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

Gleditsia Linn is widely distributed in the world and Gleditsia sinensis as an important Leguminosae specie, especially its thorns, has been used in the Chinese medicine as a chief ingredient for centuries. While the lack of genome database limits its in-depth research, especially genetic regulation and molecular developmental mechanism. In this investigation, a chromosome-level de novo genome of G. sinensis was assembled through PacBio HiFi, Illumina sequencing as well as those from Hi-C, genetic mapping and K-mer analysis. The G. sinensis harbors 786.13 Mb sized genome (contig N50=1.58 Mb, scaffold N50=51.53 Mb, 2n=28) with 36, 408 protein-coding genes. The full-length transcriptome sequencing of diverse tissues was performed to assist genome functional annotation. The comparative and evolutionary analysis unveiled that G. sinensis diverged from the Cretaceous period approximately 76.31 million years ago (Mya) and the close relationship between G. sinensis and other 8 Leguminosae species. The whole-genome duplication (WGD) analysis indicated G. sinensis underwent three WGD events and might go through another WGD event after differentiating from other Leguminosae plants. The Weighted Gene Coexpression Network Analysis based on phenotype and differentially expressed genes further demonstrated that GsinMYB should be involved in the development of thorns via regulating late thorn differentiation. This investigation provides a high level genome of Gleditsia for Leguminosae species evolution comparison and functional elucidation and also key insights for further study on the molecular regulation mechanisms of the thorns development as a special abnormal stem organ in plants and the molecular breeding of G. sinensis.