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Seabuckthorn (<jats:italic>Hippophae rhamnoides<\/jats:italic> L.) is an economically and ecologically important species within the family with richness of biologically and pharmacologically active substances. Here, we present a chromosome\u2010level genome assembly of seabuckthorn (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/hipp.shengxin.ren\/\">http:\/\/hipp.shengxin.ren\/<\/jats:ext-link>), the first genome sequence of Elaeagnaceae, which has a total length of 849.04\u2009Mb with scaffold N50 of 69.52\u2009Mb and 30\u2009864 annotated genes. Two sequential tetraploidizations with one occurring ~36\u201041 million years ago (Mya) and the last ~24\u201327\u2009Mya were inferred, resulting in expansion of genes related to ascorbate and aldarate metabolism, lipid biosynthesis, and fatty acid elongation. Comparative genomic analysis reconstructed the evolutionary trajectories of the seabuckthorn genome with the predicted ancestral genome of 14 proto\u2010chromosomes. Comparative transcriptomic and metabonomic analyses identified some key genes contributing to high content of polyunsaturated fatty acids and ascorbic acid (AsA). Additionally, we generated and analysed 55 whole\u2010genome sequences of diverse accessions, and identified 9.80 million genetic variants in the seabuckthorn germplasms. Intriguingly, genes in selective sweep regions identified through population genomic analysis appeared to contribute to the richness of AsA and fatty acid in seabuckthorn fruits, among which <jats:italic>GalLDH, GMPase<\/jats:italic> and <jats:italic>ACC<\/jats:italic>, <jats:italic>TER<\/jats:italic> were the potentially major\u2010effect causative genes controlling AsA and fatty acid content of the fruit, respectively. Our research offers novel insights into the molecular basis underlying phytochemical innovation of seabuckthorn, and provides valuable resources for exploring the evolution of the Elaeagnaceae family and molecular breeding.<\/jats:p>","DOI":"10.1111\/pbi.13802","type":"journal-article","created":{"date-parts":[[2022,3,4]],"date-time":"2022-03-04T10:27:15Z","timestamp":1646389635000},"page":"1257-1273","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":49,"title":["Genome sequence and population genomics provide insights into chromosomal evolution and phytochemical innovation of <i>Hippophae rhamnoides<\/i>"],"prefix":"10.1111","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9735-3301","authenticated-orcid":false,"given":"Liyang","family":"Yu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding &amp; Key Laboratory of Tree Breeding and Cultivation National Forestry and 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