Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 10008, China.
Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588, USA.
Plant Commun. 2023 Mar 13;4(2):100431. doi: 10.1016/j.xplc.2022.100431. Epub 2022 Sep 7.
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.
菘蓝，在中国被称为“二月兰”，是一种早春开花的观赏植物。菘蓝种子的高油含量和丰富的不饱和脂肪酸使其成为一种具有潜力的优质油料作物。在这里，我们使用纳米孔和 Hi-C 测序技术为菘蓝生成了一个全基因组组装。菘蓝的组装基因组大小约为 13 亿碱基，有 12 对染色体。通过对祖先基因组进化的研究，我们确定菘蓝的基因组经历了一次从二倍体祖先进化而来的四倍化事件，其染色体组型为转移的原 Calepineae 型。菘蓝重建亚基因组之间的比较确定了亚基因组优势的指标，表明亚基因组可能是通过异源四倍化产生的。菘蓝在系统发育上与芸薹属密切相关，菘蓝的四倍化大约发生在 857 万年前，与芸薹属的全基因组三倍化时间相近，这可能是通过一个中间的四倍化谱系产生的。然而，菘蓝的四倍化与芸薹属的六倍化是独立的，这从详细的系统发育分析和祖先基因组块的断裂和融合点的比较结果中可以看出。此外，鉴定出调控高品质油产生的多拷贝基因，突出了四倍化和串联重复在菘蓝功能创新中的作用。这些发现为植物物种的多倍体进化提供了新的见解，并将促进菘蓝的功能基因组研究和驯化/育种工作。
