Haplotype-resolved de novo genome assemblies of four coniferous tree species

ABSTRACT

Coniferous trees in gymnosperm are an important source of wood production. Because of their long lifecycle, the breeding programs of coniferous tree are time- and labor-consuming. Genomics could accelerate the selection of superior trees or clones in the breeding programs; however, the genomes of coniferous trees are generally giant in size and exhibit high heterozygosity. Therefore, the generation of long contiguous genome assemblies of coniferous species has been difficult. In this study, we employed high-fidelity (HiFi) long-read sequencing technology to sequence and assemble the genomes of four coniferous tree species, Larix kaempferi, Chamaecyparis obtusa, Cryptomeria japonica, and Cunninghamia lanceolata. Genome assemblies of the four species totaled 13.5 Gb (L. kaempferi), 8.5 Gb (C. obtusa), 9.2 Gb (C. japonica), and 11.7 Gb (C. lanceolata), which covered 99.6% of the estimated genome sizes on average. The contig N50 value, which indicates assembly contiguity, ranged from 1.2 Mb in C. obtusa to 16.0 Mb in L. kaempferi, and the assembled sequences contained, on average, 89.2% of the single-copy orthologs conserved in embryophytes. Assembled sequences representing alternative haplotypes covered 70.3–95.1% of the genomes, suggesting that the four coniferous tree genomes exhibit high heterozygosity levels. The genome sequence information obtained in this study represents a milestone in tree genetics and genomics, and will facilitate gene discovery, allele mining, phylogenetics, and evolutionary studies in coniferous trees, and accelerate forest tree breeding programs.

KEYWORDS:

• Breeding
• coniferous trees
• genome
• gymnosperm
• long-read sequencing

Acknowledgements

We thank the University of Tokyo Chiba Forest for their support and cooperation during the collection of C. lanceolata leaf samples. We also thank Y. Kishida, M. Kohara, C. Minami, K. Ozawa, H. Tsuruoka, and A. Watanabe (Kazusa DNA Research Institute) for technical assistance. This study was supported in part by the MAFF commissioned project study on “Development of efficient breeding technique aiming at forestry trees with superior carbon storage capacity” (Grant Number JPJ009841), JSPS KAKENHI (22H05172 and 22H05181), and the Kazusa DNA Research Institute Foundation.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data archiving statement

Raw sequence reads were deposited in the Sequence Read Archive (SRA) database of the DNA Data Bank of Japan (DDBJ) under the BioProject of PRJDB14450 and the accession numbers DRR413190 - DRR413200 and DRR459944 (L. kaempferi), DRR413180 - DRR413189 and DRR459943 (C. obtusa), DRR413201 - DRR413209 and DRR459945 (C. japonica), and DRR413210 - DRR413217 and DRR459946 (C. lanceolata). The assembled sequences are available at DDBJ (accession numbers: BSBM01000001-BSBM01004655 [L. kaempferi]; BSBK01000001-BSBK01015466 [C. obtusa]; BSBL01000001-BSBL01002741 [C. japonica]; and BSBN01000001-BSBN01002472 [C. lanceolata]), BreedingTrees-by-Genes (http://btg.kazusa.or.jp), and Plant GARDEN (https://plantgarden.jp).

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/13416979.2023.2267304

Additional information

Funding

The work was supported by the KAKENHI [22H05172]; KAKENHI [22H05181]; MAFF [JPJ009841].