The genus Zizania belongs to the rice tribe (Oryzeae) of the grass family Poaceae and is the closest genus to rice (Oryza sativa). Two members of the genus Zizania have been domesticated -- the annual Z. palustris, which is native to North America and is called “wild rice” as a grain crop, and the perennial Z. latifolia, which is native to Asia and called “Jiaobai” as a vegetable crop. 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 by 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.

Using a whole-genome shotgun sequencing approach, a total of 83.4 Gb of Illumina high-quality sequence data (130.1 Gb of raw data), representing approximately 140-fold genome coverage was generated. 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. These results show that continuous long-standing endophyte association can 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.

Figure 1. Evolution and phylogenetics of the Zizania genome. (a) Genome duplications in cereal genomes revealed through 4dTv analyses. Besides an ancient WGD event predating divergence of the cereals and the Zizania speciation, a recent WGD after the Zizania-Oryza divergence could be identified in the distribution of 4dTv values. (b) Clusters of orthologous and paralogous genes in Zizania and other four species of the grass family. Gene family number is listed in each of the components and species. (c) Estimation of the time of divergence (with error range shown in parentheses) of Z. latifolia and four other grasses based on orthologous single-copy gene pairs, with red dots indicating the calibration time.

This work was supported by State Key Lab of Rice Biology of China, Zhejiang Key Lab of Crop Germplasm Resources, Innovation Project of CAAS, the Gordon and Betty Moore Foundation, the National Natural Science Foundation of China (31000357 and 30921140408) and National Science and Technology Ministry of China (2012BAD27B01). The research finding has been published on Plant Journal on June 17^th, 2015.

The details are available on Plant Journal on the link bellow:

http://onlinelibrary.wiley.com/doi/10.1111/tpj.12912/abstract