The Phoebe genome sheds light on the evolution of magnoliids

Abstract

Lauraceae includes the genus <i>Phoebe</i>, and the family is linked to the evolution of magnoliids. We sequenced the genome of <i>Phoebe bournei</i> 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 <i>P. bournei</i>. 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 <i>AGL12</i>-like genes that may be related to the regulation of <i>P. bournei</i> roots and <i>FIN219</i>-like genes encoding GH3 proteins, which are involved in photomorphogenesis. <i>SAUR50</i>-like genes involved in light signal-mediated pedicel or stem development were also identified. Four <i>ATMYB46-</i> and three <i>PtrEPSP</i>-homologous genes related to lignin biosynthesis were identified. These genes may be associated with the formation of straight trunks in <i>P. bournei</i>. Overall, the <i>P. bournei</i> reference genome provides insight into the origin, evolution, and diversification of <i>Phoebe</i> and other magnoliids.