A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don

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Abstract
Background: The 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. Results: Herein, 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. Conclusions: Annotations of genes and comparisons of repeat elements with other Cupressaceae and Pinaceae species provide a fundamental resource for conifer research.
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Funding Information
  • Forestry and Forest Products Research Institute (#201421, #201406, #201906)
  • Japan Society for the Promotion of Science (JP16H06279 (PAGS), JP23H02263, JP16H06279 (PAGS))
  • National Institute for Basic Biology (Collaborative Research Program (15-829, 16-403, 17-405, 18-408, 19-420, 20-428, 21-302, 22NIBB402, and 23NIBB405), Collaborative Research Program (15-829, 16-403, 17-405, 18-408, 19-420, 20-428, 21-302, 22NIBB402, and 23NIBB405))
  • Ministry of Agriculture, Forestry and Fisheries (Agriculture, Forestry and Fisheries and Food Industry Science and Technology Research Promotion Project)
  • Bio-oriented Technology Research Advancement Institution (the research program on development of innovative technology grants (JPJ007097), (Project ID 28013B))

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