The first high-altitude autotetraploid haplotype-resolved genome
assembled (Rhododendron nivale subsp. boreale) provides new insights
into mountaintop adaptation
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.