The chromosome-scale genome of <i>Magnolia sieboldii</i> K. Koch provides insight into the evolutionary position of magnoliids and seed germination

<i>Magnolia sieboldii</i> K. Koch (<i>M. sieboldii</i>) stands as an elegant tree species within the Magnoliaceae family, esteemed for its exquisite beauty, cultural significance, and economic advantages. The species faces challenges in seed germination under natural conditions, primarily attributed to morphological dormancy. Despite its significance, the molecular mechanisms governing <i>M. sieboldii</i> seed germination remain elusive, compounded by the absence of genomic resources specific to this species. In this study, we present the first chromosome-scale genome assembly of <i>M. sieboldii</i>, with a total genome size of 2.01 Gb including 1,096 scaffolds assigned on 19 chromosomes (N50 = 102.4 Mb). Phylogenetic analyses, incorporating 13 plant species, illuminate the evolutionary independence of Magnoliids from monocots and eudicots, positioning them as a sister clade. Through RNA-seq analysis, we identify pivotal genes and pathways contributing to seed dormancy and germination. In addition, our investigation delves into the FAR1 (the far-red-impaired response) transcription factor gene family, revealing their enrichment throughout evolution and their involvement in the intricate process of seed germination. This comprehensive genome sequencing initiative offers invaluable insights into the biological attributes of <i>M. sieboldii</i>, with a specific emphasis on unraveling the complexities of seed dormancy and germination.