Genomic abundance is not predictive of tandem repeat localization in grass genomes

PLoS One. 2017 Jun 1;12(6):e0177896. doi: 10.1371/journal.pone.0177896. eCollection 2017.

Abstract

Highly repetitive regions have historically posed a challenge when investigating sequence variation and content. High-throughput sequencing has enabled researchers to use whole-genome shotgun sequencing to estimate the abundance of repetitive sequence, and these methodologies have been recently applied to centromeres. Previous research has investigated variation in centromere repeats across eukaryotes, positing that the highest abundance tandem repeat in a genome is often the centromeric repeat. To test this assumption, we used shotgun sequencing and a bioinformatic pipeline to identify common tandem repeats across a number of grass species. We find that de novo assembly and subsequent abundance ranking of repeats can successfully identify tandem repeats with homology to known tandem repeats. Fluorescent in-situ hybridization shows that de novo assembly and ranking of repeats from non-model taxa identifies chromosome domains rich in tandem repeats both near pericentromeres and elsewhere in the genome.

MeSH terms

  • Centromere
  • Genome, Plant*
  • In Situ Hybridization, Fluorescence
  • Poaceae / genetics*
  • Tandem Repeat Sequences*

Grants and funding

JRI would like to acknowledge support from USDA Hatch project CA-D-PLS-2066-H and NSF Plant Genome award IOS-0922703. PB would like to acknowledge support from the UC Davis Department of Plant Sciences and the DuPont Pioneer Howie Smith Honorary Plant Breeding Fellowship.