Supporting data for "The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP)"

<i>Magnolia sinica</i> (Magnoliaceae) is one of the most highly threatened trees endemic to Southeast Yunnan, China. In this study, we generated for the first time a high-quality chromosome-scale genome sequence from <i>M. sinica</i>, by combining Illumina and PacBio data with Hi-C mapping methods. The final assembled genome size of <i>M. sinica</i> was 1.84 Gb, with a contig N50 of ca. 45 Mb and scaffold N50 of 92 Mb. Identified repeats constituted approximately 57% of the genome, and 43,473 protein-coding genes were predicted with high support. Phylogenetic analysis showed that the magnolias form a sister clade with the eudicots and the order Ceratophyllales, while the monocots are sister to the other core angiosperms. A total of 21 individuals from the five remnant populations of <i>M. sinica</i>, as well as 22 specimens belonging to eight related Magnoliaceae species, were resequenced. The results showed that <i>M. sinica</i> had higher genetic diversity (w = 0.01126 and = 0.01158) than other related species in the Magnoliaceae. However, population structure analysis suggested that the genetic differentiation among the five <i>M. sinica</i> populations was very low. Analyses of the demographic history of the species using different models consistently revealed that two bottleneck events occurred. The contemporary effective population size of <i>M. sinica</i> was estimated to be 10.9. Additionally, different patterns of genetic loads(inbreeding and numbers of deleterious mutations) suggested constructive conservation strategies for these five different populations of <i>M. sinica</i>. Overall, this high-quality genome could be a valuable genomic resource for conservation of <i>M. sinica</i>.