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Western North America has been experiencing persistent drought exacerbated by climate change for over two decades. This extreme climate event is a clear threat to native plant communities.Artemisia tridentatais a keystone shrub species in western North America and is threatened by climate change, urbanization, and wildfire. A drought Genotype × Environment (G × E) experiment was conducted to assess phenotypic plasticity and differential gene expression inA. tridentata. The G × E experiment was performed on diploidA. tridentataseedlings from two populations (one from Idaho, USA and one from Utah, USA), which experience differing levels of drought stress during the summer months. Photosynthetic data, leaf temperature, and gene expression levels were compared between treatments and populations. The Utah population maintained higher photosynthetic rates and photosynthetic efficiency than the Idaho population under drought stress. The Utah population also exhibited far greater transcriptional plasticity than the Idaho population and expressed genes of response pathways distinct from those of the Idaho population. Populations ofA. tridentatadiffer greatly in their drought response pathways, likely due to differences in response pathways that have evolved under distinct climatic regimes. Epigenetic processes likely contribute to the observed differences between the populations.

 

Severe drought conditions and extreme weather events are increasing worldwide with climate change, threatening the persistence of native plant communities and ecosystems. Many studies have investigated the genomic basis of plant responses to drought. However, the extent of this research throughout the plant kingdom is unclear, particularly among species critical for the sustainability of natural ecosystems. This study aimed to broaden our understanding of genome-to-phenome (G2P) connections in drought-stressed plants and identify focal taxa for future research. Bioinformatics pipelines were developed to mine and link information from databases and abstracts from 7730 publications. This approach identified 1634 genes involved in drought responses among 497 plant taxa. Most (83.30%) of these species have been classified for human use, and most G2P interactions have been described within model organisms or crop species. Our analysis identifies several gaps in G2P research literature and database connectivity, with 21% of abstracts being linked to gene and taxonomy data in NCBI. Abstract text mining was more successful at identifying potential G2P pathways, with 34% of abstracts containing gene, taxa, and phenotype information. Expanding G2P studies to include non-model plants, especially those that are adapted to drought stress, will help advance our understanding of drought responsive G2P pathways. 

Open science and open data within scholarly research programs are growing both in popularity and by requirement from grant funding agencies and journal publishers. A central component of open data management, especially on collaborative, multidisciplinary, and multi-institutional science projects, is documentation of complete and accurate metadata, workflow, and source code in addition to access to raw data and data products to uphold FAIR (Findable, Accessible, Interoperable, Reusable) principles. Although best practice in data/metadata management is to use established internationally accepted metadata schemata, many of these standards are discipline-specific making it difficult to catalog multidisciplinary data and data products in a way that is easily findable and accessible. Consequently, scattered and incompatible metadata records create a barrier to scientific innovation, as researchers are burdened to find and link multidisciplinary datasets. One possible solution to increase data findability, accessibility, interoperability, reproducibility, and integrity within multi-institutional and interdisciplinary projects is a centralized and integrated data management platform. Overall, this type of interoperable framework supports reproducible open science and its dissemination to various stakeholders and the public in a FAIR manner by providing direct access to raw data and linking protocols, metadata and supporting workflow materials.

 

Abstract Increased ecological disturbances, species invasions, and climate change are creating severe conservation problems for several plant species that are widespread and foundational. Understanding the genetic diversity of these species and how it relates to adaptation to these stressors are necessary for guiding conservation and restoration efforts. This need is particularly acute for big sagebrush (Artemisia tridentata; Asteraceae), which was once the dominant shrub over 1,000,000 km2 in western North America but has since retracted by half and thus has become the target of one of the largest restoration seeding efforts globally. Here, we present the first reference-quality genome assembly for an ecologically important subspecies of big sagebrush (A. tridentata subsp. tridentata) based on short and long reads, as well as chromatin proximity ligation data analyzed using the HiRise pipeline. The final 4.2 Gb assembly consists of 5,492 scaffolds, with nine pseudo-chromosomal scaffolds (nine scaffolds comprising at least 90% of the assembled genome; n = 9). The assembly contains an estimated 43,377 genes based on ab initio gene discovery and transcriptional data analyzed using the MAKER pipeline, with 91.37% of BUSCOs being completely assembled. The final assembly was highly repetitive, with repeat elements comprising 77.99% of the genome, making the Artemisia tridentata subsp. tridentata genome one of the most highly-repetitive plant genomes to be sequenced and assembled. This genome assembly advances studies on plant adaptation to drought and heat stress and provides a valuable tool for future genomic research. 

There is a gap in the conceptual framework linking genes to phenotypes (G2P) for non-model organisms, as most non-model organisms do not yet have genomic resources readily available. To address this, researchers often perform literature reviews to understand G2P linkages by curating a list of likely gene candidates, hinging upon other studies already conducted in closely related systems. Sifting through hundreds to thousands of articles is a cumbersome task that slows down the scientific process and may introduce bias into a study. To fill this gap, we created G2PMineR, a free and open source literature mining tool developed specifically for G2P research. This R package uses automation to make the G2P review process efficient and unbiased, while also generating hypothesized associations between genes and phenotypes within a taxonomical framework. We applied the package to a literature review for drought-tolerance in plants. The analysis provides biologically meaningful results within the known framework of drought tolerance in plants. Overall, the package is useful for conducting literature reviews for genome to phenome projects, and also has broad appeal to scientists investigating a wide range of study systems as it can conduct analyses under the auspices of three different kingdoms (Plantae, Animalia, and Fungi). 

Basin big sagebrush (Artemisia tridentata subsp. tridentata) is a keystone species of the sagebrush steppe, a widespread ecosystem of western North America threatened by climate change. The study’s goal was to develop an in vitro method of propagation for this taxon to support genome sequencing and genotype-by-environment research on drought tolerance. Such research may ultimately facilitate the reintroduction of big sagebrush in degraded habitats. Seedlings were generated from two diploid mother plants (2n = 2x = 18) collected in environments with contrasting precipitation regimes. The effects of IBA and NAA on rooting of shoot tips were tested on 45 individuals and 15 shoot tips per individual. Growth regulator and individual-seedling effects on percent rooting and roots per shoot tip were evaluated using statistical and clustering analyses. Furthermore, rooted shoot tips were transferred into new media to ascertain their continued growth in vitro. The results suggest that A. tridentata is an outbred species, as shown by individuals’ effect on rooting and growth. IBA addition was the most effective method for promoting adventitious rooting, especially in top-performing individuals. These individuals also have high survival and growth rates upon transferring to new media, making them suitable candidates for generating biomass for genome sequencing and producing clones for genotype-by-environment research. 

Understanding interactions between environmental stress and genetic variation is crucial to predict the adaptive capacity of species to climate change. Leaf temperature is both a driver and a responsive indicator of plant physiological response to thermal stress, and methods to monitor it are needed. Foliar temperatures vary across leaf to canopy scales and are influenced by genetic factors, challenging efforts to map and model this critical variable. Thermal imagery collected using unoccupied aerial systems (UAS) offers an innovative way to measure thermal variation in plants across landscapes at leaf‐level resolutions. We used a UAS equipped with a thermal camera to assess temperature variation among genetically distinct populations of big sagebrush (Artemisia tridentata), a keystone plant species that is the focus of intensive restoration efforts throughout much of western North America. We completed flights across a growing season in a sagebrush common garden to map leaf temperature relative to subspecies and cytotype, physiological phenotypes of plants, and summer heat stress. Our objectives were to (1) determine whether leaf‐level stomatal conductance corresponds with changes in crown temperature; (2) quantify genetic (i.e., subspecies and cytotype) contributions to variation in leaf and crown temperatures; and (3) identify how crown structure, solar radiation, and subspecies‐cytotype relate to leaf‐level temperature. When considered across the whole season, stomatal conductance was negatively, non‐linearly correlated with crown‐level temperature derived from UAS. Subspecies identity best explained crown‐level temperature with no difference observed between cytotypes. However, structural phenotypes and microclimate best explained leaf‐level temperature. These results show how fine‐scale thermal mapping can decouple the contribution of genetic, phenotypic, and microclimate factors on leaf temperature dynamics. As climate‐change‐induced heat stress becomes prevalent, thermal UAS represents a promising way to track plant phenotypes that emerge from gene‐by‐environment interactions.

 

Climate change presents distinct ecological and physiological challenges to plants as extreme climate events become more common. Understanding how species have adapted to drought, especially ecologically important nonmodel organisms, will be crucial to elucidate potential biological pathways for drought adaptation and inform conservation strategies. To aid in genome‐to‐phenome research, a draft genome was assembled for a diploid individual ofArtemisia tridentatasubsp.tridentata, a threatened keystone shrub in western North America. While this taxon has few genetic resources available and genetic/genomics work has proven difficult due to genetic heterozygosity in the past, a draft genome was successfully assembled. Aquaporin (AQP) genes and their promoter sequences were mined from the draft genome to predict mechanisms regulating gene expression and generate hypotheses on key genes underpinning drought response. Fifty‐one AQP genes were fully assembled within the draft genome. Promoter and phylogenetic analyses revealed putative duplicates ofA. tridentatasubsp.tridentataAQPs which have experienced differentiation in promoter elements, potentially supporting novel biological pathways. Comparison with nondrought‐tolerant congener supports enrichments of AQP genes in this taxon during adaptation to drought stress. Differentiation of promoter elements revealed that paralogues of some genes have evolved to function in different pathways, highlighting these genes as potential candidates for future research and providing critical hypotheses for future genome‐to‐phenome work.