High-quality genomes of Bombax ceiba and Ceiba pentandra provide insights into the evolution of Malvaceae species and differences in their natural fiber development

Lei Shao; Shangkun Jin; Jinwen Chen; Guangsui Yang; Rui Fan; Zhiyuan Zhang; Qian Deng; Jin Han; Xiaowei Ma; Zeyu Dong; Hejun Lu; Wanying Hu; Kai Wang; Lisong Hu; Zhen Shen; Surong Huang; Ting Zhao; Xueying Guan; Yan Hu; Tianzhen Zhang; Lei Fang

doi:10.1016/j.xplc.2024.100832

High-quality genomes of Bombax ceiba and Ceiba pentandra provide insights into the evolution of Malvaceae species and differences in their natural fiber development

Plant Commun. 2024 Feb 5:100832. doi: 10.1016/j.xplc.2024.100832. Online ahead of print.

Authors

Lei Shao¹, Shangkun Jin², Jinwen Chen², Guangsui Yang³, Rui Fan⁴, Zhiyuan Zhang⁵, Qian Deng², Jin Han², Xiaowei Ma², Zeyu Dong², Hejun Lu², Wanying Hu², Kai Wang⁶, Lisong Hu⁴, Zhen Shen³, Surong Huang³, Ting Zhao¹, Xueying Guan¹, Yan Hu¹, Tianzhen Zhang¹, Lei Fang⁷

Affiliations

¹ Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China.
² Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
³ Tropical Crop Germplasm Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
⁴ Spices and Beverages Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, China.
⁵ Hainan Institute of Zhejiang University, Sanya 572025, China.
⁶ School of Life Sciences, Nantong University, Nantong 226019, China.
⁷ Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Sanya 572025, China. Electronic address: fangl@zju.edu.cn.

PMID: 38321741
DOI: 10.1016/j.xplc.2024.100832

Abstract

Members of the Malvaceae family, including Corchorus spp., Gossypium spp., Bombax spp., and Ceiba spp., are important sources of natural fibers. In the past decade, the genomes of several Malvaceae species have been assembled; however, the evolutionary history of Malvaceae species and the differences in their fiber development remain to be clarified. Here, we report the genome assembly and annotation of two natural fiber plants from the Malvaceae, Bombax ceiba and Ceiba pentandra, whose assembled genome sizes are 783.56 Mb and 1575.47 Mb, respectively. Comparative analysis revealed that whole-genome duplication and Gypsy long terminal repeat retroelements have been the major causes of differences in chromosome number (2n = 14 to 2n = 96) and genome size (234 Mb to 2676 Mb) among Malvaceae species. We also used comparative genomic analyses to reconstruct the ancestral Malvaceae karyotype with 11 proto-chromosomes, providing new insights into the evolutionary trajectories of Malvaceae species. MYB-MIXTA-like 3 is relatively conserved among the Malvaceae and functions in fiber cell-fate determination in the epidermis. It appears to perform this function in any tissue where it is expressed, i.e. in fibers on the endocarp of B. ceiba and in ovule fibers of cotton. We identified a structural variation in a cellulose synthase gene and a higher copy number of cellulose synthase-like genes as possible causes of the finer, less spinnable, weaker fibers of B. ceiba. Our study provides two high-quality genomes of natural fiber plants and offers insights into the evolution of Malvaceae species and differences in their natural fiber formation and development through multi-omics analysis.

Keywords: Malvaceae species; ancestral karyotype; fiber differentiation; genome evolution.