Woody bamboo (Bambusoideae) is renowned for its polyploidy and rare flowering. Bambusa odashimae is one of the bamboo species with the highest chromosome count (104) in the subfamily and has the highest heterozygosity of all sequenced bamboo genomes so far. Compared with other bamboo species, it can efficiently utilize exogenous hormones to regulate in vitro flowering, providing valuable insights into the hormonal regulation of bamboo flowering. Here, we generated the haplotype-resolved genome assembly of B. odashimae, despite the complexity and high chromosome number, supplemented by thirty-three transcriptomes from eleven developmental periods using a tissue culture system. The assembled genome can be divided into Haplotype I, Haplotype II, and Haplotype III, each containing A, B, and C subgenomes. Haplotype I may be derived from Dendrocalamus whereas Haplotypes II and III are closely related to Bambusa, indicating that B. odashimae has an origin involving both intergeneric and interspecific hybridizations. The high heterozygosity renders the possibility to detect abundant allele-specific expression (ASE), with ASE genes enriched in cytokinin-related pathways, likely associated with efficient cytokinin-promoted flowering. Notably, we found that the CONSTANS (CO) genes were potentially key regulators of in vitro flowering in B. odashimae. Overall, our study, based on the in vitro system combined with a high-quality reference genome, provides critical insights into the origin of this nonaploid bamboo and links hybridization and in vitro flowering in bamboo.

中文翻译：

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单倍型解析的非倍体基因组为竹子的体外开花提供了见解


木本竹（Bambusoideae）以其多倍体和罕见的开花而闻名。竹子是该亚科中染色体数最高（104）的竹种之一，也是迄今为止所有测序的竹子基因组中杂合度最高的。与其他竹种相比，它可以有效地利用外源激素来调节体外开花，为竹子开花的激素调节提供了有价值的见解。在这里，我们使用组织培养系统生成了 B. odashimae 的单倍型解析基因组组装，尽管其复杂性和染色体数量很高，并补充了来自 11 个发育阶段的 33 个转录组。组装的基因组可分为单倍型I、单倍型II和单倍型III，每个亚基因组包含A、B和C亚基因组。单倍型 I 可能源自 Dendrocalamus，而单倍型 II 和 III 与 Bambusa 密切相关，表明 B. odashimae 的起源涉及属间和种间杂交。高杂合性使得检测丰富的等位基因特异性表达（ASE）成为可能，ASE基因富含细胞分裂素相关途径，可能与有效的细胞分裂素促进开花有关。值得注意的是，我们发现 CONSTANS (CO) 基因是 B. odashimae 体外开花的潜在关键调节因子。总的来说，我们的研究基于体外系统与高质量参考基因组相结合，为这种非倍体竹子的起源提供了重要的见解，并将竹子的杂交和体外开花联系起来。