Abstract: The genus Magnolia belongs to Magnoliaceae, an early diverging lineage of the Magnoliales, and is cultivated globally for its high ornamental and commercial values. Meanwhile, as the large genus in the family Magnoliaceae, Magnolia species are regarded as highly value in phylogenetic and conservation biological studies. However, the whole genome data of Magnolia is still relatively insufficient in previous research. Here, we present a high-quality, chromosome-level genome sequence of Magnolia sinostellata (1.86 Gb) with a scaffold N50 of 85.33 Mb. The nineteen M. sinostellata genome chromosomes revealed eleven main duplications representing subgenome. Comparative genomics analysis elucidates that the variance in the number of abiotic stress resistance genes among Magnoliids species are related to different environmental adaptations. Most of the genes related to MAPK signaling and stress resistance pathways in the investigated M. sinostellata species are expanded as compared to the other species. Furthermore, the comparative genomics analysis of three Magnolia assemblies, M. sinostellata, M. biondii, and M. sieboldii reveal that large inversions enriched in terpenoid metabolic pathways, stress resistance and flavonoid biosynthesis, and DNA replication proteins. Using transcriptome sequencing data, we analyzed the expression levels of genes related to terpenoids biosynthesis (terpene synthase, TPSs) and ICE-CBF-COR gene models related to cold tolerance in various tissues and the buds under different temperature conditions. The high-quality assembly of M. sinostellata and ICE-CBF-COR bioinformatic analysis cascade provide valuable resources for studying the phylogenetic and evolution of Magnoliaceae and angiosperm, while the candidate genes will provide foundational support for molecular breeding in Magnolia species.

Key words: Chromosome duplications, Chromosome-scale genome assembly, comparative genomes, ICE-CBF-COR signaling pathways, Magnolia sinostellata, terpenoids biosynthesis