Chromosome-level de novo genome unveils the evolution of Gleditsia sinensis and thorns development

Dandan Xiao; Jiahao Liu; Jing Wang; Xiaoqian Yang; Yuzhang Yang; Ruen Yu; Chun Wang; Hongbo Gao; Yanwei Wang; Yanping Liu; Dingchen Fan; Furong Lin

doi:10.1016/j.ygeno.2025.111004

Chromosome-level de novo genome unveils the evolution of Gleditsia sinensis and thorns development

Genomics. 2025 Jan 23:111004. doi: 10.1016/j.ygeno.2025.111004. Online ahead of print.

Authors

Dandan Xiao¹, Jiahao Liu¹, Jing Wang¹, Xiaoqian Yang¹, Yuzhang Yang¹, Ruen Yu¹, Chun Wang¹, Hongbo Gao¹, Yanwei Wang², Yanping Liu³, Dingchen Fan⁴, Furong Lin⁵

Affiliations

¹ State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
² State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China. Electronic address: ywwang@bjfu.edu.cn.
³ Henan Academy of Forestry, Henan, Zhengzhou 450008, China. Electronic address: liuyp@hnagri.org.cn.
⁴ Henan Academy of Forestry, Henan, Zhengzhou 450008, China. Electronic address: fandc@hnagri.org.cn.
⁵ State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, China. Electronic address: linfr@caf.ac.cn.

PMID: 39863186
DOI: 10.1016/j.ygeno.2025.111004

Abstract

Gleditsia sinensis Lam. (G. sinensis) as an important species within the Leguminosae family, has been utilized in Chinese medicine for centuries, and its thorns serve as a chief medicinal ingredient. The absence of a comprehensive genome database has hindered its in-depth research. In this investigation, a chromosome-level de novo genome assembly of G. sinensis 'Yulin No.1' was achieved, which harbors a 786.13 Mb sized genome with 36,408 protein-coding genes and experiences two WGD events. The comparative and evolutionary analysis unveiled the close phylogenetic relationship between G. sinensis and eight other Leguminosae species. The WGCNA and gene family analysis further indicated that GsinMYB was involved in the development of thorns. This investigation offered a high-level genome of G. sinensis, facilitating comparisons in Leguminosae species evolution and functional elucidation. It also provided key insights for further research on the molecular regulation mechanisms of thorn development in plants and the molecular breeding of G. sinensis.

Keywords: Evolution; G. sinensis; Genome; MYB gene family; Thorns.