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An improved and robust method to efficiently deplete repetitive elements from complex plant genomes.

Hiroyuki Ichida1, Tomoko Abe1

  • 1RIKEN Nishina Center for Accelerator-Based Science, Saitama 351-0198, Japan.

Plant Science : an International Journal of Experimental Plant Biology
|March 3, 2019
PubMed
Summary

This study introduces a new method using a modified adapter and duplex-specific nuclease (DSN) to efficiently remove repetitive DNA sequences from complex plant genomes. This improves sequencing accuracy for important genes in crops like wheat.

Keywords:
Duplex-specific nucleaseGenome reductionNext-generation sequencingRiceWheat

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Large and complex genomes in agricultural species pose challenges for genomic analysis.
  • Repetitive sequences can dominate genomes, obscuring important genetic information.

Purpose of the Study:

  • To develop an improved short-read library preparation method for efficient elimination of repetitive DNA elements.
  • To enhance the sequencing of low-copy genes and protein-coding sequences in complex genomes.

Main Methods:

  • Designed a novel hairpin-structured adapter for short-read library preparation.
  • Employed duplex-specific nuclease (DSN) for enzymatic depletion of repetitive elements.
  • Applied the method to rice and various wheat cultivars (diploid, tetraploid, hexaploid).

Main Results:

  • DSN treatment significantly reduced ribosomal DNA abundance in rice and wheat.
  • Whole-genome sequencing showed a dramatic decrease in retrotransposons and DNA transposons.
  • Sequencing reads from low-copy genes and protein-coding sequences increased by over 50%.

Conclusions:

  • The developed method effectively removes repetitive sequences from complex plant genomes.
  • This technique is valuable for improving genome-based approaches in wheat and other large-genome crops.