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Reference Genome for the Highly Transformable Setaria viridis ME034V.

Peter M Thielen1, Amanda L Pendleton2,3, Robert A Player1

  • 1Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723.

G3 (Bethesda, Md.)
|July 23, 2020
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Summary

A new genome assembly for the model plant Setaria viridis (green foxtail) accession ME034V was created using ultra-long nanopore sequencing. This high-quality genome resource reveals significant structural variations and aids future cereal crop improvement.

Keywords:
MinIONOxford Nanopore Technologieslong-read assemblystructural variation

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Area of Science:

  • Genomics
  • Plant Biology
  • Bioinformatics

Background:

  • Setaria viridis (green foxtail) is a key C4 model for cereal crop research.
  • The transformable ME034V accession lacked a sequenced genome, limiting its research potential.

Purpose of the Study:

  • To generate a high-quality, de novo genome assembly for the Setaria viridis ME034V accession.
  • To characterize the genome's structure, including genes and repetitive elements.
  • To compare the ME034V genome with other Setaria genomes and identify structural variations.

Main Methods:

  • Utilized ultra-long nanopore sequencing for a highly contiguous de novo assembly.
  • Performed genome annotation to identify protein-coding genes and repetitive elements.
  • Conducted comparative genomics and phylogenomic analyses against existing Setaria genomes and a diversity panel.

Main Results:

  • Generated a 397 Mb highly contiguous genome assembly for ME034V (estimated genome size 401 Mb).
  • Annotated 37,908 protein-coding genes and identified over 300,000 repetitive elements (46% of the genome).
  • Discovered numerous unique polymorphic structural variants, including deletions potentially linked to retrotransposition events.

Conclusions:

  • The high-continuity ME034V genome assembly, enabled by ultra-long DNA sequencing, significantly enhances genetic resources for Setaria research.
  • Identification of structural variations underscores the need for accurate genome references in genetic studies.
  • This genome resource is expected to be highly valuable for the Setaria research community and cereal crop improvement efforts.