Comparative plastome analyses and genomic resource development in wild rice (Zizania spp., Poaceae) using genome skimming data

Wild rice (Zizania spp.), a major aquatic crop of North America and East Asia, has been globally recognized for its superior nutritional and health benefits. However, genomic resources available for molecular breeding and germplasm exploration of Zizania are still scarce, which have impeded the industrial and commercial production of wild rice. Here, we used a genome skimming strategy to retrieve plastome information (including whole plastome sequences, plastome-divergent hotspots and plastome-derived SSRs) of Zizania species/cultivars, and identify polymorphic nuclear SSRs within this genus. All the Zizania plastomes ranged in length from 136,278 to 136,502 bp, and exhibited the typical quadripartite structure with identical gene content, GC content, gene order, and IR/SC boundary structure. Eight common cultivars of Z. latifolia shared almost the same whole-plastome haplotype. Comparative plastome analyses of Zizania revealed that the top ten most variable regions (π > 7.65 × 10⁻³) are all intergenic regions (ndhC-trnV, ndhE-ndhG, ndhF-rpl32, psaA-ycf3, psaI-ycf4, psbK-psbI, rpl32-trnL, trnG-trnfM, trnR-rps14 and trnY-trnD). A total of 36, 35 and 29 plastome-derived SSRs were identified in Z. latifolia, Z. aquatica and Z. palustris, respectively. Based on multiple assembled nuclear sequences, we also developed 290 polymorphic nuclear SSRs within this genus. Phylogenomic analyses based on the whole plastome sequences and 77 protein coding genes strongly supported two well-supported Zizania clades, corresponding strictly to the East Asian clade of Z. latifolia, as well as the North American clade of Z. aquatica and Z. palustris. All Z. latifolia cultivars formed a monophyletic group, implying a single domestication origin of them. Overall, the accumulated genetic resources described here will not only facilitate further phylogeographic and population genetic studies on Zizania, but also be useful for commercial/industrial exploitation of this economically significant genus.