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

Abstract

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.

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

“…Our results suggest a polygenic basis of drought tolerance, consistent with previous GWAS in other complex traits in conifer species, with candidate genes distributed in different chromosomes or scaffolds, and small to moderate effect sizes (Baison et al, 2020;De La Torre et al, 2021a;Weiss et al, 2020). The exact location of candidate genes in the SESE genome could only be determined at the scaffold level, as the current assembly of the reference genome is not chromosome-scale (Neale et al, 2021). Univariate methods identified 78 new significant associations for SESE, 27 of them were consistently found by all three univariate and multivariate GWAS methods in this study.…”

“…Here, we report notable phenotypic variation for several drought-related traits among natural populations (or groves) of both SEGI and SESE grown in a common garden. The development of genome-wide methods, gene identification, functional annotation, and location in the species genomes has only been possible due to the recent sequencing of reference genomes for both species (Neale et al, 2021;Scott et al, 2020).…”

“…For that purpose, SESE seedlings measured in this study have been planted in long-term common gardens in California, where different phenotypes can be evaluated as trees mature. This new resource, together with our newly sequenced reference genomes of SEGI and SESE (Neale et al, 2021;Scott et al, 2020) will help to develop future genomic studies in the species. A thorough knowledge of the interconnection among plasticity, genomics, and physiological processes is needed to predict species responses to future warmer conditions and to design conservation and management strategies.…”

“…Coast redwood (Sequoia sempervirens [D. Don] Endl.) (SESE) is also slow-growing and long-lived but differs from SEGI in that it is hexaploid (genome size is 26.5 Gbp; Neale et al, 2021) and often reproduces asexually. The species once had a nearly continuous distribution along the Pacific Coast in Oregon and California, but natural populations were severely reduced by intensive logging beginning in the nineteenth and twentieth centuries (Breidenbach et al, 2020;Burns et al, 2018).…”

Chromosome-scale genome assembly of the diploid oat Avena longiglumis reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses

“…Assembled plant genome sizes range from 61 Mbp ( Genlisea tuberosa , bladderwort [63]) to 26,454 Gbp ( Sequoia sempervirens , coast redwood [64]). The ALO assembly falls into this range, and a combination of ONT, Illumina and Hi-C sequence approaches was essential for the high continuity chromosome level assemblies with high presence of core genes, as is for many important crop genomes, particularly cereals, with genomes larger than 2 Gbp (barley [65]; wheat [66, 67]).…”