The genome assembly and annotation of Magnolia biondii Pamp., a phylogenetically, economically, and medicinally important ornamental tree species

Magnolia biondii Pamp. (Magnoliaceae, magnoliids) is a phylogenetically,
economically, and medicinally important ornamental tree species widely
grown and cultivated in the north-temperate regions of China. Contributing
a genome sequence for M. biondii will help resolve phylogenetic
uncertainty of magnoliids and further understand individual trait
evolution in Magnolia. We assembled a chromosome-level reference genome of
M. biondii using ~67, ~175, and ~154 Gb of raw DNA sequences generated by
Pacific Biosciences Single-molecule Real-time sequencing, 10X genomics
Chromium, and Hi-C scaffolding strategies, respectively. The final genome
assembly was ∼2.22 Gb with a contig N50 of 269.11 Kb and a BUSCO complete
gene ratio of 91.90%. About 89.17% of the genome length was organized to
19 chromosomes, resulting in a scaffold N50 of 92.86 Mb. The genome
contained 48,319 protein-coding genes, accounting for 22.97% of the genome
length, in contrast to 66.48% of the genome length for the repetitive
elements. We confirmed a Magnoliaceae specific WGD event that might have
probably occurred shortly after the split of Magnoliaceae and Annonaceae.
Functional enrichment of the Magnolia specific and expanded gene families
highlighted genes involved in biosynthesis of secondary metabolites,
plant-pathogen interaction, and response to stimulus, which may improve
ecological fitness and biological adaptability of the lineage.
Phylogenomic analyses recovered a sister relationship of magnoliids and
Chloranthaceae, which are sister to a clade comprising monocots and
eudicots. The genome sequence of M. biondii could empower trait
improvement, germplasm conservation, and evolutionary studies on rapid
radiation of early angiosperms.