Genomics and Applied Biology 2024, Vol.15, No.2, 75-88 http://bioscipublisher.com/index.php/gab 75 Systematic Review Open Access Comparative Genomics: Insights into the Evolutionary History of Eucommia ulmoides XinXie 1,3, Atul Kumar Srivastava 3, Mehran Khan3, Yichen Zhao2 , Degang Zhao1,2 1 Plant Conservation and Breeding Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology, Biotechnology Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China 2 The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Tea Sciences， Guizhou University, Guiyang, 550025, China 3 College of Agriculture, Guizhou University, Guiyang, 550025, China Co-corresponding authors: yczhao@gzu.edu.cn; dgzhao@gzu.edu.cn Genomics and Applied Biology, 2024, Vol.15, No.2 doi: 10.5376/gab.2024.15.0010 Received: 05 Feb., 2024 Accepted: 08 Mar., 2024 Published: 19 Mar., 2024 Copyright © 2024 Xie et al., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Xie X., Srivastava A.K., Khan M., Zhao Y.C., and Zhao D.G., 2024, Comparative genomics: insights into the evolutionary history of Eucommia ulmoides, Genomics and Applied Biology, 15(2): 75-88 (doi: 10.5376/gab.2024.15.0010) Abstract Eucommia ulmoides, commonly known as the hardy rubber tree, is a unique and economically significant tree species with applications in rubber production as well as traditional medicine. This review delves into the evolutionary history of E. ulmoides through comparative genomics, highlighting key findings from recent genomic studies. High-quality genome assemblies have revealed significant insights into the genetic architecture and evolutionary mechanisms of this tree. Notably, the genome of E. ulmoides has undergone a whole-genome duplication event, contributing to its complex genomic structure and the expansion of gene families involved in rubber biosynthesis and stress responses. Comparative analyses of chloroplast genomes have identified heterogeneous sequence divergence and mutation hotspots, providing valuable information for conservation genetics. Transcriptome studies have uncovered sex-biased gene expression and potential sex-determination genes, shedding light on the genetic basis of sexual dimorphism in this dioecious species. Additionally, high-density genetic maps and QTL analysis have facilitated the identification of growth-related traits, paving the way for genetic improvement and breeding programs. This review presents a comprehensive understanding of the evolutionary history and genomic innovations of E. ulmoides, offering new perspectives for its conservation and utilization. Keywords Eucommia ulmoides; Comparative genomics; Whole-genome duplication; Rubber biosynthesis; Chloroplast genome; Sex-biased gene expression; QTL analysis 1 Introduction Eucommia ulmoides, commonly known as the Hardy Rubber Tree, is a unique and economically significant tree endemic to China. It belongs to the monotypic family Eucommiaceae and is renowned for its medicinal and industrial applications. The tree is a source of gutta-percha, a natural rubber, and various secondary metabolites with pharmacological properties, such as aucubin and chlorogenic acid (Li et al., 2020; Liu et al., 2021b). This species has garnered attention not only for its economic value but also for its ecological importance, including applications in landscaping, wind sheltering, and sand fixation (Jin et al., 2020). The genetic and genomic studies of E. ulmoides have revealed its complex evolutionary history. It has undergone multiple whole-genome duplication events, including a recent duplication approximately 27.3 million years ago and an earlier γ paleohexaploidization event (Li et al., 2020; Du et al., 2023). These events have significantly contributed to the expansion of its genome and the diversification of its genetic traits. The high-quality chromosome-level genome assemblies for both male and female E. ulmoides have provided valuable resources for understanding the genetic basis of its unique traits, such as sex differentiation and α-linolenic acid biosynthesis (Du et al., 2023). The primary objective of this study is to conduct a comprehensive comparative genomics analysis of E. ulmoides to gain deeper insights into its evolutionary history and genetic diversity. By leveraging high-quality genome assemblies and advanced genomic technologies, this study aims to elucidate the evolutionary events by
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