Whole Genome Assembly and Annotation of Northern Wild Rice (Zizania palustris L.), a North American Grain

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Description of data (7.38 KB)
Northern Wild Rice (Zizania palustris L.) genome (cultivar Itasca-C12) GFF3 file OLD NAMES (95.94 MB)
Northern Wild Rice (Zizania palustris L.) genome (cultivar Itasca-C12) FASTA file NEW NAMES (1.2 GB)
Duplications.tsv file from OrthoFinder run for Figure 2 (28.05 MB)
Duplications.tsv file from OrthoFinder run for rice relatives (10.83 MB)
Orthogroups.GeneCount.tsv for the entire (20-member) run of OrthoFinder incl. Z. latifolia (3.54 MB)
Orthogroups.GeneCount.tsv file for Figure 2 (767.32 KB)
Orthogroups.GeneCount.tsv file for rice relatives (761.79 KB)
Orthogroups.tsv file from OrthoFinder run for Figure 2 (4.15 MB)
Orthogroups.tsv file from OrthoFinder run for rice relatives (3.27 MB)
Orthogroups.UnassignedGenes.tsv file from OrthoFinder run for entire (20-member) run of OrthoFinder incl. Z. latifolia (4.26 MB)
Orthogroups.UnassignedGenes.tsv file from OrthoFinder run for Figure 2 (1.98 MB)
Orthogroups.UnassignedGenes.tsv file from OrthoFinder run for rice relatives (700.22 KB)
genes with Biological Process GO terms (238.76 KB)
genes with Cellular Component GO terms (460.84 KB)
genes with Molecular Function GO terms (858.09 KB)
Duplications.tsv file for the entire (20-member) run of OrthoFinder incl. Z. latifolia (257.85 MB)
Duplications.tsv file for the entire (20-member) run of OrthoFinder incl. Z. latifolia (257.85 MB)
Duplications.tsv file for the entire (20-member) run of OrthoFinder incl. Z. latifolia (257.85 MB)
Orthogroups.tsv file from OrthoFinder run for the entire (20-member) run of OrthoFinder incl. Z. latifolia (25.17 MB)
Tau values for all tissues (4.6 MB)
Tau values without root tissue (4.18 MB)
counts per million (cpm) values for all tissues (6.21 MB)
Use this file to translate original gene names (beginning with "FUN") to newer "ZP" names (1.58 MB)
Annotation file with old and new gene names, genomic position, predicted function, gene ontology information, and tissue-specific counts (cpm) (11.64 MB)

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Title

Whole Genome Assembly and Annotation of Northern Wild Rice (Zizania palustris L.), a North American Grain

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Published Date

2021-07-23

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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.

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Funding information

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.

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https://doi.org/10.13020/ha32-4735

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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 (DRUM), https://doi.org/10.13020/ha32-4735.

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