The genome assembly and annotation ofMagnolia biondiiPamp., a phylogenetically, economically, and medicinally important ornamental tree species

Abstract

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.

Conserved and non-conserved triggers of 24-nt reproductive phasiRNAs in eudicots

“…We previously characterized the presence of miR2275 loci in 209 genomes of flowering plants spanning different clades of eudicots and monocots (Xia et al, 2019); however, that analysis excluded the magnoliids as there were no sequenced genomes at that time. Therefore, we investigated a recently published sequence genome of a magnoliid species, Magnolia biondii , (Dong et al, 2020). We found nine unique mature miR2275 sequences derived from 11 precursors (Supplemental Figure 6A), three of which appear to be polycistronic precursors, an example locus is shown in Supplemental Figure 6B (see also Supplemental Table 5).…”