ArticleBMC genomics2024
A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don.
Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
- Review
- Population history rather than tree age contributes to the evolutionary importance of ancient trees in an endangered conifer.Nature plants · 2026Article
- Chromosomal evolution and speciation inferred from chromosome-scale genome assemblies in three Cupressaceae species.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Genomic insights into the improvement of Chinese fir from ancient domestication continuum to modern breeding.Nature communications · 2026Article
- Positional identification of a candidate gene for MALE STERILITY 2 (MS2) by linkage mapping and transcriptomic data in Cryptomeria japonica D. Don.BMC genomics · 2026Article
- Natural selection and recombination interact to structure genome-wide variation in pines.The Plant journal : for cell and molecular biology · 2026Article
- 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
- Climate-Associated Genetic Variation and Projected Genetic Offsets forEvolutionary applications · 2025Article
- Convergent Patterns of Karyotype Evolution Underlying Karyotype Uniformity in Conifers.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Transcriptome differentiation in Cryptomeria japonica trees with different origins growing in the north and south of Japan.PloS one · 2025Article
- Photoprotective pigment plasticity and cold acclimation strategies inForestry research · 2025Article
- Improvement of genome editing efficiency by Cas9 codon optimization in Japanese cedar (Plant biotechnology (Tokyo, Japan) · 2024Article
- A genome sequence for the threatened whitebark pine.G3 (Bethesda, Md.) · 2024Article
- Identification and high-throughput genotyping of single nucleotide polymorphism markers in a non-model conifer (Abies nordmanniana (Steven) Spach).Scientific reports · 2023Article
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17 authors.
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Abstract
backgroundThe Japanese cedar (Cryptomeria japonica D. Don) is one of the most important Japanese forest trees, occupying approximately 44% of artificial forests and planted in East Asia, the Azores Archipelago, and certain islands in the Indian Ocean. Although the huge genome of the species (ca. 9 Gbp) with abundant repeat elements may have represented an obstacle for genetic analysis, this species is easily propagated by cutting, flowered by gibberellic acid, transformed by Agrobacterium, and edited by CRISPR/Cas9. These characteristics of C. japonica recommend it as a model conifer species for which reference genome sequences are necessary.
resultsHerein, we report the first chromosome-level assembly of C. japonica (2n = 22) using third-generation selfed progeny (estimated homozygosity rate = 0.96). Young leaf tissue was used to extract high molecular weight DNA (> 50 kb) for HiFi PacBio long-read sequencing and to construct an Hi-C/Omni-C library for Illumina short-read sequencing. The 29× and 26× genome coverage of HiFi and Illumina reads, respectively, for de novo assembly yielded 2,651 contigs (9.1 Gbp, N50 contig size 12.0 Mbp). Hi-C analysis mapped 97% of the nucleotides on 11 chromosomes. The assembly was verified through comparison with a consensus linkage map comprising 7,781 markers. BUSCO analysis identified ∼ 91% conserved genes.
conclusionsAnnotations of genes and comparisons of repeat elements with other Cupressaceae and Pinaceae species provide a fundamental resource for conifer research.
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