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

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.

裸子植物中的针叶树是木材生产的重要来源。由于其生命周期漫长，针叶树的育种项目往往耗时耗力。基因组学可加速育种项目中优良林木或无性系的选育进程；然而，针叶树的基因组通常体量庞大且杂合度较高。因此，获取针叶树物种的长片段连续基因组组装体一直颇具挑战。本研究采用高保真（high-fidelity, HiFi）长读长测序技术，对日本落叶松（Larix kaempferi）、日本扁柏（Chamaecyparis obtusa）、日本柳杉（Cryptomeria japonica）和杉木（Cunninghamia lanceolata）四种针叶树的基因组进行测序与组装。四个物种的基因组组装结果总长度分别为13.5 Gb（日本落叶松）、8.5 Gb（日本扁柏）、9.2 Gb（日本柳杉）以及11.7 Gb（杉木），平均覆盖了预估基因组大小的99.6%。反映组装连续性的重叠群N50值范围为日本扁柏的1.2 Mb至日本落叶松的16.0 Mb，组装序列平均包含89.2%的有胚植物保守单拷贝直系同源基因。代表等位单倍型的组装序列覆盖了基因组的70.3%~95.1%，表明这四种针叶树基因组均具有较高的杂合度。本研究获得的基因组序列信息是林木遗传学与基因组学研究的一座里程碑，将助力针叶树的基因发掘、等位基因挖掘、系统发育学与进化研究，并推动林木育种项目的进程。