The Phoebe genome sheds light on the evolution of magnoliids

Shi-Pin Chen,Yu Li,Xing-Yu Liao,Liang Ma,Yuan-Fang Xiong,Li He,Bin Liu,Bao Liu,Shuangquan Zou ,Xuedie Liu ,Li Feng ,Yuting Jiang ,Jinlin Feng ,Weihong Sun ,Zhiwen Wang ,Diyang Zhang ,Shuzhen Jiang ,Siren Lan ,Xia Yu,Zhong‐Jian Liu

doi:10.1038/s41438-020-00368-z

Abstract

Lauraceae includes the genus Phoebe, and the family is linked to the evolution of magnoliids. We sequenced the genome of Phoebe bournei Nanmu. The assembled genome size was 989.19 Mb, with a contig N50 value of 2.05 Mb. A total of 28,198 protein-coding genes were annotated in P. bournei. Whole-genome duplication (WGD) analysis showed that Lauraceae has experienced two WGD events; the older WGD event occurred just before the divergence of Lauraceae and Magnoliales, and the more recent WGD was shared by all lineages of Lauraceae. The phylogenetic tree showed that magnoliids form a sister clade to monocots and eudicots. We also identified 63 MADS-box genes, including AGL12-like genes that may be related to the regulation of P. bournei roots and FIN219-like genes encoding GH3 proteins, which are involved in photomorphogenesis. SAUR50-like genes involved in light signal-mediated pedicel or stem development were also identified. Four ATMYB46- and three PtrEPSP-homologous genes related to lignin biosynthesis were identified. These genes may be associated with the formation of straight trunks in P. bournei. Overall, the P. bournei reference genome provides insight into the origin, evolution, and diversification of Phoebe and other magnoliids.

Highlights

Introduction Lauraceae belongs toLaurales, which together withCanellales, Piperales, and Magnoliales, constitute the magnoliids, including 9000 species[1,2,3]
Benchmarking Universal Single-Copy Orthologs (BUSCO)[18] assessment showed that the completeness of the gene set of the assembled genome was 95% (Supplementary Table 3), and the Illumina read alignment rate was 98.87% (Supplementary Table 4), indicating that the P. bournei genome assembly was of high quality and could be used for subsequent analysis
Whole-genome duplication (WGD) analysis suggested that Piperales and Magnoliales have both experienced one WGD event, and that Lauraceae has experienced two WGD events, where the older WGD event is shared with Magnoliales and the younger with other Lauraceae species

Summary

Introduction

Introduction Lauraceae belongs toLaurales, which together withCanellales, Piperales, and Magnoliales, constitute the magnoliids, including 9000 species[1,2,3]. The relationships among the magnoliids, eudicots, and monocots remain unclear, even after the publication of four magnoliid genomes[4,5,6,7,8]. The genomes of Piper nigrum, Persea americana, and Liriodendron chinense support the magnoliids as a sister clade of monocots and eudicots[4,5,6], while the genome of stout camphor Cinnamomum kanehirae supports magnoliids as a sister clade of eudicots[7]. The conflicts in terms of phylogenetic tree location indicate that additional genomic data are needed to more Lauraceae. Lauraceae is an important economic and ecological family including 2850 species of herbs, shrubs, and trees, mainly distributed in tropical and subtropical regions of Asia and South America[9].

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Results

Conclusion