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

Shanshan Dong,Huan Liu,Ernest Wu,Lu Chen,Min Liu,Yamei Shen,Xun Gong,Zhen Yao ,Xiaoan Lang,Ting Yang,Xingtan Zhang,Tian Deng,Xing Guo,Yiqing Gong,Fei Chen,Linzhou Li,Dongming Fang,Yaling Wang,Yang Liu,Shouzhou Zhang

doi:10.1038/s41438-021-00471-9

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. 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.

Highlights

Introduction The family MagnoliaceaeJuss., with more than300 species[1] worldwide, comprises two genera, Liriodendron L., which includes only two species, and Magnolia L., which includes the others[2]
Magnoliids are resolved as sister to eudicots and monocots, with weak support[8,9,10,12], which is in agreement with the large-scale plastome phylogenomic analysis of land plants, Viridiplantae, and angiosperms[15,16,17]
The raw scaffold assembly was further improved with PacBio long reads and 10X Genomics short reads, resulting in an assembled genome size of 2.23 Gb represented by 9510 scaffolds, with a scaffold N50 of 92.86 Mb (Table 1)

Summary

Introduction

Introduction The family MagnoliaceaeJuss., with more than300 species[1] worldwide, comprises two genera, Liriodendron L., which includes only two species, and Magnolia L., which includes the others[2]. Phylogenomic analyses based on these genomic data have led to controversial taxonomic placements of magnoliids. Magnoliids are resolved as sister to eudicots, with relatively strong support[11], which is consistent with the results of a phylotranscriptomic analysis of 92 streptophytes[13] and 20 representative angiosperms[14]. Magnoliids are resolved as sister to eudicots and monocots, with weak support[8,9,10,12], which is in agreement with the large-scale plastome phylogenomic analysis of land plants, Viridiplantae, and angiosperms[15,16,17]. As phylogenetic inferences rely heavily on the sampling of lineages and genes, as well as analytical methods[5], these controversial taxonomic placements of magnoliids relative to monocots and eudicots need to be further examined with more genomic data from magnoliids

Methods

Results

Discussion

Conclusion