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The first high-altitude autotetraploid haplotype-resolved genome assembled (Rhododendron nivale subsp. boreale) provides new insights into mountaintop adaptation
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  • Zhen-Yu Lyu,
  • Xiong-Li Zhou,
  • Si-Qi Wang,
  • Gao-Ming Yang,
  • Wen-Guang Sun,
  • Jie-Yu Zhang,
  • Rui Zhang,
  • Shi-Kang Shen
Zhen-Yu Lyu
Yunnan University
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Xiong-Li Zhou
Yunnan University
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Si-Qi Wang
Yunnan University
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Gao-Ming Yang
Yunnan University
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Wen-Guang Sun
Yunnan Normal University
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Jie-Yu Zhang
Yunnan Normal University
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Rui Zhang
Yunnan University
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Shi-Kang Shen
Yunnan University

Corresponding Author:[email protected]

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Abstract

Rhododendron nivale subsp. boreale Philipson et M. N. Philipson is a kind of ornamental alpine woody flower from mountaintop scrub at an altitude of approximately 4000 meters. Despite ecological significance, the lack of genomic resources has hindered a comprehensive understanding of its evolutionary and adaptive characteristics in high-altitude environments. In this work, we sequenced and assembled the genome of R. nivale subsp. boreale, which is an assembly of the first subgenus Rhododendron and the first high-altitude woody flowering autotetraploid. The assembly included 52 pseudochromosomes, which belonged to 4 haplotypes, harbor 127,810 predicted protein-coding genes. Comparative genomic analysis revealed that R. nivale subsp. boreale originated as a neopolyploid resulting from R. nivale and experienced two rounds of ancient polyploidy event. Transcriptional expression analysis showed that the expression differences of alleles were common, randomly distributed in the genome. We identified signatures of positive selection involved not only in adaptations to mountaintop ecosystem (response to UV radiation and developmental regulation), but also in strategy of autotetraploid reproduction (meiotic stabilization). Notably, highly expressed ERF VIIs aid survival in hypoxic mountaintop environments. Meanwhile, the expanded families was enriched in brassinosteroid (BR) biosynthesis, which enhances adaptability to the dramatic changes in alpine weather, is likely mediated by the increased number of cytochrome P450 (CYP) genes. This valuable genome of mountaintop woody flowering autotetraploids not only provides genetic resources for studying high-altitude polyploid formation but also provides new insights for understanding the evolution and adaptation mechanism of high-altitude plants.