A chromosome-level genome assembly of Styphnolobium japonicum combined with comparative genomic analyses offers insights on the evolution of flavonoid and lignin biosynthesis

Styphnolobium japonicum is an important industrial crop that is widely used as a source of flavonoids. In this study, the first chromosome-scale reference genome of S. japonicum was provided by combining Illumina and nanopore sequencing and high-throughput chromatin conformation capture technology. The genome of S. japonicum is 520 Mb and has an N50 contig that is 4.77 Mb. The contig could be clustered into 14 pseudochromosomes. A total of 32,551 genes that encode proteins were annotated in the genome. Comparative and phylogenetic analyses of the genome revealed the phylogenetic placement of this plant, which indicates that S. japonicum experienced two whole-genome duplication (WGD) events. The genes retained after the WGD were shared by members of the papilionoideae. A comparative genomic analysis revealed that the expansion and contraction of the flavonoid pathway gene families was the reason that the production of flavonoids was enhanced. This reference genome enabled the prediction of 17 genes that are involved in the flavonoid and lignin biosynthetic gene families. Collectively, S. japonicum could have undergone adaptive evolution to promote its growth by enhancing the production of flavonoids and altering the composition of lignin.