Chromosome-level genome assembly of Manglietia pachyphylla

Chuqiao Tang; Jiamei Yang; Shuai Yuan; Yuling Li

doi:10.1038/s41597-026-07475-x

Chromosome-level genome assembly of Manglietia pachyphylla

Sci Data. 2026 May 27. doi: 10.1038/s41597-026-07475-x. Online ahead of print.

Authors

Chuqiao Tang^{1

2}, Jiamei Yang¹, Shuai Yuan³, Yuling Li⁴

Affiliations

¹ College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
² State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
³ State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China. shuaiyuan@scbg.ac.cn.
⁴ College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China. ylli@scau.edu.cn.

PMID: 42204154
DOI: 10.1038/s41597-026-07475-x

Abstract

Manglietia pachyphylla, an endangered evergreen tree within the Magnoliaceae family, is renowned for its exceptional ornamental value in landscape horticulture. Despite its classification as a Category II nationally protected plant species in China, the genetic basis of its adaptive traits and conservation priorities remains poorly understood. To address this, we present the first chromosome-scale genome assembly of M. pachyphylla utilizing an integrated approach combining PacBio HiFi long-read and Hi-C chromosome conformation capture sequencing technologies. The assembled genome spans 2.15 Gb (contig N50 = 43.57 Mb), exhibiting a heterozygosity rate of 0.78% and repeat content of 78.64%, predominantly comprising long terminal repeat (LTR) retrotransposons (52.86%). Hi-C scaffolding anchored 99.57% of the assembly to 19 pseudochromosomes, achieving a BUSCO completeness score of 96.4%. Annotation revealed 42,505 putative protein-coding genes, with 84.46% of predicted genes were functionally annotated. Phylogenomic analysis positioned M. pachyphylla and Oyama sieboldii clustered together in a well-supported group. This high-contiguity genome assembly enables future investigations into adaptive evolution, functional genomics, and evidence-based conservation strategies for this endangered species.