Utilizing a comparative approach to assess genome evolution during diploidization in Artemisia tridentata, a keystone species of western North America.

PREMISE: Polyploidization is often followed by diploidization. Diploidization is generally studied using synthetic polyploid lines and/or crop plants, but rarely using extant diploids or nonmodel plants such as Artemisia tridentata. This threatened western North American keystone species has a large genome compared to congeneric Artemisia species; dominated by diploid and tetraploid cytotypes, with multiple origins of tetraploids with genome size reduction. METHODS: The genome of an A. tridentata sample was resequenced to study genome evolution and compared to that of A. annua, a diploid congener. Three diploid genomes of A. tridentata were compared to test for multiple diploidization events. RESULTS: The A. tridentata genome had many chromosomal rearrangements relative to that of A. annua, while large-scale synteny of A. tridentata chromosome 3 and A. annua chromosome 4 was conserved. The three A. tridentata genomes had similar sizes (4.19-4.2 Gbp), heterozygosity (2.24-2.25%), and sequence (98.73-99.15% similarity) across scaffolds, and in k-mer analyses, similar patterns of diploid heterozygous k-mers (AB = 41%, 47%, and 47%), triploid heterozygous k-mers (AAB = 18-21%), and tetraploid k-mers (AABB = 13-17%). Biallelic SNPs were evenly distributed across scaffolds for all individuals. Comparisons of transposable element (TE) content revealed differential enrichment of TE clades. CONCLUSIONS: Our findings suggest population-level TE differentiation after a shared polyploidization-to-diploidization event(s) and exemplify the complex processes of genome evolution. This research approached provides new resources for exploration of abiotic stress response, especially the roles of TEs in response pathways.

A genotype × environment experiment reveals contrasting response strategies to drought between populations of a keystone species (Artemisia tridentata; Asteraceae).

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 tridentata is 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 in A. tridentata. The G × E experiment was performed on diploid A. tridentata seedlings 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 of A. tridentata differ 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.

Meta-Analysis Reveals Challenges and Gaps for Genome-to-Phenome Research Underpinning Plant Drought Response.

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.

A haploid pseudo-chromosome genome assembly for a keystone sagebrush species of western North American rangelands.

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.

Potential distributional shifts in North America of allelopathic invasive plant species under climate change models.

Predictive studies play a crucial role in the study of biological invasions of terrestrial plants under possible climate change scenarios. Invasive species are recognized for their ability to modify soil microbial communities and influence ecosystem dynamics. Here, we focused on six species of allelopathic flowering plants-Ailanthus altissima, Casuarina equisetifolia, Centaurea stoebe ssp. micranthos, Dioscorea bulbifera, Lantana camara, and Schinus terebinthifolia-that are invasive in North America and examined their potential to spread further during projected climate change. We used Species Distribution Models (SDMs) to predict future suitable areas for these species in North America under several proposed future climate models. ENMEval and Maxent were used to develop SDMs, estimate current distributions, and predict future areas of suitable climate for each species. Areas with the greatest predicted suitable climate in the future include the northeastern and the coastal northwestern regions of North America. Range size estimations demonstrate the possibility of extreme range loss for these invasives in the southeastern United States, while new areas may become suitable in the northeastern United States and southeastern Canada. These findings show an overall northward shift of suitable climate during the next few decades, given projected changes in temperature and precipitation. Our results can be utilized to analyze potential shifts in the distribution of these invasive species and may aid in the development of conservation and management plans to target and control dissemination in areas at higher risk for potential future invasion by these allelopathic species.

A draft genome provides hypotheses on drought tolerance in a keystone plant species in Western North America threatened by climate change.

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 of Artemisia tridentata subsp. 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 of A. tridentata subsp. tridentata AQPs 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.

G2PMineR: A Genome to Phenome Literature Review Approach.

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).

Genetic insights into the evolution of genera with the eastern Asia-eastern North America floristic disjunction: a transcriptomics analysis.

PREMISE: Large disjunctions in species distributions provide excellent opportunities to study processes that shape biogeographic patterns. One such disjunction is the eastern Asia-eastern North America (EA-ENA) floristic disjunction. For many genera with this disjunction, species richness is greater in EA than in ENA; this pattern has been attributed, in part, to higher rates of molecular evolution and speciation in EA. Longer branch lengths have been found in some EA clades, relative to their ENA sister clades, suggesting that the EA lineages have evolved at a higher rate, possibly due to environmental heterogeneity, potentially contributing to the species richness anomaly. METHODS: To evaluate whether rates of molecular evolution are elevated in EA relative to ENA, we used transcriptomes from species in 11 genera displaying this disjunction. Rates of molecular evolution were estimated for up to 385 orthologous nuclear loci per genus. RESULTS: No statistically significant differences were identified in pairwise comparisons between EA and ENA sister species, suggesting equal rates of molecular evolution for both species; the data also suggest similar selection pressures in both regions. For larger genera, evidence likewise argues against more species-rich clades having higher molecular evolutionary rates, regardless of region. Our results suggest that genes across multiple gene ontology categories are evolving at similar rates under purifying selection in species in both regions. CONCLUSIONS: Our data support the hypothesis that greater species richness in EA than ENA is due to factors other than an overall increase in rates of molecular evolution in EA.

Identification and functional characterization of the Marshallia (Asteraceae) Clade III Cytokinin Response Factor (CRF).

Cytokinin Response Factor (CRF) genes are a subgroup of AP2/ERF domain-containing transcription factors that are defined by the CRF domain, from which five clades of CRF genes have been identified. Clade III CRFs are strongly induced by cytokinin, as well as other abiotic stress factors, such as oxidative stress. While this appears well studied for the Clade III CRFs in Arabidopsis and tomato, there have been almost no studies done outside of these model systems. This study expands upon that and represents the first CRF research in the Sunflower family, Asteraceae. Fifty Asterid Clade III CRF protein sequences were examined, and novel Clade III CRF C-terminus motifs were identified. Clade III CRF genes of Marshallia mohrii and M. caespitosa were assembled from genome-skimming and transcriptomic data. Expression experiments were conducted on M. caespitosa to test responsiveness to both cytokinin and oxidative stress. Low levels of basal expression for the McCRF1 were found to be strongly induced in both treatment groups. These are the first experiments to show regulation of a nuclear gene in a Marshallia species, and these results suggest there is broad conservation in the sequence, form, and regulation of Clade III CRF genes and proteins.

Cytokinin Response Factor 5 has transcriptional activity governed by its C-terminal domain.

Cytokinin Response Factors (CRFs) are AP2/ERF transcription factors involved in cytokinin signal transduction. CRF proteins consist of a N-terminal dimerization domain (CRF domain), an AP2 DNA-binding domain, and a clade-specific C-terminal region of unknown function. Using a series of sequential deletions in yeast-2-hybrid assays, we provide evidence that the C-terminal region of Arabidopsis CRF5 can confer transactivation activity. Although comparative analyses identified evolutionarily conserved protein sequence within the C-terminal region, deletion experiments suggest that this transactivation domain has a partially redundant modular structure required for activation of target gene transcription.