The carbon concentrating mechanism—C4 photosynthesis—represents a classic example of convergent evolution. While how this important trait originated and evolved remains largely enigmatic. The spider-flower Gynandropsis gynandra is a valuable leafy vegetable crop and medicinal plant that has also been recognized as a C4 model species. Here we present a high-quality chromosome-scale annotated genome assembly of G. gynandra through a combination of ONT, HiFi and Hi-C technology. The seventeen super scaffolds cover 98.66% of the estimated genome (997.61 Mb), with a contig N50 of 11.43 Mb and a scaffold N50 of 51.02 Mb. Repetitive elements occupy up to 71.91% of its genome, and over half are LTR-RTs derived from recent bursts, contributing to genome size expansion. Strikingly, LTR-RT explosion also played a critical role in C4 evolution by altering expression features of photosynthesis-associated genes via preferential insertion in promoters. Integrated multi-omics analyses of G. gynandra and the ornamental horticulture C3 relative Tarenaya hassleriana reveal that species-specific whole-genome duplication, gene family expansion, recent LTR-RT amplification and more recent tandem duplication events have all facilitated evolution of C4 photosynthesis, revealing uniqueness of C4 evolution in the Cleome genus. Moreover, high leaf vein density and heat stress resilience are associated with shifted gene expression patterns. The mode of C3-to-C4 transition found here yields new insights into evolutionary convergence of a complex plant trait. The availability of this reference-grade genomic resource makes G. gynandra an ideal model system facilitating efforts toward C4-aimed crop engineering.

The carbon concentrating mechanism-C4 photosynthesis-represents a classic example of convergent evolution. While how this important trait originated and evolved remains largely enigmatic. Here we present a high-quality chromosome-scale annotated genome assembly of the spider-flower Gynandropsis gynandra, a valuable leafy vegetable crop and medicinal plant that has also been recognized as an emerging C4 model species. Repetitive elements occupy up to 71.91% of its genome, and over half are LTR-RTs derived from recent bursts, contributing to genome size expansion. Strikingly, LTR-RT explosion also played a critical role in C4 evolution by altering expression features of photosynthesis-associated genes via preferential insertion in promoters. Synteny analysis in the Cleome genus unveils that an independent species-specific whole-genome duplication in G. gynandra, which we name Gg-α, occurred after divergence from its close relative C3 plant Tarenaya hassleriana. Integrated multi-omics profiling demonstrates that Gg-α, gene family expansion, recent LTR-RT amplification and more recent species-specific tandem duplication events have all facilitated the evolution of C4 photosynthesis, revealing uniqueness of C4 evolution in this lineage. Moreover, high leaf vein density and heat stress resilience are associated with shifted gene expression patterns. Altogether, this mode of C3-to-C4 transition yields new insights into evolutionary convergence of a complex plant trait.