Title
Whole Genome Assembly and Annotation of Northern Wild Rice (Zizania palustris L.), a North American Grain
Published Date
2021-07-23
Authors
Group
University of Minnesota Cultivated Wild Rice Breeding and Genetics Lab
Author Contact
Kimball, Jennifer A (jkimball@umn.edu)
Type
Dataset
Abstract
Northern Wild Rice (NWR; Zizania palustris L.) 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 United States. Using long- and short-range sequencing, Hi-C scaffolding, and RNA-seq data from eight tissues, we generated a whole genome de novo assembly and annotation of NWR. The assembly is 1.29 Gb, highly repetitive (~76.0%), and contains 46,421 protein-coding genes. Comparative analyses revealed conservation of large syntenic blocks with Oryza sativa L., which were used to identify putative seed shattering genes. Estimates of divergence times revealed the Zizania genus diverged from Oryza ~26-30 million years ago (MYA), while NWR and Zizania latifolia diverged from one another ~6-8 MYA. Comparative genomics revealed evidence of a whole genome duplication in NWR ~5.3 MYA after the NWR-Z. latifolia speciation event. This high-quality genome assembly and annotation provides is a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.
Funding information
Sponsorship:
This work was supported by the Minnesota Cultivated Wild Rice Council and by the State of Minnesota, Agricultural Research, Education, Extension, and Technology Transfer program.
Referenced by
submission pending
License
Attribution 3.0 United States
Suggested Citation
Haas, Matthew W; Kono, Thomas; Macchietto, Marissa; Millas, Reneth; McGilp, Lillian; Shao, Mingqin; Duquette, Jacques; Hirsch, Candice N; Kimball, Jennifer A.
(2021). Whole Genome Assembly and Annotation of Northern Wild Rice (Zizania palustris L.), a North American Grain.
Retrieved from the Data Repository for the University of Minnesota,
https://doi.org/10.13020/ha32-4735.