The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids.

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. Determining the genome sequence of M. biondii would help resolve the phylogenetic uncertainty of magnoliids and improve the understanding of individual trait evolution within the Magnolia genus. We assembled a chromosome-level reference genome of M. biondii using ~67, ~175, and ~154 Gb of raw DNA sequences generated via 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 value of 269.11 kb and a BUSCO complete gene percentage of 91.90%. Approximately 89.17% of the genome was organized into 19 chromosomes, resulting in a scaffold N50 of 92.86 Mb. The genome contained 47,547 protein-coding genes, accounting for 23.47% of the genome length, whereas 66.48% of the genome length consisted of repetitive elements. We confirmed a WGD event that occurred very close to the time of the split between the Magnoliales and Laurales. Functional enrichment of the Magnolia-specific and expanded gene families highlighted genes involved in the biosynthesis of secondary metabolites, plant-pathogen interactions, and responses to stimuli, which may improve the ecological fitness and biological adaptability of the lineage. Phylogenomic analyses revealed a sister relationship of magnoliids and Chloranthaceae, which are sister to a clade comprising monocots and eudicots. The genome sequence of M. biondii could lead to trait improvement, germplasm conservation, and evolutionary studies on the rapid radiation of early angiosperms.

Development of EST-SSR markers and their application in an analysis of the genetic diversity of the endangered species Magnolia sinostellata.

Magnolia sinostellata is an endemic species of Magnoliaceae that is narrowly distributed in the south of Zhejiang Province, China. To explore the genetic diversity and population structure of this endangered species, this study developed sequence tag-simple sequence repeat (EST-SSR) markers based on transcriptome data of M. sinostellata. In total, 25472 SSRs were identified among 110644 unique assembled sequences with a total of 90.83 Mb and an average frequency of 23.02%. The mononucleotide (33.53%) and dinucleotide (42.08%) motifs appeared to be the most abundant. In total, 150 potential loci were randomly selected to validate the quality of the developed SSR markers; an effective PCR rate of 32.00% and a polymorphism rate of 15.33% were obtained for these loci. After performing sequencing and cloning for validation, 23 pairs of SSR primers were retained and used to characterize the genetic diversity and population structure of M. sinostellata. Overall, 204 alleles were amplified. The results of Shannon's information index (I), heterozygosity (Ho), heterozygosity (He) and Nei's expected heterozygosity (H) indicated rich genetic diversity in M. sinostellata. However, the high inbreeding coefficient and differential coefficient suggest that serious genetic drift occurred within populations, and genetic differentiation is apparent among the populations. Consequently, although M. sinostellata has high genetic diversity among populations, it is still in a serious and dangerous condition. Habitat destruction caused by human activities is the main threat to this species, and enhancing the species abundance by adopting some conservation measures should be favourable for saving the species.

The complete chloroplast genome of Magnolia sinostellata (Magnoliaceae), a rare and endangered species of China.

Magnolia sinostellata Chiu & Chen is a rare and endangered species endemic to subtropical China. Here we assembled and annotated the complete chloroplast (cp) genome of M. sinostellata. The chloroplast genome of M. sinostellata is 160,076 bp in length and encodes 79 protein-coding genes, 30 transfer RNA (tRNA) genes and four ribosomal RNA (rRNA) genes. The maximum-likelihood (ML) phylogenetic analysis result reveals that M. sinostellata is most closely related to M. biondii.