The Orychophragmus violaceus genome

Orychophragmus violaceus, a plant of the genus Orychophragmus in Brassicaceae, gets its name 'Er-yue-lan' as its flowering starts in February of the lunar calendar. The seeds of O. violaceus have high oil content and rich unsaturated fatty acids. Meanwhile, O. violaceus can also be eaten as a leafy vegetable, 'Zhuge' in China. Therefore, O. violaceus has high ornamental value, edible value, and economic value (Fig. 1). With the development of genome sequencing technology and bioinformatics, it is possible to explore the genes involved in these traits at the genome level. Recently, two reports have obtained a high-quality O. violaceus genome at the chromosome level using second- and third-generation sequencing technology, and explored its evolution and genes related to important agronomic traits.

Figure 1. 

The photograph of Orychophragmus violaceus plant with blooming flowers. Credit: Veer Photo.

One report was originated from the Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, and relevant cooperative institutions (DOI: 10.1016/j.xplc.2022.100431). In the study, Nanopore and Hi-C sequencing were used to obtain a high-quality genome of O. violaceus containing 12 chromosomes, with a genome size of 1.34 Gb and Scaffold N50 of 100.34 Mb. A total of 55,389 protein-coding genes were detected, and 98% of 1,614 BUSCO genes were identified in the O. violaceus genome.

Studies have shown that the large-scale expansion of repetitive sequences is the reason why the O. violaceus genome is larger than other diploid genomes of Brassicaceae. It was found that O. violaceus experienced a specific genomic tetraploid event, and its karyotype is tPCK, which is the same as that of Brassica vegetable crops such as Chinese cabbage. The study reconstructed two sets of ancestral genomes of O. violaceus, named Ov1 and Ov2. It was found that the gene density of Ov1 was higher than that of Ov2, and more genes were a higher expression in Ov1 than Ov2. These results indicate that subgenome dominance exists in O. violaceus, and its ancient polyploidy belongs to the allotetraploid. The genome tetraploidy of O. violaceus occurred about 8.57 million years ago, which is similar to the ancient hexaploidy of common genomes of Brassica species. However, the ancient tetraploid event of O. violaceus is independent of the ancient hexaploid event of Brassica, which indicates that O. violaceus is not the tetraploid ancestor of Brassicaceae crops.

Through genomics and transcriptomics analysis of O. violaceus, it was found that DGAT1, FAD2, and FAD6, the key genes for oil biosynthesis, simultaneously expanded and retained more gene copies through ancient tetraploid and tandem repeat, and the copy number expansion of these genes played an important role in the formation of high yield oil of O. violaceus.

Another report came from the College of Plant Science and Technology, Huazhong Agricultural University, and relevant cooperative institutions (DOI: 10.1016/j.xplc.2022.100432). Pacbio and Hi-C sequencing techniques were used in the study to obtain a high-quality genome at the chromosome level of O. violaceus, with a size of 1.25 Gb. A total of 61,097 protein-coding genes were identified, and 97.8% of the BUSCO genes were identified in the genome of O. violaceus.

O. violaceus is a diploid undergoing an extra whole-genome duplication (WGD) after the Brassicaceae specific α-WGD event. Karyotype analysis showed that most chromosomes were broken and rearranged relative to tPCK karyotype of the ancestor species. According to karyotype comparison with the genome of Isatis indigotica, the evolutionary process of the O. violaceus genome is different from that of related species of Brassica.

Through transcriptomic analysis of O. violaceus seeds at different development stages, it was found that there were no new genes different from those in Brassica napus from the functional annotation of genes expressed at the peak of dihydroxy fatty acid synthesis, including FAD2, FAE1, and other genes known to participate in the synthesis of special fatty acids. Furthermore, OvDGAT genes (OvDGAT1-1, OvDGAT1-2) were identified as candidate genes related to the synthesis of dihydroxy fatty acids in O. violaceus. The study provides an important reference for the future industrial utilization of special fatty acids through genetic engineering transformation and the use of the O. violaceus gene as a genetic resource.

In summary, the two studies mentioned above have assembled a high-quality genome of O. violaceus, enriching our understanding of the evolutionary process of ancient polyploidy of Brassicaceae. It provides abundant data resources for comparative genomics and functional genomics research of O. violaceus and other Brassicaceae crops.