gene expression and regulators, chemotype and agronomic traits opens the door to use the expression of well-characterised genes associated with carbohydrate metabolism, particularly in the starch and sucrose pathway, for the early selection of high biomass-yielding genotypes from large Miscanthus populations.

In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of metadata in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic interchange format across domains but can lead to inconsistency between files in the presentation of metadata. To enable fully autonomous machine actionable data flow, generic elements need to be further specified. We strongly support the merits of the FAIR principles and see the need to facilitate them also through technical implementation specifications. They form a basis for the proposed VCF extensions here. We have learned from the existing application of VCF that the definition of relevant metadata using controlled standards, vocabulary and the consistent use of cross-references via resolvable identifiers (machine-readable) are particularly necessary and propose their encoding. VCF is an established standard for the exchange and publication of genotyping data. Other data formats are also used to capture variant data (for example, the HapMap and the gVCF formats), but none currently have the reach of VCF. For the sake of simplicity, we will only discuss VCF and our recommendations for its use, but these recommendations could also be applied to gVCF. However, the part of the VCF standard relating to metadata (as opposed to the actual variant calls) defines a syntactic format but no vocabulary, unique identifier or recommended content. In practice, often only sparse descriptive metadata is included. When descriptive metadata is provided, proprietary metadata fields are frequently added that have not been agreed upon within the community which may limit long-term and comprehensive interoperability. To address this, we propose recommendations for supplying and encoding metadata, focusing on use cases from plant sciences. We expect there to be overlap, but also divergence, with the needs of other domains.

Recognizing that university statements about equity, diversity, and inclusion are often cosmetic, performative, or at best, aspirational, rather than indicative of on-campus realities, this project analyzes interpretations of student identity and diversity through publicly available materials. The primary purpose of this research was to investigate how university messages about equity, diversity, and inclusion, available through public websites, are interpreted by faculty and students. Using a students-as-partners approach, we identified and analyzed themes based on our own perceptions and understandings of each of five university websites University of Calgary (Canada), University of Alabama (USA), Deakin University (Australia), University of Exeter (UK), and Portland State University (USA). While equity, diversity, and inclusion are signature initiatives at many universities, we found that analyses of their websites suggest that the ways in which those are operationalized differ. The patterns identified suggest that messaging through university websites can promote or detract from equity, diversity, and inclusion in university settings, and we observed differences in the ways in which institutions operationalized and represented initiatives related to equity, diversity, and inclusion. Exploring how these efforts at our five institutions are messaged to and interpreted by students provides a better understanding of the institutional priorities and the assumed values identified by student co-researchers. The use of student co-researchers proved an especially valuable contribution to this analysis to gain perspectives about presentations of student identity and diversity. Using this form of embedded research, we identify the limited presentations of and perceptions around diversity at institutions of higher education cited by student co-researchers.

The Welsh Transplantation and Immunogenetics Laboratory (WTAIL) is responsible for managing patient work-up for haematopoietic stem cell transplantation (HSCT), the only potentially curative option for many haematological and non-haematological conditions. Work-up requires regular communication between WTAIL and the transplanting clinicians, facilitated by weekly multidisciplinary team (MDT) meetings, to agree decisions and proceed through each work-up stage. Effective communication and minimising error are critical, as transplanting cells from a suboptimal donor could have severe or fatal consequences for the patient. We reviewed our HSCT patient management and identified issues including staff dissatisfaction with the inefficiency of the current (paper-based) system and concern about the potential for incidents caused by errors in manual transcription of patient information and tracking clinical decisions. Another driver for change was the COVID-19 pandemic, which prevented the usual face-to-face MDT meetings in which staff would show clinicians the paper records and reports; the shift to online MDT required new ways of sharing data. In this project we developed a new central reference point for our patient management data along with electronic patient summary sheets, designed with an eye to improving safety and efficiency. Over several improvement cycles we tested and refined the summary sheets with staff and clinicians and experimented with videoconferencing to facilitate data sharing. We conducted interviews with staff from which we concluded that the new process successfully reduced transcription and duplication and improved communication with the clinicians during the pandemic. Despite an increase in workload due to build-up of active patient work-up cases during the pandemic, staff reported that the new summaries enabled them to cope well. A key initiative was creation of a ‘Task and Finish’ group that helped establish continual improvement culture and identified additional areas for improvement which have been followed up in further improvement projects.

Miscanthus sacchariflorus (Maxim.) Hack. is a highly productive C4 perennial rhizomatous biofuel grass crop. M. sacchariflorus is among the most widely distributed species in the genus, particularly at cold northern latitudes, and is one of the progenitor species of the commercial M. × giganteus genotypes. We generated a 2.54 Gb whole-genome assembly of the diploid M. sacchariflorus cv. “Robustus 297” genotype, which represented ~59% of the expected total genome size. We later anchored this assembly using the chromosomes from the M. sinensis genome to generate a second assembly with improved contiguity. We annotated 86,767 and 69,049 protein-coding genes in the unanchored and anchored assemblies, respectively. We estimated our assemblies included ~85% of the M. sacchariflorus genes based on homology and core markers. The utility of the new reference for genomic studies was evidenced by a 99% alignment rate of the RNA-seq reads from the same genotype. The raw data, unanchored and anchored assemblies, and respective gene annotations are publicly available.

This paper reflects on what we learnt about teaching geography during the COVID-19 pandemic. We interrogate how we, as geography educators working in different contexts, navigated the novel teaching spaces created during the pandemic using two key registers; courageous and compassionate pedagogies. Our premise is that understanding in more nuanced form the approaches we took to creating courageous and compassionate education during the pandemic may help geography educators to thrive when delivering future-facing education. Our approach was to write and share vignettes of our pandemic teaching upon which we (asynchronously) collectively reflected; creating emergent themes described in this paper. This approach to structured peer learning derives from our commitment to education as a collective endeavour. We argue that the disruption caused by the early pandemic required geography educators to focus attention explicitly on areas previously taken as given. Geography educators slowed down by: (1) recognising educator and student embodiment in a novel context; (2) prioritising listening, acknowledging and sharing with students; and (3) paying attention to and respecting difference amongst learners and colleagues. We propose that consciously adopting these approaches will support geography educators and their students in rapidly changing circumstances across educational, employment and climate contexts.

In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of metadata in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic interchange format across domains but can lead to inconsistency between files in the presentation of metadata. To enable fully autonomous machine actionable data flow, generic elements need to be further specified. We strongly support the merits of the FAIR principles and see the need to facilitate them also through technical implementation specifications. They form a basis for the proposed VCF extensions here. We have learned from the existing application of VCF that the definition of relevant metadata using controlled standards, vocabulary and the consistent use of cross-references via resolvable identifiers (machine-readable) are particularly necessary and propose their encoding. VCF is an established standard for the exchange and publication of genotyping data. Other data formats are also used to capture variant data (for example, the HapMap and the gVCF formats), but none currently have the reach of VCF. For the sake of simplicity, we will only discuss VCF and our recommendations for its use, but these recommendations could also be applied to gVCF. However, the part of the VCF standard relating to metadata (as opposed to the actual variant calls) defines a syntactic format but no vocabulary, unique identifier or recommended content. In practice, often only sparse descriptive metadata is included. When descriptive metadata is provided, proprietary metadata fields are frequently added that have not been agreed upon within the community which may limit long-term and comprehensive interoperability. To address this, we propose recommendations for supplying and encoding metadata, focusing on use cases from plant sciences. We expect there to be overlap, but also divergence, with the needs of other domains.

In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of (meta-) data in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic interchange format across domains but can lead to inconsistency between files in the presentation of metadata. To enable fully autonomous machine actionable data flow, generic elements need to be further specified. We strongly support the merits of the FAIR principles and see the need to facilitate them also through technical implementation specifications. VCF files are an established standard for the exchange and publication of genotyping data. Other data formats are also used to capture variant call data (for example, the HapMap format and the gVCF format), but none currently have the reach of VCF. In VCF, only the sites of variation are described, whereas in gVCF, all positions are listed, and confidence values are also provided. For the sake of simplicity, we will only discuss VCF and our recommendations for its use. However, the part of the VCF standard relating to metadata (as opposed to the actual variant calls) defines a syntactic format but no vocabulary, unique identifier or recommended content. In practice, often only sparse (if any) descriptive metadata is included. When descriptive metadata is provided, proprietary metadata fields are frequently added that have not been agreed upon within the community which may limit long-term and comprehensive interoperability. To address this, we propose recommendations for supplying and encoding metadata, focusing on use cases from the plant sciences. We expect there to be overlap, but also divergence, with the needs of other domains.

Delft-born Adriaen van de Venne (1580–1662) is an artist well-known for his genre scenes, portraits, and book illustrations. He also created images with great moralistic and comic value, such as his painting Hoe dienen wij bij een!, made between c. 1614 and 1662. This painting portrays two brown and black-spotted owls in the guise of humans skating on a frozen lake. As other more conventional birds soar above the distant skeletal trees, these feathered creatures both wear contemporary clothing. The male owl also clenches a rope in his beak with a pair of glasses knotted at the end. This same rope attaches behind him to the female owl's chest, but instead of spectacles, her end holds several dead mice. Above the two anthropomorphic animals floats a banderole, which translates to 'How well we go together!' Although scholars believe van de Venne intended this work as lighthearted with only a vague message of foolishness, I contend that through the artist's use of iconographic imagery and well-known proverbs and themes, van de Venne produced a humorous painting with a moralizing and didactic message which condemned the vice of adultery and warned the male audience about the dangers of a cunning woman. [ABSTRACT FROM AUTHOR]

1. The tobacco hornworm, Manduca sexta, has been an important model system in insect biology for more than 50 years. In nature, M. sexta successfully utilises a range of host plants that vary in quality. The consequences of laboratory domestication and rearing on artificial diet for fitness of phytophagous insects on natural host plants have not been explored. 2. We examine the evolutionary divergence of two domesticated laboratory populations and a field population (separated for more than 40 years, or > 250 laboratory generations) of M. sexta with respect to performance and fitness on two natural host plants: a typical host plant, tobacco ( Nicotiana tabacum) and a novel host plant, devil's claw ( Proboscidea louisianica). 3. For both field and laboratory populations, rearing on devil's claw resulted in animals with lower survival, smaller final size, longer development time, and reduced size-corrected fecundity than animals reared on tobacco. Reductions in some fitness components (survival and fecundity) were greater for the laboratory population animals than the field population animals. 4. When reared on tobacco, the laboratory population animals had similar or larger pupal masses and slightly shorter development times than when reared on artificial diet, suggesting that laboratory domestication on artificial diet has not greatly affected the ability of M. sexta to perform well on a typical natural host plant. 5. Although field and laboratory populations exhibited qualitatively similar responses to host-plant quality, i.e. reduced performance on devil‘s claw, the magnitude of this reduction differed across populations, with the domesticated laboratory populations having greater reductions in performance than the field population. The use of domesticated populations as models for responses of field populations may therefore be more appropriate for considering environmental conditions that are relatively benign or near-optimal, than when exploring responses to extreme or stressful conditions. [ABSTRACT FROM AUTHOR]

Background: Previous studies suggest that psychotropic drug changes may signal an acute period of time whereby a person is highly vulnerable to fall. It is unknown whether certain classes of psychotropic agents are less safe with respect to the acute risk of falls. Our purpose was to compare fall rates in the 7 days following a change of an antidepressant, antipsychotic, or benzodiazepine. We also identified specific times when residents are at high risk for falls with respect to a psychotropic drug change. Methods: Residents in our one-year study included 851 long term care residents from two nursing home facilities in Boston, MA, U.S.A. (May 2010 - May 2011). Drug changes (i.e., new prescriptions or increased dose of a previously used drug) were ascertained using the computerized provider order entry system, whereas falls were ascertained by incident reports. Negative binomial regression was used to compare the rate of falls following a drug change between medication classes. Further, we calculated the rate of falls for each of the 7 days before and 7 days after a psychotropic drug change. Results: Forty-eight percent of residents were prescribed a new prescription or increased dose of a psychotropic drug during the study. The rate of falls was similar in the 7 days following a change to a SSRI versus non-SSRI antidepressant (11.9 versus 14.4 falls/1,000 person years; p = 0.58), a typical versus an atypical antipsychotic (25.4 versus 17.1 falls/1,000 person years; p = 0.10), or a short versus long acting benzodiazepine (15.2 versus 13.9 falls/1,000 person years; p = 0.23). Fall risk was highest on day 4 before the drug change (19.0 falls/1,000 person days), on the day of the drug change through 2 days after the drug change (17.6-20.3 falls/1,000 person days), and 5-6 days after the drug change (17.6-19.0 falls/1,000 person days). Conclusions: In the nursing home, risk of falls was similar following a psychotropic drug change of any class. We observed higher fall risk in the days before, but mostly after the drug change. We recommend that nursing home residents be closely monitored following a psychotropic drug change in an effort to reduce falls.

Red clover (Trifolium pratense L.) is a highly adaptable forage crop for temperate livestock agriculture. Genetic variation can be identified, via molecular techniques, and used to assess diversity among populations that may otherwise be indistinguishable. Here we have used genotyping by sequencing (GBS) to determine the genetic variation and population structure in red clover natural populations from Europe and Asia, and varieties or synthetic populations. Cluster analysis differentiated the collection into four large regional groups: Asia, Iberia, UK, and Central Europe. The five varieties clustered with the geographical area from which they were derived. Two methods (BayeScan and Samβada) were used to search for outlier loci indicating signatures of selection. A total of 60 loci were identified by both methods, but no specific genomic region was highlighted. The rate of decay in linkage disequilibrium was fast, and no significant evidence of any bottlenecks was found. Phenotypic analysis showed that a more prostrate and spreading growth habit was predominantly found among populations from Iberia and the UK. A genome wide association study identified a single nucleotide polymorphism (SNP) located in a homologue of the VEG2 gene from pea, associated with flowering time. The identification of genetic variation within the natural populations is likely to be useful for enhancing the breeding of red clover in the future.