Recent decade has witnessed significant advances in studies of speciation and adaptive evolution using sequencing technology.However, investigation on plant speciation at genome level is scarce, particularly in terms of structural and functional aspects.Two wild rice species, Oryza nivara and O.rufipogon are sympatric and distinct morphologically and ecologically.Oryza nivara is annual, photoperiod insensitive, self-fertilized, and adapted to seasonally dry habitats, whereas O.ruflpogon is perennial, photoperiod sensitive, largely cross-fertilized, and adapted to persistently wet habitats.Our previous studies have demonstrated the ecological divergence between species in the presence of significant gene flow, implying that natural selection plays a primary role in driving the divergence of the two Oryza species.