Chromosome‐Level Reference Genome Assembly Provides Insights Into C21 Steroid Saponins Biosynthesis in Cynanchum atratum

Cynanchum atratum, a perennial medicinal plant belonging to the genus Cynanchum in the Apocynaceae family, is rich in C21 steroidal saponins. This study presented a chromosome-level genome assembly of C. atratum using PacBio long-read sequencing technology. The assembly resulted in a 361.85 Mb genome with a contig N50 of 5.13 Mb, of which 86.55% was scaffolded into 11 pseudochromosomes. Among the 18 871 predicted protein-coding genes, 98.3% have been functionally annotated. Comparative genomic analyses reveal the evolutionary dynamics of C. atratum and a notable contrast between contracted and expanded gene families. Transcriptome sequencing was performed using root, stem, and leaf samples collected in August from 1- and 2-year-old plants. LC-MS quantification across 4 months revealed that leaves were the main accumulation tissue of cynatratoside-C (CyC), and the highest content was detected in leaves of 2-year-old plants in October. cynatratoside-C correlation of metabolite content with gene expression patterns led to the identification of 11 CYP and 16 UGT genes potentially involved in the biosynthesis of CyC, and as well as a putative biosynthetic gene cluster on chromosome 3. Based on the genome and transcriptome, a putative biosynthetic pathway for CyC was further proposed.