Abstract
Apocynum venetum L., a saline-alkali-tolerant plant valued for its high-quality bast fiber in textile manufacturing and medicinal compounds in traditional medicine, serves as a key economic species in saline-alkali regions with additional phytoremediation applications. However, its natural populations are becoming increasingly threatened by rapid environmental change and anthropogenic activities. To inform conservation and sustainable utilization, we generated a chromosome-level genome assembly of A. venetum (234.73 Mb; contig N50 = 19.11 Mb, scaffold N50 = 20.46 Mb) using PacBio HiFi, Illumina and Hi-C technologies, and performed whole-genome resequencing of 109 individuals spanning China's saline-alkali regions. Population genetic analyses revealed that the Xinjiang population exhibited the highest level of genetic diversity and strong genetic differentiation from the other populations. Demographic analyses indicated that most populations underwent significant population declines during the late Last Glacial Maximum, followed by recovery in western and northern populations, whereas the eastern coastal populations maintained consistently low effective population sizes. Genome-environment association analyses identified candidate adaptive loci, including a flavonol 4'-sulfotransferase (4'-ST) gene, potentially linked to saline-alkali tolerance and flavonoid biosynthesis. Our findings provide critical insights into the evolutionary history and adaptive mechanisms of A. venetum, offering genomic tools for conservation prioritization and the development of stress-resilient cultivars through marker-assisted breeding.