High quality genome of potherb mustard XC (Brassica juncea var. multiceps) provides new insight into leaf shape variation1

The potherb mustard ‘Xuecai’ (XC) cultivar is a cruciferous vegetable that is popular as a fresh and a pickled vegetable. On the basis of 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 has been found to be 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 genomic collinearity regions, SNPs, and indels were identified. Quintuple 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 copy number increase and the high expression 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 insight into the variation and evolution of important traits through comparative analysis of the sequenced genome.