Chromosome‐level de novo genome assembly and whole‐genome resequencing of the threatened species Acanthochlamys bracteata (Velloziaceae) provide insights into alpine plant divergence in a biodiversity hotspot

Abstract

The Hengduan Mountains region is an important hotspot of alpine plant diversity and endemism. Acanthochlamys bracteata is a species of a threatened monotypic genus endemic to the Hengduan Mountains. In this study, we present a high‐quality, chromosome‐level reference genome for A. bracteata, constructed using long reads, short reads and Hi‐C technology. We characterized its genetic diversity, population structure, demographic history and gene flow by resequencing individuals collected across its distribution. Comparative genomics analyses based on sequence information from single‐copy orthologous genes revealed that A. bracteata and Dioscorea rotundata diverged ~104.5 million years ago. Whole‐genome resequencing based on population genetic analysis revealed that the division of the 14 populations into 10 distinct clusters reflected geographical divergence, and three separate high levels of gene flow occurred sequentially between isolated populations of the Hengduan Mountains, a finding which is consistent with the turnover between ice ages and interglacial periods. Our findings indicate that Quaternary climatic changes played an important role in shaping the genetic structure and demographic trajectories of A. bracteata, and provide critical insights into the genetic status and evolutionary history of this poorly understood species, and possibly other alpine plants with a similar distribution. This study demonstrates the usefulness of population genomics for evaluating the effects of past climatic changes and identifying conservation units for the conservation and management of threatened species. Our high‐quality genome represents a valuable resource for future studies of the underlying molecular mechanisms of adaptive evolution and provides insight for further comparative genomic analysis with other Velloziaceae species.

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Speciation patterns of related species under the hybrid zone: A case study of three sclerophyllous oaks in the east Himalaya–Hengduan Mountains

“…During this period, alpine plants had been affected by climatic turbulence. For example, the effective population size of Acanthochlamys bracteata (Velloziaceae) had continued to decline, and experienced two bottlenecks during succession between glacial and interglacial periods (Xu et al, 2022). Based on the population dynamic history analysis (Figure 5b), the effective population size of the three sclerophyll oaks showed an overall declining trend during the Pleistocene and flattened during the Holocene.…”

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