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.

An Overview of the Practices and Management Methods for Enhancing Seed Production in Conifer Plantations for Commercial Use

Flowering, the beginning of the reproductive growth, is a significant stage in the growth and development of plants. Conifers are economically and ecologically important, characterized by straight trunks and a good wood quality and, thus, conifer plantations are widely distributed around the world. In addition, conifer species have a good tolerance to biotic and abiotic stress, and a stronger survival ability. Seeds of some conifer species, such as Pinus koraiensis, are rich in vitamins, amino acids, mineral elements and other nutrients, which are used for food and medicine. Although conifers are the largest (giant sequoia) and oldest living plants (bristlecone pine), their growth cycle is relatively long, and the seed yield is unstable. In the present work, we reviewed selected literature and provide a comprehensive overview on the most influential factors and on the methods and techniques that can be adopted in order to improve flowering and seed production in conifers species. The review revealed that flowering and seed yields in conifers are affected by a variety of factors, such as pollen, temperature, light, water availability, nutrients, etc., and a number of management techniques, including topping off, pruning, fertilization, hormone treatment, supplementary pollination, etc. has been developed for improving cone yields. Furthermore, several flowering-related genes (FT, Flowering locus T and MADS-box, MCMI, AGAMOUS, DEFICIENCES and SRF) that play a crucial role in flowering in coniferous trees were identified. The results of this study can be useful for forest managers and for enhancing seed yields in conifer plantations for commercial use.

Neofusicoccum parvum, a New Agent of Sequoia Canker and Dieback Identified in Geneva, Switzerland

Fungi were isolated in pure cultures from decaying giant sequoias in Geneva (Switzerland). Isolates were genetically identified by ITS rDNA sequencing. Young giant sequoia trees were artificially infected with a pure culture of Botryosphaeria parva. Henle-Koch’s Postulates demonstrated that Botryosphaeria parva was pathogenic to Sequoiadendron giganteum. When analysing the microorganisms associated to canker and dieback symptoms in a giant sequoias (Sequoiadendron giganteum) in Geneva, the fungus Neofusicoccum parvum (Pennycook & Samuels) Crous, Slippers & A.J.L. Phillips, teleomorph Botryosphaeria parva (Pennycook & Samuels) Crous, Slippers & A.J.L. Phillips, was isolated, whereas such symptoms are commonly associated to Fusicoccum aesculi (teleomorph Botryosphaeria dothidea). These two fungal species belong to the same genus Botryosphaeria of the Botryosphaeriaceae family. Because Neofusicoccum parvum was causing cankers and diebacks in other woody species around the world, we extended the analysis to other trees displaying sequoia dieback symptoms in order to evaluate the involvement of Neofusicoccum parvum in such increasing symptoms in sequoias in Geneva. Dried twigs, trunk, and branch cankers from diseased trees were sampled on several distinct sites. From all samples, isolated fungi in pure cultures showed a phenotype typical of Botryosphaeriaceae species. Isolates were then genetically identified at the species level. Subsequently Neofusicoccum parvum was inoculated to young giant sequoia trees, re-isolated in pure culture from provoked symptoms, and re-identified to fulfil Henle-Koch’s postulates. The identification confirmed that Neofusicoccum parvum was present on all sites, while Fusicoccum aesculi was retrieved only once alone. The inoculation of Neofusicoccum parvum isolates on young sequoias demonstrated for the first time that this fungus was able to develop cankers in Sequoiadendron gigantean. Neofusicoccum parvum could, therefore, be the major cause for dying of giant sequoias in the Geneva Lake area.

Patterns of Fine-Scale Spatial Genetic Structure and Pollen Dispersal in Giant Sequoia (Sequoiadendron giganteum)

Research Highlights: Patterns of dispersal shape the distribution and temporal development of genetic diversity both within and among populations. In an era of unprecedented environmental change, the maintenance of extant genetic diversity is crucial to population persistence. Background and Objectives: We investigate patterns of pollen dispersal and spatial genetic structure within populations of giant sequoia (Sequoiadendron giganteum). Materials and Methods: The leaf genotypes of established trees from twelve populations were used to estimate the extent of spatial genetic structure within populations, as measured by the Sp statistic. We utilized progeny arrays from five populations to estimate mating parameters, the diversity of the pollen pool, and characteristics of pollen dispersal. Results: Our research indicates that giant sequoia is predominantly outcrossing, but exhibits moderate levels of bi-parental inbreeding (0.155). The diversity of the pollen pool is low, with an average of 7.5 pollen donors per mother tree. As revealed by the Sp-statistic, we find significant genetic structure in ten of twelve populations examined, which indicates the clustering of related individuals at fine spatial scales. Estimates of pollen and gene dispersal indicate predominantly local dispersal, with the majority of pollen dispersal <253 m, and with some populations showing fat-tailed dispersal curves, suggesting potential for long-distance dispersal. Conclusions: The research presented here represent the first detailed examination of the reproductive ecology of giant sequoia, which will provide necessary background information for the conservation of genetic resources in this species. We suggest that restoration planting can mitigate potential diversity loss from many giant sequoia populations.