The Genome of Phoebe zhennan (Lauraceae) and Comparative Genomics of Phoebe

Abstract

Phoebe zhennan is a Chinese endemic and valuable timber species of Phoebe (Lauraceae). It is known for its fragrant, high-value wood and is the primary source of the renowned “golden-thread nanmu.” In this study, we present a chromosome-level genome assembly of P. zhennan, consisting of 12 chromosomes (979.28 Mb; scaffold N50: 87.69 Mb) with an estimated 26,262 protein-coding genes. Whole-genome duplication (WGD) analysis revealed that P. zhennan has undergone two WGD events: an older one shared by Magnoliales and Laurales, and a younger one shared by Lauraceae and Calycanthaceae species. Phylogenetic analysis showed that magnoliids (together with Chloranthales) form a sister clade to monocots. We identified 197 members of the MYB gene family and further selected 44 MYB genes that may be associated with phenylpropanoid lignin biosynthesis, including 28 genes acting as positive regulatory transcription factors and 16 as negative regulators. Gene expression analysis indicated that PzMYB6 is highly expressed in the cambium, suggesting it may play a critical regulatory role in the lignin biosynthesis pathway of P. zhennan. Overall, this chromosome-level reference genome provides new insights into the genome evolution of Phoebe and offers essential genetic resources for the rational utilization and conservation of this valuable timber species.

Keywords

chromosome-level genome / Lauraceae / lignin biosynthesis / MYB gene family / Phoebe zhennan

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2025 The Author(s). Integrative Conservation published by John Wiley & Sons Australia, Ltd on behalf of Xishuangbanna Tropical Botanical Garden (XTBG).