High-quality genome of <i>Firmiana hainanensis</i> provides insights into the evolution of Malvaceae subfamilies and the mechanism of their wood density formation

Zeyu Dong; Shangkun Jin; Rui Fan; Pengcheng Sun; Lei Shao; Ting Zhao; Haojie Jiang; Zhiyuan Zhang; Haihong Shang; Xueying Guan; Yan Hu; Tianzhen Zhang; Fuyuan Zhu; Lei Fang

doi:10.1016/j.jgg.2024.12.009

Volume 52 Issue 6

Jun. 2025

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Article Navigation > Journal of Genetics and Genomics > 2025 > 52(6): 812-825

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High-quality genome of Firmiana hainanensis provides insights into the evolution of Malvaceae subfamilies and the mechanism of their wood density formation

doi: 10.1016/j.jgg.2024.12.009

a. Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Key Lab of Plant Factory for Plant Factory Generation-Adding Breeding of Ministry of Agriculture and Rural Affairs, The Advanced Seed Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China;
b. Hainan Institute of Zhejiang University, Sanya, Hainan 572025, China;
c. Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China;
d. Spices and Beverages Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan 571533, China;
e. College of Life Sciences, Nanjing Forestry University, Nanjing, Jiangsu 210037, China

Funds:

YSPTZX202139)

the Research Startup Funding from Hainan Institute of Zhejiang University (0202-6602-A12201) and the Distinguished Discipline Support Program of Zhejiang University (226-2024-00205, 226-2022-00100).

This research was supported by the National Key R&D Program of China (2022YFF1001400), postdoctoral innovative talents support program (517000-X92308), the specific research fund of The Innovation Platform for Academicians of Hainan Province (YSPTZX202154

Received Date: 2024-09-27
Accepted Date: 2024-12-10
Rev Recd Date: 2024-12-10

Available Online: 2025-07-11

Publish Date: 2024-12-19

Abstract

Abstract

The Malvaceae family, the most diverse family in the order Malvales, consists of nine subfamilies. Within the Firmiana genus of the Sterculioideae subfamily, most species are considered globally vulnerable, yet their genomes remain unexplored. Here, we present a chromosome-level genome assembly for a representative Firmiana species, F. hainanensis, 2n = 40, totaling 1536 Mb. Phylogenomic analysis shows that F. hainanensis and Durio zibethinus have the closest evolutionary relationship, with an estimated divergence time of approximately 21 millions of years ago (MYA) and distinct polyploidization events in their histories. Evolutionary trajectory analyses indicate that fissions and fusions may play a crucial role in chromosome number variation (2n = 14 to 2n = 96). Analysis of repetitive elements among Malvaceae reveals that the Tekay subfamily (belonging to the Gypsy group) contributes to variation in genome size (ranging from 324 Mb to 1620 Mb). Additionally, genes associated with P450, peroxidase, and microtubules, and thereby related to cell wall biosynthesis, are significantly contracted in F. hainanensis, potentially leading to its lower wood density relative to Hopea hainanensis. Overall, our study provides insights into the evolution of chromosome number, genome size, and the genetic basis of cell wall biosynthesis in Malvaceae species.
- Malvaceae species,
- Genome evolution,
- Ancestral karyotype,
- Transposable elements,
- Cell wall biosynthesis

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