A chromosome-level genome assembly of Callerya speciosa sheds new light on the biosynthesis of root-specific isoflavonoids

The edible tuberous roots of the legume Callerya speciosa (Champ. Ex Benth.) Schot are medicinally important and are a rich source of isoflavonoids. The accumulation of isoflavonoids in the roots is critically important for enhancing the quality of C. speciosa. There is thus a need to develop approaches to manipulate isoflavonoid biosynthesis and breed cultivars that better accommodate the needs of consumers. One of the major impediments to achieving these goals is a lack of available genetic information for C. speciosa. In this study, we present a chromosome-level genome assembly for C. speciosa (total size of 668.5 Mb) using Nanopore single-molecule sequencing and Hi-C technology; a total of 41,467 protein-coding genes were annotated in this genome assembly. The assembled genome comprised 303 contigs and 34 scaffolds, and the contig and scaffold N50 values were 4.18 and 87.4 Mb, respectively. The scaffolds were clustered into eight pseudochromosomes. Metabolites involved in flavonoid biosynthesis in five different tissues were identified via metabolic data. Furthermore, we developed a regulatory network for root-specific isoflavonoid biosynthesis in C. speciosa using gene-to-metabolite correlation analysis and weighted gene co-expression network analysis. A total of nine CsMYBs in the regulatory network were identified as key candidate transcription factors (TFs) that likely play important roles in regulating the content of isoflavonoids in the roots of C. speciosa. Yeast one-hybrid assays revealed interactions between structural genes involved in isoflavonoid biosynthesis and candidate MYB TFs. The reference genome and large-scale transcriptomic and metabolic data presented in our study provide valuable resources that will aid future efforts to enhance the quality of C. speciosa, as well as other agricultural traits.