Haplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations

Yinguang Hou, Junwei Gan, Zeyu Fan, Lei Sun, Vanika Garg, Yu Wang, Shanying Li, Pengfei Bao, Bingchen Cao, Rajeev K. Varshney and Hansheng Zhao ()
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Yinguang Hou: International Centre for Bamboo and Rattan
Junwei Gan: International Centre for Bamboo and Rattan
Zeyu Fan: International Centre for Bamboo and Rattan
Lei Sun: International Centre for Bamboo and Rattan
Vanika Garg: Murdoch University
Yu Wang: International Centre for Bamboo and Rattan
Shanying Li: International Centre for Bamboo and Rattan
Pengfei Bao: International Centre for Bamboo and Rattan
Bingchen Cao: International Centre for Bamboo and Rattan
Rajeev K. Varshney: Murdoch University
Hansheng Zhao: International Centre for Bamboo and Rattan

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract Moso bamboo (Phyllostachys edulis), an ecologically and economically important forest species in East Asia, plays vital roles in carbon sequestration and climate change mitigation. However, intensifying climate change threatens moso bamboo survival. Here we generate high-quality haplotype-based pangenome assemblies for 16 representative moso bamboo accessions and integrated these assemblies with 427 previously resequenced accessions. Characterization of the haplotype-based pangenome reveals extensive genetic variation, predominantly between haplotypes rather than within accessions. Many genes with allele-specific expression patterns are implicated in climate responses. Integrating spatiotemporal climate data reveals more than 1050 variations associated with pivotal climate factors, including temperature and precipitation. Climate-associated variations enable the prediction of increased genetic risk across the northern and western regions of China under future emissions scenarios, underscoring the threats posed by rising temperatures. Our integrated haplotype-based pangenome elucidates moso bamboo’s local climate adaptation mechanisms and provides critical genomic resources for addressing intensifying climate pressures on this essential bamboo. More broadly, this study demonstrates the power of long-read sequencing in dissecting adaptive traits in climate-sensitive species, advancing evolutionary knowledge to support conservation.

Date: 2024
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DOI: 10.1038/s41467-024-52376-5

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