ArticleG3 (Bethesda, Md.)2022
Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin.
Article in G3 (Bethesda, Md.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 49 citations in OpenAlex.
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- Genomic insights into the improvement of Chinese fir from ancient domestication continuum to modern breeding.Nature communications · 2026Article
- Decoding the genome of Brainea insignis reveals insights into fern evolution and conservation.Nature communications · 2025Article
- Transcriptomic and enzymological evidence for plastid peptidoglycan synthesis in the gymnosperm Picea abies.The Plant journal : for cell and molecular biology · 2025Article
- NGATHA carpel development genes evolved in the common ancestor of seed plants.The Plant journal : for cell and molecular biology · 2025Article
- Construction of Ancestral Chromosomes in Gymnosperms and the Application in Comparative Genomic Analysis.Plants (Basel, Switzerland) · 2025Article
- Occurrence of aneuploidy across the range of coast redwood (Sequoia sempervirens).G3 (Bethesda, Md.) · 2025Article
- Conifers Concentrate Large Numbers of NLR Immune Receptor Genes on One Chromosome.Genome biology and evolution · 2024Article
- Piece and parcel of gymnosperm organellar genomes.Planta · 2024Review
- A genome sequence for the threatened whitebark pine.G3 (Bethesda, Md.) · 2024Article
- High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers.G3 (Bethesda, Md.) · 2024Article
- Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response.G3 (Bethesda, Md.) · 2023Article
- Identification and high-throughput genotyping of single nucleotide polymorphism markers in a non-model conifer (Abies nordmanniana (Steven) Spach).Scientific reports · 2023Article
- The Metasequoia genome and evolutionary relationships among redwoods.Plant communications · 2023Article
- Mabs, a suite of tools for gene-informed genome assembly.BMC bioinformatics · 2023Article
- A gap-free genome assembly of Chlamydomonas reinhardtii and detection of translocations induced by CRISPR-mediated mutagenesis.Plant communications · 2023Article
- The need for masked genomes in gymnosperms.Frontiers in plant science · 2023Article
- Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica).BMC plant biology · 2022Article
- The western redcedar genome reveals low genetic diversity in a self-compatible conifer.Genome research · 2022Article
- Evolution of complex genome architecture in gymnosperms.GigaScience · 2022Article
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Authors and funding
16 authors at 5 institutions in 1 country.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.