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

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.This research was made possible by 2 NSF Idaho EPSCoR grants (award numbers OIA-1757324 and OIA-1826801), as well as a Dovetail Genomics Tree of Life Award.Introduction Materials and methods Sample collection, in vitro tissue propagation, and biomass production Flow cytometry and genome complexity analysis PacBio and Omni-C sequence data generation PacBio long-read de novo assembly and validation Pseudomolecule construction with HiRise Genome annotation RNA sequencing Repeat identification Functional annotation Results and discussion Validation of genome assembly and annotation Genome complexity and evidence of past polyploidization Comparing the A. tridentata and A. annua genome assemblies Applications of the sagebrush reference genome Data availability Acknowledgments Literature cite

Seen, but Not Heard?: Evaluating the Visibility of Plants in the Conservation Translocation Literature

Human activities are affecting the sustainability of functional ecosystems worldwide, with an estimated 100-1000x increase in recent extinction rates due to anthropogenic factors. Conservation translocations —or the movement of organisms to enhance recovery efforts— are an important tool to combat anthropogenic impacts such as climate change, habitat loss, fragmentation, and barriers to dispersal that can lead to reduced adaptive capacity and extinction. While exemplars in conservation translocation science have largely included vertebrates, fewer models exist for plants, despite their ecological importance as sources of food and habitat. In order to develop best management practices for improved plant translocation success, we evaluate the visibility of plants in the conservation translocation literature using the newly developed R-package LitRevieweR. Preliminary results indicate that plants constitute a mere 17% of IUCN conservation translocation case studies, but comprise 40% of peer-reviewed literature found through Scopus. Literature mining peer-reviewed studies and current IUCN Conservation Translocation Guidelines has revealed language specific to plant conservation translocations, including the words important to plant translocation success (e.g., soil microbial communities, and climate change). We recommend the development of IUCN conservation translocation guidelines specific to plants using this informed approach to increase plant conservation and restoration success worldwide

Hot Takes: A Comprehensive Review of Genes That Help Plants Survive Drought

Increasing temperatures and aridity negatively affect plant communities, including the recruitment of keystone ecological species like big sagebrush (Artemisia tridentata). While research on the genomic basis of plant resilience towards drought has been conducted in crops and model plants, fewer studies have evaluated natural plant communities. We provide a resource for identifying genes underpinning drought across a broad range of plants using a literature mining approach with the newly developed package LitRevieweR. Our results confirm that most peer-reviewed studies on drought resistance in plants are conducted on model and crop species that already have genomic resources available. This approach also identified over 4K genes associated with drought. Top-reported genes (e.g., AER, PER, and GWD) show associations with dozens of biological processes including proteogenesis, photosynthesis, stress response, and immune response. Our research will be used to construct networks for genome to phenome research, with applicability to assessing adaptive capacity of natural plant communities towards drought, pointedly big sagebrush. We anticipate this research informing future restoration efforts for sagebrush and other plant species by ensuring individuals have the adaptive capacity to endure future drought conditions