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Article|01 Mar 2021|OPEN
The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids
Min Liu1, Shanshan Dong2,1, Yang Liu1,2, Fei Chen3, Ting Yang2, Lu Chen1, Xingtan Zhang4, Xing Guo2, Dongming Fang2, Linzhou Li2, Tian Deng1, Zhangxiu Yao1, Xiaoan Lang1, Yiqing Gong1, Ernest Wu5, Yaling Wang6, Yamei Shen7, Xun Gong8, Huan Liu9,2, & Shouzhou Zhang1,
1State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
2Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, China
3Nanjing Forestry University, Nanjing 210037, China
4Fujian Agriculture and Forestry University, Fuzhou 350000, China
5University of British Columbia, Vancouver BC, Canada
6Xi’an Botanical Garden, Xi’an 710061, China
7Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
8Kunming Botanical Garden, Chinese Academy of Sciences, Kunming 650201, China
9Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark

Horticulture Research 8,
Article number: 38 (2021)
doi: 10.1038/hortres.2021.38
Views: 293

Received: 11 Jan 2020
Revised: 28 Oct 2020
Accepted: 12 Dec 2020
Published online: 01 Mar 2021

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.