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

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.

Population structure and hybridization under contemporary and future climates in a heteroploid foundational shrub species (Artemisia tridentata)

“…In A. tridentata , polyploid populations have been widely found and are abundant across its distribution ( McArthur and Sanderson, 1999 ). Recent studies suggest independent origins of the tetraploids ( Richardson et al., 2012 ), as well as cycles of polyploidization and possible re-diploidization ( Melton et al., 2022 ). These findings indicate that WGD is an evolutionary mechanism and adaptive process of ecological importance in this taxonomic group.…”

“…Each filtered read file was mapped against the A. tridentata reference genome ( Melton et al., 2022 ), using the maximum exact match (MEM) algorithm (BWA 0.7.17, Li and Durbin, 2010 ). The resulting SAM files were sorted by reference coordinates and annotated with read groups (picard tools 2.9.2; available from https://broadinstitute.github.io/picard/ ).…”

“…The demultiplexed files were then filtered for polyG tails (-g), adapter content (-a), and a minimum length of 139 bp (fastp, Chen et al, 2018; available at https://github.com/OpenGene/fastp). Each filtered read file was mapped against the A. tridentata reference genome (Melton et al, 2022), using the maximum exact match (MEM) algorithm (BWA 0.7.17, Li and Durbin, 2010). The resulting SAM files were sorted by reference coordinates and annotated with read groups (picard tools 2.9.2; available from https://broadinstitute.github.io/picard/).…”

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

“…tridentata were selected for comparison. The IDT3 (Rockville, ID, USA) and UTT2 (La Sal, UT, USA) samples represent individuals from previously studied populations (Barron et al, 2020;Martinez et al, 2023;Melton et al, 2022aMelton et al, , 2023 that are maintained in vitro at Boise State University (Boise, ID, USA) for G2P and G×E research (Barron et al, 2020). These populations occur in regions with distinct climatic regimes; UTT2 experiences shorter summer drought stress, which is relieved by the North American monsoon annually, while IDT3 experiences longer durations of summer drought stress and does not receive rain from the North American monsoon.…”

“…Another individual, designated IDT2, sampled from a natural population in Orchard, Idaho, United States was used in a previous genomic study (NCBI SRA accessions SRR14309371, SRR14309372, and SRR14309373; Melton et al, 2021) and also included in the present study. The IDT3 reference genome sample (NCBI SRA accessions SRR17870775 and SRR17863368; Melton et al, 2022a) was used in these T A B L E 1 Locality and environmental data for the areas from which individuals were sampled. One sample, IDT2, represents a natural population, while IDT3 and UTT2 represent in vitro propagated lines developed from plants grown from seeds sampled from natural populations.…”