Whole‐genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole‐genome duplication in the Zizania genus

Abstract

Zizania palustris L. (northern wild rice, NWR) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural and agricultural significance, specifically in the Great Lakes region of the USA. Using flow cytometry, we first estimated the NWR genome size to be 1.8 Gb. Using long-and short-range sequencing, Hi-C scaffolding and RNA-seq data from eight tissues, we generated an annotated whole-genome de novo assembly of NWR. The assembly was 1.29 Gb in length, highly repetitive (approx. 76.0%) and contained 46 421 putative protein-coding genes. The expansion of retrotransposons within the genome and a whole-genome duplication (WGD) after the Zizania-Oryza speciation event have both led to an increase in the genome size of NWR in comparison with Oryza sativa L. and Zizania latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed the conservation of large syntenic blocks between NWR and O. sativa, which were used to identify putative seed-shattering genes. Estimates of divergence times revealed that the Zizania genus diverged from Oryza approximately 26-30 million years ago (26-30 MYA), whereas NWR and Z. latifolia diverged from one another approximately 6-8 MYA. Comparative genomics confirmed evidence of a WGD in the Zizania genus and provided support that the event occurred prior to the NWR-Z. latifolia speciation event. This genome assembly and annotation provides a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.

Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis

“…These results might explain why Chinese wild rice has a genome larger than O. sativa . Notably, the repetitive rate in the genome of northern wild rice (76.40%) 36 is higher than that in Chinese wild rice Huai’an (52.89%), which might explain why northern wild rice has a larger genome than Chinese wild rice. We then used three strategies (ab initio prediction, a homology-based strategy, and transcriptomic support) to predict the protein-coding genes (Supplementary Fig.…”

“…3e ), which is consistent with the previous findings 31 . Zizania – Oryza speciation events have both led to an increase in the genome size of northern wild rice (1.29 Gb) 36 in comparison with that of rice (390.30 Mb) and Chinese wild rice (547.38 Mb) (Table 1 ). Moreover, a peak centering on Ks of ~0.25 was observed between the O. sativa and Z. latifolia pairs.…”

“…Significant genome collinearity has been observed between northern wild rice and rice 36 , 39 , 40 . Similarly, in this study, significant genome collinearity was observed between Chinese wild rice and rice (Supplementary Fig.…”

“…To the best of our knowledge, 10 seed-shattering-related genes have been identified in rice (i.e., qSH1 , OsGRF4/PT2 , OsSh1 , OsNPC1 , sh4/SHA1 , SHAT , OsLG1 , SH5 , sh-h/OsCPL1 , and SSH1 ) (Supplementary Table 8 ). Moreover, 17 seed-shattering-related genes have been identified in northern wild rice through collinearity between seed-shattering-related genes of rice and northern wild rice 36 . Based on genome collinearity and gene homolog analyses between the genomes of Chinese wild rice and rice, we identified 29 candidate genes potentially related to seed shattering in Chinese wild rice (Supplementary Fig.…”

“…Furthermore, our assembly of Huai’an (contig N50 = 4.78 Mb) exhibits a 367.69 × longer contig N50 than HSD2 (contig N50 = 13 kb) 31 . Recently, Haas et al 36 generated a high-quality genome for northern wild rice and anchored 98.53% of the sequences to 15 chromosomes. The chromosome-level genome will support future studies of molecular genetic breeding and genome evolution in wild rice and the genus Zizania .…”