The high quality genome of potherb mustard Xuecai (Brassica juncea var. multiceps) provides new insights into leaf shape variation

The potherb mustard Xuecai (XC) cultivar is a cruciferous vegetable that is popular either fresh or pickled. Due to the deep notches in the edges of leaves in mustard XC, this plant can be said to have multipinnately lobed leaves. The net photosynthesis of lobed leaves is significantly greater than that of simple leaves. However, the molecular mechanism of leaf shape variation has not been determined. Here, we used HiFi and Hi-C data to assemble the XC genome. The genome was 961.72 Mb in size, with a contig N50 value of 6.565 Mb. The XC genome was compared with four previously sequenced mustard genomes, and the genomic collinearity regions, SNPs, and indels were identified. Five BjRCO genes were found on chromosome (Chr.) A10 in potherb mustard XC when the BjRCO gene locus was compared against other sequenced B. juncea genomes. Segmental duplication was found to contribute to the BjRCO gene copy number. The transcript expression of BjRCO genes was greater in multipinnately lobed leaves than in sawtooth-like leaves. Together, these findings indicate that both the greater copy number and the expression level of BjRCO genes regulate leaf shape from simple to complex in B. juncea. Gene editing of the BjRCO gene from XC changed the leaf shape from multipinnately lobed to simple. The high-quality XC genome sequence not only provides new insight into B. juncea leaf-type genomics but also helps in deciphering leaf shape variation. Our study provides insights into the variation and evolution of important traits in Brassica plants through a comparative analysis of the sequenced genomes.