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

Matthew Haas, Thomas Kono, Marissa Macchietto, Reneth Millas, Lillian McGilp, Mingqin Shao, Jacques Duquette, Yinjie Qiu, Candice N. Hirsch, Jennifer Kimball

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1802-1818
Number of pages17
JournalPlant Journal
Volume107
Issue number6
Early online dateJul 26 2021
DOIs
StatePublished - Sep 2021

Bibliographical note

Funding Information:
The authors would like to thank the staff at the University of Minnesota Genomics Center (UMGC) and acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing resources that contributed to the research results reported in this article. 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. JK conceived the study. TK and MM performed the genome annotation. MS and JD collected plant material and prepared the samples for sequencing. YQ and LM performed flow cytometry. MH, TK, MM, YQ, RM and LM performed data analysis. All authors contributed to data interpretation. JK and MH wrote the article with significant contributions from CNH and input from all authors. The authors declare that they have no conflicts of interest associated with this work.

Funding Information:
The authors would like to thank the staff at the University of Minnesota Genomics Center (UMGC) and acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing resources that contributed to the research results reported in this article. 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.

Publisher Copyright:
© 2021 Society for Experimental Biology and John Wiley & Sons Ltd

Keywords

  • PacBio sequencing
  • RNA-seq
  • Zizania palustris
  • annotation
  • de novo assembly
  • northern wild rice
  • whole-genome duplication

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't

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