Woody bamboos (Bambusoideae) are 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, based on the in vitro system combined with a high-quality reference genome, our study provides critical insights into the origin of this nonaploid bamboo and links hybridization and in vitro flowering in bamboos.

中文翻译：

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单倍型解析的非倍体基因组为竹子体外开花提供了见解


木本竹 （Bambusoideae） 以其多倍体和稀有的开花而闻名。Bambusa odashimae 是该亚科中染色体计数最高 （104） 的竹种之一，也是迄今为止所有测序竹子基因组中杂合性最高的。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，为竹子开花的荷尔蒙调节提供有价值的见解。在这里，我们生成了 B. odashimae 的单倍型分辨基因组组装，尽管复杂性和高染色体数量，但使用组织培养系统补充了来自 11 个发育时期的 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，每个都包含 A、B 和 C 亚基因组。单倍型 I 可能来源于 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，其中 ASE 基因富含细胞分裂素相关途径，可能与细胞分裂素促进的高效开花有关。值得注意的是，我们发现 CONSTANS （CO） 基因可能是 B. odashimae 体外开花的关键调节因子。总体而言，基于体外系统结合高质量的参考基因组，我们的研究为这种非倍体竹子的起源提供了重要见解，并将杂交和竹子体外开花联系起来。