Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin

Sequencing, assembly, and annotation of the 26.5 Gbp hexaploid genome of coast redwood (Sequoia sempervirens) was completed leading toward discovery of genes related to climate adaptation and investigation of the origin of the hexaploid genome. Deep-coverage short-read Illumina sequencing data from haploid tissue from a single seed were combined with long-read Oxford Nanopore Technologies sequencing data from diploid needle tissue to create an initial assembly, which was then scaffolded using proximity ligation data to produce a highly contiguous final assembly, SESE 2.1, with a scaffold N50 size of 44.9 Mbp. The assembly included several scaffolds that span entire chromosome arms, confirmed by the presence of telomere and centromere sequences on the ends of the scaffolds. The structural annotation produced 118,906 genes with 113 containing introns that exceed 500 Kbp in length and one reaching 2 Mb. Nearly 19 Gbp of the genome represented repetitive content with the vast majority characterized as long terminal repeats, with a 2.9:1 ratio of Copia to Gypsy elements that may aid in gene expression control. Comparison of coast redwood to other conifers revealed species-specific expansions for a plethora of abiotic and biotic stress response genes, including those involved in fungal disease resistance, detoxification, and physical injury/structural remodeling and others supporting flavonoid biosynthesis. Analysis of multiple genes that exist in triplicate in coast redwood but only once in its diploid relative, giant sequoia, supports a previous hypothesis that the hexaploidy is the result of autopolyploidy rather than any hybridizations with separate but closely related conifer species.

Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia

Dissecting the genomic basis of local adaptation is a major goal in evolutionary biology and conservation science. Rapid changes in the climate pose significant challenges to the survival of natural populations, and the genomic basis of long-generation plant species is still poorly understood. Here, we investigated genome-wide climate adaptation in giant sequoia and coast redwood, two iconic and ecologically important tree species. We used a combination of univariate and multivariate genotype–environment association methods and a selective sweep analysis using non-overlapping sliding windows. We identified genomic regions of potential adaptive importance, showing strong associations to moisture variables and mean annual temperature. Our results found a complex architecture of climate adaptation in the species, with genomic regions showing signatures of selective sweeps, polygenic adaptation, or a combination of both, suggesting recent or ongoing climate adaptation along moisture and temperature gradients in giant sequoia and coast redwood. The results of this study provide a first step toward identifying genomic regions of adaptive significance in the species and will provide information to guide management and conservation strategies that seek to maximize adaptive potential in the face of climate change.

Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia

Drought is a major limitation for survival and growth in plants. With more frequent and severe drought episodes occurring due to climate change, it is imperative to understand the genomic and physiological basis of drought tolerance to be able to predict how species will respond in the future. In this study, univariate and multitrait multivariate GWAS methods were used to identify candidate genes in two iconic and ecosystem-dominating species of the western US, coast redwood and giant sequoia, using ten drought-related physiological and anatomical traits and genome wide sequence-capture SNPs. Population level phenotypic variation was found in carbon isotope discrimination, osmotic pressure at full turgor, xylem hydraulic diameter and total area of transporting fibers in both species. Our study identified new 78 new marker x trait associations in coast redwood and six in giant sequoia, with genes involved in a range of metabolic, stress and signaling pathways, among other functions. This study contributes to a better understanding of the genomic basis of drought tolerance in long-generation conifers and helps guide current and future conservation efforts in the species.

A Novel Approach to Modelling Stand-Level Growth of an Even-Aged Forest Using a Volume Productivity Index with Application to New Zealand-Grown Coast Redwood

Empirical growth models are widely used to predict the growth and yield of plantation tree species, and the precise estimation of site quality is an important component of these models. The most commonly used proxy for site quality in growth models is Site Index (SI), which describes the mean height of dominant trees at a specified base age. Although SI is widely used, considerable research shows significant site-dependent variation in height for a given volume, with this latter variable more closely reflecting actual site productivity. Using a national dataset, this study develops and describes a stand-level growth and yield model for even-aged New Zealand-grown coast redwood (Sequoia sempervirens). We used a novel modelling approach that quantifies site quality using SI and a volume-based index termed the 300 Index, defined as the volume mean annual increment at age 30 years for a reference regime of 300 stems ha−1. The growth model includes a number of interrelated components. Mean top height is modelled from age and SI using a polymorphic Korf function. A modified anamorphic Korf function is used to describe tree quadratic mean diameter (Dq) as a function of age, stand density, SI and a diameter site index. As the Dq model includes stand density in its formulation, it can predict tree growth for different stand densities and thinning regimes. The mortality model is based on a simple attritional equation improved through incorporation of the Reineke stand density index to account for competition-induced mortality. Using these components, the model precisely estimates stand-level volume. The developed model will be of considerable value to growers for yield projection and regime evaluation. By more robustly describing the site effect, the growth model provides researchers with an improved framework for quantifying and understanding the causes of spatial and temporal variation in plantation productivity.

Initial Floristic Response to High Severity Wildfire in an Old-Growth Coast Redwood (Sequoia sempervirens (D. Don) Endl.) Forest

Climate driven increases in fire frequency and severity are predicted for Mediterranean climatic zones, including the Pacific coast of California. A recent high severity wildfire that burned in the Santa Cruz Mountains affected a variety of vegetation types, including ancient coast redwood (Sequoia sempervirens (D. Don) Endl.) stands. The purpose of this study was to characterize the survival and initial recovery of vegetation approximately six months after the fire. We sampled thirty randomly selected points in an old-growth coast redwood forest to examine and compare survival, crown retention, and post fire regeneration of trees by species, and the recovery of associated understory plant species. Sequoia sempervirens exhibited the highest post-fire survival (95%), with lower survival rates for subcanopy hardwood associates including tanoak (Notholithocarpus densiflorus (Hook. & Arn.) Manos) (88%), coast live oak (Quercus agrifolia Nee.) (93%), Pacific wax myrtle (Myrica californica (Cham. & Schltdl.) Wilbur) (75%), Pacific madrone (Arbutus menziesii Pursh) (71%), and the lowest survival recorded for the canopy codominant Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) (15%). Canopy retention and post fire regeneration were also highest for S. sempervirens and lowest for P. menziesii, indicating that S. sempervirens had a competitive advantage over P. menziesii following high severity crown fire. Both canopy survival and regeneration were greater for larger height and diameter trees; and basal sprouting was positively associated with tree height and diameter for S. sempervirens and N. densiflorus. Observed recovery of understory species was modest but included the reemergence of coast redwood associated herbaceous species. The robust nature of survival and recovery of S. sempervirens following this extreme fire event suggest that the removal of scorched, and the seeding or planting of trees, following this type of fire is contraindicated. The decline of P. menziesii is of concern, however, and suggests that repeated high severity fires driven by climate change could eventually lead to vegetation type conversion.

Fuel load, stand structure, and understory species composition following prescribed fire in an old-growth coast redwood (Sequoia sempervirens) forest

Background With the prevalence of catastrophic wildfire increasing in response to widespread fire suppression and climate change, land managers have sought methods to increase the resiliency of landscapes to fire. The application of prescribed burning in ecosystems adapted to fire can reduce fuel load and fire potential while minimizing impacts to the ecosystem as a whole. Coast redwood forests have historically experienced fire from both natural and anthropogenic sources, and are likely to respond favorably to its reintroduction. Results Random sampling was conducted in three burned sites and in three unburned sites, in an old-growth coast redwood (Sequoia sempervirens [D. Don] Endl.) forest. Data were collected on fuel, forest structure, and understory species composition and compared between treatments. Downed woody fuel, duff depth, litter depth, and density of live woody fuels were found to be significantly lower on sites treated with fire compared to unburned sites. Density of the dominant overstory canopy species, coast redwood and Douglas-fir (Pseudotsuga menziesii var. menziesii [Mirb.] Franco), remained consistent between treatments, and the abundance of herbaceous understory plant species was not significantly altered by burning. In addition, both downed woody fuel and live fuel measures were positively correlated with time since last burn, with the lowest measures on the most recently burned sites. Conclusions Our results indicated that the use of prescribed burning in old-growth redwood forests can provide beneficial reductions in live and dead surface fuels with minimal impacts to overstory trees and understory herbaceous species.