The Phoebe genome sheds light on the evolution of magnoliids

Shi-Pin Chen; Wei-Hong Sun; Yuan-Fang Xiong; Yu-Ting Jiang; Xue-Die Liu; Xing-Yu Liao; Di-Yang Zhang; Shu-Zhen Jiang; Yu Li; Bin Liu; Liang Ma; Xia Yu; Li He; Bao Liu; Jin-Lin Feng; Li-Zhen Feng; Zhi-Wen Wang; Shuang-Quan Zou; Si-Ren Lan; Zhong-Jian Liu

doi:10.1038/s41438-020-00368-z

The Phoebe genome sheds light on the evolution of magnoliids

Hortic Res. 2020 Sep 1:7:146. doi: 10.1038/s41438-020-00368-z. eCollection 2020.

Authors

Shi-Pin Chen^{1

2}, Wei-Hong Sun^{1

2}, Yuan-Fang Xiong^{1

2}, Yu-Ting Jiang^{1

2}, Xue-Die Liu^{1

2}, Xing-Yu Liao^{1

2}, Di-Yang Zhang^{1

2}, Shu-Zhen Jiang^{1

2}, Yu Li^{1

2}, Bin Liu^{1

2}, Liang Ma², Xia Yu², Li He², Bao Liu², Jin-Lin Feng², Li-Zhen Feng², Zhi-Wen Wang³, Shuang-Quan Zou^{1

2}, Si-Ren Lan^{1

2}, Zhong-Jian Liu^{2

4

5}

Affiliations

¹ College of Forestry, Fujian Agriculture and Forestry University, 350002 Fuzhou, China.
² Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at the College of Landscape Architecture, Fujian Agriculture and Forestry University, 350002 Fuzhou, China.
³ PubBio-Tech, 430070 Wuhan, China.
⁴ Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, 325005 Wenzhou, China.
⁵ Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, 250100 Jinan, China.

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.

Keywords: Genome; Genome evolution.