High-quality genomes of Bombax ceiba and Ceiba pentandra provide insights into evolution of Malvaceae species and differentiation of natural fiber

The Malvaceae family of plants is an important source of natural fiber, containing Corchorus spp., Gossypium spp., Bombax spp., Ceiba spp., etc. In the past decade, genomes of several Malvaceae species have been assembled; however, the evolution of Malvaceae species and the differentiation of their fiber development are still unclear. Here, we report the assembly and annotation of two natural fiber plants of Malvaceae, Bombax ceiba and Ceiba pentandra, whose genome sizes are 783.56 Mb and 1,575.47 Mb, respectively. Comparative analysis revealed that whole genome duplication and Gypsy long terminal repeat retroelements were the major causes of differences in chromosome number (2n = 14 to 2n = 96) and genome size (234 Mb to 2,676 Mb) within Malvaceae species, and reported an ancestral karyotype with 11 proto-chromosomes for Malvaceae, providing new insights into the evolutionary trajectories. MYB-MIXTA-like 3 was relatively conserved in Malvaceae species with a function in fiber cell-fate determination on epidermis. Its function can be fulfilled wherever the tissue MYB-MIXTA-like 3 expressed, i.e. fiber on the endocarp of B. ceiba and the ovule fiber of cotton. We identified prematurely terminating structural variation of cellulose synthase genes and a higher copy number of cellulose synthase-like genes as the possible cause for the finer and less spinnable fiber with lower strength in B. ceiba than in cotton. In sum, our study provides two high-quality genomes of natural fiber plants and insights toward understanding the evolution of Malvaceae species and the differentiation of natural fiber formation and development through multi-omics analysis.