The genus Zizania, the closest genus to rice (Oryza sativa), belongs to the rice tribe (Oryzeae) of the grass family Poaceae. Two members of the genus Zizania have been domesticated -- the annual Z. palustris, called “wild rice” as a grain crop native to North America, and the perennial Z. latifolia, called “Jiaobai” as a vegetable crop native to Asia and. However, the ancient cereal crop Gu (Zizania latifolia) near the Taihu Lake basin of the low Yangtze in Chinese history, was replaced by rice and disappeared about 1000 years ago. Meanwhile, the domestication of Z. latifolia into Jiaobai was made possible through persistent infection by a fungal endophyte, Ustilago esculenta, resulting in enlarged edible stems and loss of flowering. The long-standing plant-pathogen symbiotic relationship provides a valuable genetic resource for the study of the adaptive differentiation of a defined long-term microbial infection on host genome dynamics.

Recently, using a whole-genome shotgun sequencing approach, researchers from China National Rice Research Institute (CNRRI) of CAAS conducted a research and generated a total of 83.4 Gb of Illumina high-quality sequence data (130.1 Gb of raw data), representing approximately 140-fold genome coverage. 43,703 protein-coding genes were predicted, including a large number of NBS type resistance gene, based on ab initio and homology-based (including transcriptomic sequences generated by RNA-Seq) approaches. There is a high genomic synteny between Zizania and Oryza, and 1498 syntenic blocks between them were identified, which cover 50.9% of total genes. Genomic comparative analysis revealed that cultivated Z. latifolia has a significantly smaller repertoire of immune receptors compared with wild Z. latifolia. There are widespread gene losses/mutations and expression changes in the plant-pathogen interaction pathway in Jiaobai. Research findings showed that continuous long-standing endophyte association could have a major effect on the evolution of the structural and transcriptomic components of the host genome (Figure 1). The analysis of the mechanism of the interaction between fungi and plants has important theoretical significance and application value for the innovation of agricultural breeding and plant protection.