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Chromosome-Level Genome Assembly Identifies RIRE2 and CACTA Transposable Elements at the Sub1 Locus in

Na-Hyun Shin1, Ji-Hun Hwang2, Moaine El Baidouri3,4

  • 1Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Republic of Korea.

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Summary

Researchers identified novel transposable elements within the rice Sub1 QTL, providing the first complete reference sequence. These elements contain regulatory sequences that may enhance submergence tolerance in rice.

Keywords:
De novo assemblySub1RiceSubmergence toleranceTransposable elements

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Area of Science:

  • Genetics
  • Plant Biology
  • Genomics

Background:

  • Rice (Oryza sativa) is vulnerable to complete submergence, a major threat to crop yield.
  • The Sub1A-1 allele confers submergence tolerance but its regulatory regions are not fully characterized.

Purpose of the Study:

  • To provide a complete reference sequence of the rice Sub1 QTL, including flanking regulatory regions.
  • To identify and characterize transposable elements within the Sub1 locus and their potential regulatory roles.

Main Methods:

  • Chromosome-level genome assemblies of IR64-Sub1 and IR64sj were used.
  • Identification and characterization of transposable elements (TEs) including LTR-retrotransposons and CACTA elements.
  • Motif analysis to identify transcription factor binding sites within TEs.

Main Results:

  • The Sub1 locus contains two novel transposable elements: a RIRE2 retrotransposon and a CACTA element.
  • The CACTA element contains two genes with expression patterns similar to Sub1A-1 under submergence.
  • ERF-family binding motifs are enriched in the CACTA element's promoter regions.

Conclusions:

  • This study provides the first complete reference sequence of the Sub1 QTL.
  • TE-associated regulatory sequences are potential contributors to submergence-responsive gene transcription.
  • Establishes a genomic foundation for developing flood-resilient rice varieties.