Supporting data for "The chromosome-level genome assembly of an endangered herb Bergenia scopulosa provides insights into local adaptation and genomic vulnerability under climate change"

Global climate change poses severe threats to biodiversity and ecosystem stability. Rapid climate oscillations potentially lead to species geographic range shifts, population declines and even extinctions. The rare and endangered species, being critical components of regional biodiversity, hold the key to understanding local adaptation and evolutionary processes shaping species distributions. Therefore, assessing the evolutionary mechanisms of local adaptation and population vulnerability under climate change is crucial for developing conservation strategies of endangered species.br /In this study, we assembled a high-quality, chromosome-level genome of the rare and endangered herb iBergenia scopulosa/i in the Qinling Mountains in East Asia and re-sequenced 37 individual genomes spanning its entire geographic distributional ranges. By integrating population genetics, landscape genomics, and climate datasets, a substantial number of adaptive SNP loci associated with climate variables were identified. The genotype-environment association analysis showed that some cold-tolerant genes have played pivotal roles in cold environmental adaptation of iB. scopulosa/i. These findings are further corroborated through evolutionary analysis of gene family and qPCR validation. Population genomic analysis revealed two distinct genetic lineages in iB. scopulosa/i. The western lineage showed higher genomic vulnerability and more rare cold-tolerance alleles, suggesting its heightened sensitivity to impending climate shifts and should be given priority conservation in the management practices.br /These findings provide novel insights into local adaptation and genomic vulnerability of iB. scopulosa/i under climate change in the Qinling Mountains in East Asia. Additionally, the study also offers valuable guidance for formulating conservation strategies for the rare and endangered plants.