Search

Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

BackgroundThe process of crop domestication often consists of two stages: initial domestication, where the wild species is first cultivated by humans, followed by diversification, when the domesticated species are subsequently adapted to more environments and specialized uses. Selective pressure to increase sugar accumulation in certain varieties of the cereal crop Sorghum bicolor is an excellent example of the latter; this has resulted in pronounced phenotypic divergence between sweet and grain-type sorghums, but the genetic mechanisms underlying these differences remain poorly understood.ResultsHere we present a new reference genome based on an archetypal sweet sorghum line and compare it to the current grain sorghum reference, revealing a high rate of nonsynonymous and potential loss of function mutations, but few changes in gene content or overall genome structure. We also use comparative transcriptomics to highlight changes in gene expression correlated with high stalk sugar content and show that changes in the activity and possibly localization of transporters, along with the timing of sugar metabolism play a critical role in the sweet phenotype.ConclusionsThe high level of genomic similarity between sweet and grain sorghum reflects their historical relatedness, rather than their current phenotypic differences, but we find key changes in signaling molecules and transcriptional regulators that represent new candidates for understanding and improving sugar metabolism in this important crop.

AbstractArctic destinations are continually reshaping their global identities to manage external expectations about the region. Existing portrayals of Greenland often stereotype the area as untouched wilderness or oversimplify its social, economic, and cultural realities. Our study combines visual analysis of cultural landscape and cultural ecosystem services (CES) to unveil a novel narrative in Greenland’s sustainable tourism branding we termed ‘landscape as homeland’. Empirically this research is based on the photographic database of Greenland’s national destination marketing organization. We explore Greenland’s destination branding as a strategic tool to define local meanings of sustainable tourism, homeland, and “Arcticness” in a branding that distinctively positions itself amidst Arctic destinations. Using pictured landscape as a dwelling place discerns locally valued CES, and realigns tourist engagements toward a culturally and ecologically integrated relationship. Applications of these findings extend to other rapidly changing regions seeking to expand economic opportunities, harnessing the synergy between destination branding and sustainable tourism. We reflect on the efficacy of our integrated CES and cultural landscape research to reveal local framings of the tourism-sustainability tension. We highlight the role of destination marketing organizations to bridge the gap between local identity, visitor expectations, and sustainable tourism development. [ABSTRACT FROM AUTHOR]

Secondary contact between closely related taxa represents a "moment of truth" for speciation—an opportunity to test the efficacy of reproductive isolation that evolved in allopatry and to identify the genetic, behavioral, and/or ecological barriers that separate species in sympatry. Sex chromosomes are known to rapidly accumulate differences between species, an effect that may be exacerbated for neo-sex chromosomes that are transitioning from autosomal to sex-specific inheritance. Here we report that, in the Solomon Islands, two closely related bird species in the honeyeater family—Myzomela cardinalis and Myzomela tristrami—carry neo-sex chromosomes and have come into recent secondary contact after ~1.1 my of geographic isolation. Hybrids of the two species were first observed in sympatry ~100 years ago. To determine the genetic consequences of hybridization, we use population genomic analyses of individuals sampled in allopatry and in sympatry to characterize gene flow in the contact zone. Using genome-wide estimates of diversity, differentiation, and divergence, we find that the degree and direction of introgression varies dramatically across the genome. For sympatric birds, autosomal introgression is bidirectional, with phenotypic hybrids and phenotypic parentals of both species showing admixed ancestry. In other regions of the genome, however, the story is different. While introgression on the Z/neo-Z-linked sequence is limited, introgression of W/neo-W regions and mitochondrial sequence (mtDNA) is highly asymmetric, moving only from the invading M. cardinalis to the resident M. tristrami. The recent hybridization between these species has thus enabled gene flow in some genomic regions but the interaction of admixture, asymmetric mate choice, and/or natural selection has led to the variation in the amount and direction of gene flow at sex-linked regions of the genome. Author summary: When an invasive species colonizes an island and interacts with a closely related resident species, we are provided with a rare opportunity to study the consequences of interbreeding and the factors that keep species distinct. Regions of the genome that evolve rapidly and/or influence mate choice may be especially likely to act as incidental barriers to gene flow. The red Myzomela cardinalis, birds in the honeyeater family, have invaded Makira in the Solomon Islands, coming into contact with the endemic, all black Myzomela tristrami. We used population genomic analyses of individuals in geographic isolation, and those in geographic contact, to understand the history of these two species and the consequences of their recent range overlap. We found that sex-specific regions of the genome (i.e., sex chromosomes) were either limited in their ability to move between species, or only moved in one direction, from the invading M. cardinalis to the resident M. tristrami. This work highlights how certain regions of the genome may be especially important in defining species boundaries and the generation and maintenance of biodiversity. [ABSTRACT FROM AUTHOR]

The UK Met Office state‐of‐the‐art, deterministic, convection‐permitting, coupled land‐atmosphere, regional weather forecasting system, known as the UKV or UK Variable resolution model (Tang et al. Meteorological Applications, 2013; 20:417–426), has been operational since 2015. Science updates are regularly made to the UKV land surface data assimilation scheme when those updates improve predictions of screen temperature and humidity, since these quantities have a direct impact on atmospheric states and weather forecasts. Less attention has been paid to whether UKV soil moisture analyses are close to independent, in‐situ soil moisture observations, partly because it is difficult to make meaningful comparisons between 1.5 km2 gridded model outputs and traditional point sensor measurements. Soil moisture is recognized to be important when hydrological forecasts for runoff and rivers are required. This is because soil moisture controls the extent to which rainfall can infiltrate the soil, and the amount of surface runoff affects the timing of peak river flows (Ward & Robinson, Principles of Hydrology. McGraw‐Hill Publishing Company; 2000; Singh et al. Water Resources Research, 2021, 57, e2020WR028827). Gómez et al. (Remote Sensing, 2020; 12:3691) report benefits to river flow forecasts when using soil moisture data assimilation in the UKV system instead of a daily downscaled product from the Met Office global model. The Met Office measures soil temperature and soil moisture at Cardington (Osborne & Weedon, Journal of Hydrometeorology, 2021, 22:279–295); there is no other UK Met Office site at which soil moisture is measured. In this study, we use field‐scale (~200 m radius) soil moisture measurements from the UK Centre for Ecology and Hydrology's (UKCEH's) COSMOS‐UK network to provide independent verification and analysis of UKV soil moisture during summer 2018, an unusually dry period in the United Kingdom. We find that the match to COSMOS‐UK soil moisture observations is generally good, and that changes made to the land data assimilation approach during a recent operational upgrade had a generally beneficial impact on UKV soil moisture analyses under very dry conditions. [ABSTRACT FROM AUTHOR]

Dignity--dig*ni*ty | \ 'dig-ne-te--The 'quality or state of being worthy, honored, or esteemed.' (1) When I think about all that is wrong in the world--the threat to democracy in the [...]

This study evaluates the efficacy of bias-correction (BC) and data assimilation (DA) techniques in refining hydrological model predictions. Both approaches are routinely used to enhance hydrological forecasts, yet there have been no studies that have systematically compared their utility. We focus on the application of these techniques to improve operational river flow forecasts in a diverse dataset of 316 catchments in the UK, using the Ensemble Streamflow Prediction (ESP) method applied to the GR4J hydrological model. This framework is used in operational seasonal forecasting, providing a suitable testbed for method application. Assessing the impacts of these two approaches on model performance and forecast skill, we find that BC yields substantial and generalised improvements by rectifying errors post-simulation. Conversely, DA, adjusting model states at the start of the forecast period, provides more subtle enhancements, with the biggest effects seen at short lead times in catchments impacted by snow accumulation/melting processes in winter and spring, and catchments with high Base Flow Index (BFI) during summer months. The choice between BC and DA involves trade-offs, considering conceptual differences, computational demands, and uncertainty handling. Our findings emphasise the need for selective application based on specific scenarios and user requirements. This underscores the potential for developing a selective system (e.g., decision-tree) to refine forecasts effectively and deliver user-friendly hydrological predictions. While further work is required to enable implementation, this research contributes insights into the relative strengths and weaknesses of these forecast enhancement methods. These could find application in other forecasting systems, aiding the refinement of hydrological forecasts and meeting the demand for reliable information by end-users. [ABSTRACT FROM AUTHOR]

Background: There is a concerning rise in antifungal‐resistant dermatophytosis globally, with resistance to terbinafine conferred by point mutations in the squalene epoxidase (SQLE) gene. Objectives: Report changes in the prevalence and profile of SQLE mutations in onychomycosis patients in the United States. Methods: A longitudinal cohort study of toenail samples was collected from suspected onychomycosis patients over an 18‐month period from 2022 to 2023. Samples were submitted from across the United States and subjected to multiplex real‐time polymerase chain reactions for dermatophyte detection, with further screening of SQLE mutations at four known hotspots (393Leu, 397Phe, 415Phe and 440His). Results: A total of 62,056 samples were submitted (mean age: 57.5 years; female: 60.4%). Dermatophytes were detected in 38.5% of samples, primarily Trichophyton rubrum complex (83.6%) and T. mentagrophytes complex (10.7%). A survey of SQLE mutations was carried out in 22,610 dermatophyte samples; there was a significant increase in the prevalence of SQLE mutations between the first quarter of 2022 and the second quarter of 2023 (29.0 to 61.9 per 1000 persons). The Phe397Leu substitution was the predominant mutation; Phe415Ser and His440Tyr have also emerged which were previously reported as minor mutations in skin samples. The temporal change in mutation rates can be primarily attributed to the Phe415Ser substitution. Samples from elderly patients (>70 years) are more likely to be infected with the T. mentagrophytes complex including strains harbouring the Phe415Ser substitution. Conclusion: The prevalence of SQLE mutations among onychomycosis patients with Trichophyton infections may be underestimated. Older individuals may have a higher risk. [ABSTRACT FROM AUTHOR]