Li W, Zhang QJ, Zhu T, Tong Y, Li K, Shi C, Zhang Y, Liu YL, Jiang JJ, Liu Y, Xia EH, Huang H, Zhang LP, Zhang D, Shi C, Jiang WK, Zhao YJ, Mao SY, Jiao JY, Xu PZ, Yang LL, Gao LZ.

Plant Direct. 2020 Jun 11;4(6):e00232.

Abstract

Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable number of lineage-specific gene families associated with the self-incompatibility (SI) and formation of reproductive separation. We show how lineage-specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage-specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome-wide expansion of genes encoding NBS-LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata.

See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7287411/

Figure 3: Evolutionary dynamics of the R‐genes in the nine Oryza genomes

We positioned these orthologous R‐genes to definite genomic locations across the SAT chromosomes in Figure 3, displaying an almost unequal distribution of the amplified NBS‐encoding genes throughout the entire genome, among which Chromosome 11 harbored the utmost number of R‐genes for all these nine rice species. They will evidently offer a large number of candidate loci for further functional genomic studies on disease resistance and rice breeding programs.