Haplotype-resolved nonaploid genome provides insights into in vitro flowering in bamboos

Abstract

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.

Acknowledgements

We would like to thank Choun-Sea Lin, Fu-Hui Wu, Jun He, Chun-Fang Li, and Cun-Fu Li for their assistance in building the in vitro tissue culture system. This research was facilitated by Germplasm Bank of Wild Species (GBOWS). This work was supported by the National Natural Science Foundation of China (grants 31670227 to Z.-H.G. and 32120103003 to D.-Z.L.), the Program of Science and Technology Talents Training in Yunnan Province (202105AC160022 to P.-F.M.) and Ten Thousand Talent Program of Yunnan Province (YNWR-QNBJ-2020-297 to P.-F.M.)

Author contributions

D.-Z. L., Z.-H. G., and P.-F. M. designed the study; Y.-J. W. built in vitro tissue culture systems; Sampling was performed by L.M. and Y.-J. W.; Y.-J. W., Y.-Z. Y., L.Z. and K.-C. Q. analyzed data. Y.-J. W., C.G., P.-F.M., Z.-H. G., and D.-Z. L. wrote and edited the manuscript; All authors approved the final version of the manuscript.

Data availability statement

Raw data and assembly genome underlying this article are available in Science Data Bank (https://doi.org/10.57760/sciencedb.12511). Transcriptome sequencing data were deposited in Science Data Bank (https://cstr.cn/31253.11.sciencedb.12528).

Conflict of interest statement

.No conflict of interest is declared.

Supplementary Information

Supplementary material are available at Horticulture Research online.

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