BAL31-NGS approach for identification of telomeres de novo in large genomes

Methods. 2017 Feb 1;114:16-27. doi: 10.1016/j.ymeth.2016.08.017. Epub 2016 Sep 3.

Abstract

This article describes a novel method to identify as yet undiscovered telomere sequences, which combines next generation sequencing (NGS) with BAL31 digestion of high molecular weight DNA. The method was applied to two groups of plants: i) dicots, genus Cestrum, and ii) monocots, Allium species (e.g. A. ursinum and A. cepa). Both groups consist of species with large genomes (tens of Gb) and a low number of chromosomes (2n=14-16), full of repeat elements. Both genera lack typical telomeric repeats and multiple studies have attempted to characterize alternative telomeric sequences. However, despite interesting hypotheses and suggestions of alternative candidate telomeres (retrotransposons, rDNA, satellite repeats) these studies have not resolved the question. In a novel approach based on the two most general features of eukaryotic telomeres, their repetitive character and sensitivity to BAL31 nuclease digestion, we have taken advantage of the capacity and current affordability of NGS in combination with the robustness of classical BAL31 nuclease digestion of chromosomal termini. While representative samples of most repeat elements were ensured by low-coverage (less than 5%) genomic shot-gun NGS, candidate telomeres were identified as under-represented sequences in BAL31-treated samples.

Keywords: BAL31; NGS; RepeatExplorer; Tandem Repeats Finder; Tandem Repeats Merger; Telomere.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Allium / genetics*
  • Cestrum / genetics*
  • Chromosomes, Plant
  • Endodeoxyribonucleases / metabolism*
  • Genome, Plant*
  • Genomics
  • High-Throughput Nucleotide Sequencing / methods*
  • Sequence Analysis, DNA / methods*
  • Telomere / genetics*

Substances

  • Endodeoxyribonucleases
  • exonuclease Bal 31