The origin and evolution of the diosgenin biosynthetic pathway in yam

Abstract

Diosgenin, mainly produced by Dioscorea species, is a traditional precursor of most hormonal drugs in the pharmaceutical industry. The mechanisms that underlie the origin and evolution of diosgenin biosynthesis in plants remain unclear. After sequencing the whole genome of Dioscorea zingiberensis , we revealed the evolutionary trajectory of the diosgenin biosynthetic pathway in Dioscorea and demonstrated the de novo biosynthesis of diosgenin in a yeast cell factory. First, we found that P450 gene duplication and neo-functionalization, driven by positive selection, played important roles in the origin of the diosgenin biosynthetic pathway. Subsequently, we found that the enrichment of diosgenin in the yam lineage was regulated by CpG islands, which evolved to regulate gene expression in the diosgenin pathway and balance the carbon flux between the biosynthesis of diosgenin and starch. Finally, by integrating genes from plants, animals, and yeast, we heterologously synthesized diosgenin to 10 mg/l in genetically-engineered yeast. Our study not only reveals the origin and evolutionary mechanisms of the diosgenin biosynthetic pathway in Dioscorea , but also introduces an alternative approach for the production of diosgenin through synthetic biology.

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

“…Notably, the distantly related D. zingiberensis has a haploid complement of n=10, compared with n=20 found in D. alata, D. rotundata , and D. dumetorum . We find that the D. zingiberensis chromosomes 22 were formed from ancestral, D. alata -like chromosomes and/or chromosome arms by combinations of end-to-end and centric fusions and translocations ( Fig. 2a, Supplementary Fig.…”

“…While comparisons with the draft genome assembly of T. zeylanicus (Ks = 0.804 to D. alata ) further suggest that the delta paleotetraploidy may have preceded the origin of the family Dioscoreaceae, the fragmentation of the T. zeylanicus assembly precludes a definitive assessment. The timing of the delta duplication (estimated to be 64 Mya 22 ) is contemporaneous with the K/T boundary and a cluster of successful paleopolyploidies 36 .…”

“…Here we describe a chromosome-scale reference genome for D. alata and a dense 10k marker consensus genetic linkage map from five populations involving seven distinct parental genotypes. Comparison of the D. alata reference genome with the recently sequenced genomes of the distantly related D. rotundata 21 and D. zingiberensis 22 reveals substantial conservation of chromosome structure between D. alata and D. rotundata but considerable rearrangement relative to more deeply divergent D. zingiberensis lineage. Analysis of the D. alata genome supports the existence of ancient polyploidy events shared across Dioscoreales, and reveals chromosome rearrangements after the most recent pan-Dioscoreales genome duplication.…”

PCPD: Plant cytochrome P450 database and web-based tools for structural construction and ligand docking

“…However, a small proportion of the plant P450s have been functionally characterized, due to the high cost required for screening a P450 enzyme with a specific catalytic function. Some studies have exploited the potentials of comparative genomic or transcriptomic analysis to reduce the screening scope [ [7] , [8] , [9] ]. However, to our knowledge, no universal method can obviously assist the mining and functional analysis of plant P450 enzymes.…”

Uncovering the genetic diversity of yams (Dioscorea spp.) in China by combining phenotypic trait and molecular marker analyses

“…Moreover,Dioscorea is mainly dioecious, rarely flowering, and has difficult forming mature seeds (Bressan et al , 2011). The development of medicinal ingredients from a few species of yam has long been emphasized in China (Li et al, 2018;Lebot et al, 2018;Cheng et al, 2020), but the analysis of the resource types and genetic diversity of yam is insufficient. Moreover, several studies only focused on D. alata , and the method of resource evaluation is relatively simple (Siqueira et al, 2014;Arnau et al, 2017;Wu et al, 2019).…”