Whole genome duplication in coast redwood ( Sequoia sempervirens ) and its implications for explaining the rarity of polyploidy in conifers (original) (raw)
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G3 Genes|Genomes|Genetics
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 c...
The American Midland Naturalist, 2011
We developed a suite of tetranucleotide microsatellite loci and applied them to a study of genetic variation across the geographic range of coast redwood [Sequoia sempervirens (D. Don) Endl.]. The objectives of the study were to determine if the microsatellite loci could provide useful information on genetic diversity in this hexaploid species and to investigate earlier reports of divergent lineages within coast redwood. The microsatellite loci were highly variable, yielding a total of 142 alleles. Up to six alleles were detected in each individual consistent with the ploidy of coast redwood and suggesting that parental genomes must have been at least partially homologous. This does not rule out autoployploidy in the evolution of the redwood genome. We treated the microsatellite alleles as presence-absence data and we also estimated full genotypes assuming peak intensities varied with allele dosage. Both types of analyses revealed similar trends. Variation within the 17 watersheds sampled, explained most of the genetic diversity, with less than 4% of the variation attributable to watersheds. Our data showed a weak divergence between more or less continuous populations north of 36.8uN (the Sonoma-Mendocino county border) and disjunct populations south of this latitude. This is further north than indicated from earlier studies of marker systems that would be under selection and may reflect a demographic break. In view of the importance of clonal growth, we suggest that redwood may have difficulty adapting to new climatic conditions or of migrating into displaced habitats with anticipated climate change. Furthermore, the southern lineage of populations is likely to be at greatest risk and is therefore of conservation priority.
American Journal of Botany, 2004
The ecology and evolutionary potential of coast redwood (Sequoia sempervirens) is significantly influenced by the important role clonal spread plays in its reproduction and site persistence. In nine second-growth stands, amplified fragment length polymorphisms (AFLPs) were used to identify redwood clonal architecture. Clones (multistem genets) dominated sites by representing an average of 70% of stems measured, ranging in size from two to 20 stems. As a result, a relatively small number of genets can monopolize a disproportionate amount of site resources, are more likely to persist over time, and have greater on-site genetic representation. Clones were not limited to fairy-ring structures, but consisted of a wide range of shapes including concentric rings, ring chains, disjunct. and linear structures. Between-ramet distances of up to 40 m were measured, indicating that clonal reproduction is not limited to basal sttlmp resprouting. Clonal structure in second-growth stands was similar to earlier reports from old growth, emphasizing the importance of site persistence and long-term, gradual site development. Smaller ramet numbers per genet in old growth is probably due to local within-genet self thinning. Management and conservation of redwoods will benefit from a better understanding of the dynamics and structure of clonal spread in these forests.
Genetic constitution and diversity in four narrow endemic redwoods from the family Cupressaceae
Euphytica, 2009
The genetic constitution and diversity of four relictual redwoods are discussed in this review. These include monotypic genera of the family Cupressaceae: coast redwood (Sequoia sempervirens), giant sequoia (Sequoiadendron giganteum), dawn redwood (Metasequoia glyptostroboides), and alerce (Fitzroya cupressoides). All four species are narrow endemics, share a number of common phenotypic traits, including red wood, and are threatened species. Fossil history suggests that the ancestors of redwoods probably originated during the Cretaceous and Tertiary periods and Xourished thereafter for millions of years. Towards the end of the Tertiary period began their decline and struggle for existence that continued during the subsequent geologic upheavals and climate changes, until the survival of the presentday redwoods in the current restricted locations in the world (USA, China, and South America). Although two species, Sequoiadendron and Metasequoia, are diploids (2n = 22), and the other two are polyploids: Fitzroya a tetraploid (2n = 4x = 44), and Sequoia a hexaploid (2n = 6x = 66); they all share the same basic chromosome number x = 11. The genome size in the hexaploid Sequoia is one of the largest (31,500 MB) in the conifers, while the genome sizes of diploid Metasequoia and Sequoiadendron are about one-third (ยป10,000 MB) of Sequoia. Genetic diversity in the redwoods is lower than most other gymnosperms, except in Sequoia, which seems to rank near the upper quarter of the coniferous forest trees. Genomic research is sparse in the redwoods, and should be pursued for a better understanding of their genome structure, function, and adaptive genetic diversity.
Polyploidy in the Conifer Genus Juniperus: An Unexpectedly High Rate
Frontiers in Plant Science
Recent research suggests that the frequency of polyploidy may have been underestimated in gymnosperms. One notable example is in the conifer genus Juniperus, where there are already a few reports of polyploids although data are still missing for most species. In this study, we evaluated the extent of polyploidy in Juniperus by conducting the first comprehensive screen across nearly all of the genus. Genome size data from fresh material, together with chromosome counts, were used to demonstrate that genome sizes estimated from dried material could be used as reliable proxies to uncover the extent of ploidy diversity across the genus. Our analysis revealed that 16 Juniperus taxa were polyploid, with tetraploids and one hexaploid being reported. Furthermore, by analyzing the genome size and chromosome data within a phylogenetic framework we provide the first evidence of possible lineage-specific polyploidizations within the genus. Genome downsizing following polyploidization is moderate, suggesting limited genome restructuring. This study highlights the importance of polyploidy in Juniperus, making it the first conifer genus and only the second genus in gymnosperms where polyploidy is frequent. In this sense, Juniperus represents an interesting model for investigating the genomic and ecological consequences of polyploidy in conifers.
Applications in plant sciences, 2015
Identifying clonal lineages in asexually reproducing plants using microsatellite markers is complicated by the possibility of nonidentical genotypes from the same clonal lineage due to somatic mutations, null alleles, and scoring errors. We developed and tested a clonal identification protocol that is robust to these issues for the asexually reproducing hexaploid tree species coast redwood (Sequoia sempervirens). Microsatellite data from four previously published and two newly developed primers were scored using a modified protocol, and clones were identified using Bruvo genetic distances. The effectiveness of this clonal identification protocol was assessed using simulations and by genotyping a test set of paired samples of different tissue types from the same trees. Data from simulations showed that our protocol allowed us to accurately identify clonal lineages. Multiple test samples from the same trees were identified correctly, although certain tissue type pairs had larger genet...
PLOS ONE, 2020
Coast redwood (Sequoia sempervirens) naturally growing in southern Oregon and northern California is one of the few conifer tree species that are polyploid. Despite its unique ecological and economic importance, its population genetic structure is still insufficiently studied. To obtain additional data on its population genetic structure we genotyped 317 samples collected from populations in California (data set C) and 144 trees growing in a provenance trial in France (data set F) using 12 nuclear (five random nuclear genomic nSSRs and seven expressed sequence tag EST-SSRs) and six chloroplast (cpSSRs) microsatellite or simple sequence repeat (SSR) markers, respectively. These data sets were also used as reference to infer the origin of 147 coast redwood trees growing in Germany (data set G). Coast redwood was introduced to Europe, including Germany as an ornamental species, decades ago. Due to its fast growth and high timber quality, it could be considered as a potential commercial...
Journal of Computational Biology, 2009
Recent analyses of plant genomic data have found extensive evidence of ancient whole genome duplication (or polyploidy) events, but there are many unresolved questions regarding the number and timing of such events in plant evolutionary history. We describe the first exact and efficient algorithm for the Episode Clustering problem, which, given a collection of rooted gene trees and a rooted species tree, seeks the minimum number of locations on the species tree of gene duplication events. Solving this problem allows one to place gene duplication events onto nodes of a given species tree and potentially detect large-scale gene duplication events. We examined the performance of an implementation of our algorithm using 85 plant gene trees that contain genes from a total of 136 plant taxa. We found evidence of large-scale gene duplication events in Populus, Gossypium, Poaceae, Asteraceae, Brassicaceae, Solanaceae, Fabaceae, and near the root of the eudicot clade that are consistent with previous genomic evidence. However, a lack of phylogenetic signal within the gene trees can produce erroneous evidence of large-scale duplication events, especially near the root of the species tree. Although the results of our algorithm should be interpreted cautiously, they provide hypotheses for precise locations of large-scale gene duplication events with data from relatively few gene trees and can complement other genomic approaches to provide a more comprehensive view of ancient large-scale gene duplication events.
Clonal Spread in Second-Growth Stands of Coast Redwood, Sequoia sempervirens1
Coast redwood (Sequoia sempervirens) is one of the rare conifers to reproduce successfully through clonal spread. The importance of this mode of reproduction in stand development is largely unknown. Understanding the importance of clonal spread and the spatial structure of clones is crucial for stand management strategies that would aim to maximize genetic diversity. We have developed genetic markers to identify the clonal structure of nine second- growth redwood stands in Jackson Demonstration State Forest, California. Clonal spread was found to be important in the development of these stands, with an average of 6.7 stems being assigned as ramets of the same genet. Although fairy ring structures were commonly identified, we also detected a range of other spatial structures in these second-growth redwood stands. We also detected mixed genets within perceived fairy rings. The extent of clones and their spatial structure may have important evolutionary implications and will also have ...
2017
During this century, climate warming and altered precipitation patterns will lead to habitat changes that may be beneficial to some long-lived tree species and detrimental to others. Paleoendemics, with limited and disjunct distributions will face the greatest challenges, as migration rates will be too slow to keep pace with rapid environmental change and populations at the receding edges are eroded through mal-adaption. Giant sequoia (Sequoiadendron giganteum (Lindl.) Buchholz) is an iconic Sierra Nevada tree species with populations that tend to be small and highly fragmented (particularly in the northern range), making them especially vulnerable to environmental change. Maintenance of genetic variation is an important determinant of population persistence that, in part, depends on gene flow within and between populations. The research presented here describes: 1) the distribution of genetic diversity among population pairs distributed across the range of giant sequoia, and 2) the...