Magnolia sinica (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
M. sinica, by combining Illumina and PacBio data with Hi-C mapping methods. The final assembled genome size of
M. sinica 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
M. sinica, as well as 22 specimens belonging to eight related Magnoliaceae species, were resequenced. The results showed that
M. sinica had higher genetic diversity (θw = 0.01126 and θπ = 0.01158) than other related species in the Magnoliaceae. However, population structure analysis suggested that the genetic differentiation among the five
M. sinica 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
M. sinica 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
M. sinica. Overall, this high-quality genome could be a valuable genomic resource for conservation of
M. sinica.
