The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceaepolyploidizationandits distinct traits

Authors

Kang Zhang, Chinese Academy of Agricultural Sciences
Yinqing Yang, Chinese Academy of Agricultural Sciences
Xin Zhang, Chinese Academy of Agricultural Sciences
Lingkui Zhang, Chinese Academy of Agricultural Sciences
Yu Fu, Chinese Academy of Agricultural Sciences
Zhongwei Guo, Chinese Academy of Agricultural Sciences
Shumin Chen, Chinese Academy of Agricultural Sciences
Jian Wu, Chinese Academy of Agricultural Sciences
James C. Schnable, University of Nebraska-LincolnFollow
Keke Yi, Chinese Academy of Agricultural Sciences
Xiaowu Wang, Chinese Academy of Agricultural Sciences
Feng Cheng, Chinese Academy of Agricultural Sciences

Date of this Version

11-14-2022

Citation

Zhang et al., The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceae polyploidization and its distinct traits, Plant Communications (2022), https://doi.org/10.1016/j.xplc.2022.100431

Comments

Open access

Abstract

Orychophragmus violaceus, referred to as ‘‘eryuelan’’ (February orchid) in China, is an early-flowering ornamental plant. The high oil content and abundance of unsaturated fatty acids in O. violaceus seeds make it a potential high-quality oilseed crop. Here, we generated a whole-genome assembly for O. violaceus using Nanopore and Hi-C sequencing technologies. The assembled genome of O. violaceus was ~1.3 Gb in size, with 12 pairs of chromosomes. Through investigation of ancestral genome evolution, we determined that the genome of O. violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype. Comparisons between the reconstructed subgenomes of O. violaceus identified indicators of subgenome dominance, indicating that subgenomes likely originated via allotetraploidy. O. violaceus was phylogenetically close to the Brassica genus, and tetraploidy in O. violaceus occurred approximately 8.57 million years ago, close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid lineage. However, the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica, as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks. Moreover, identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O. violaceus. These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O. violaceus.