The genome of Eleocharis vivipara elucidates the genetics of C_(3)–C_(4)photosynthetic plasticity and karyotype evolution in the Cyperaceae

Eleocharis vivipara,an amphibious sedge in the Cyperaceae family,has several remarkable properties,most notably its alternate use of C_(3)photosynthesis underwater and C_(4)photosynthesis on land.However,the absence of genomic data has hindered its utility for evolutionary and genetic research.Here,we present a high-quality genome for E.vivipara,representing the first chromosome-level genome for the Eleocharis genus,with an approximate size of 965.22 Mb mainly distributed across 10 chromosomes.Its Hi–C pattern,chromosome clustering results,and one-to-one genome synteny across two subgroups indicates a tetraploid structure with chromosome count 2n=4x=20.Phylogenetic analysis suggests that E.vivipara diverged from Cyperus esculentus approximately 32.96million years ago(Mya),and underwent a wholegenome duplication(WGD)about 3.5 Mya.Numerous fusion and fission events were identified between the chromosomes of E.vivipara and its close relatives.We demonstrate that E.vivipara has holocentromeres,a chromosomal feature which can maintain the stability of such chromosomal rearrangements.Experimental transplantation and cross-section studies showed its terrestrial culms developed C_(4)Kranz anatomy with increased number of chloroplasts in the bundle sheath(BS)cells.Gene expression and weighted gene co-expression network analysis(WGCNA)showed overall elevated expression of core genes associated with the C_(4)pathway,and significant enrichment of genes related to modified culm anatomy and photosynthesis efficiency.We found evidence of mixed nicotinamide adenine dinucleotide-malic enzyme and phosphoenolpyruvate carboxykinase type C_(4)photosynthesis in E.vivipara,and hypothesize that the evolution of C_(4)photosynthesis predates the WGD event.The mixed type is dominated by subgenome A and supplemented by subgenome B.Collectively,our findings not only shed light on the evolution of E.vivipara and karyotype within the Cyperaceae family,but also provide valuable insights into the transition between C_(3)and C_(4)photosynthesis,offering promising avenues for crop improvement and breeding.