Genomic abundance is not predictive of tandem repeat localization in grass genomes
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 appl...
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Published in: | PloS one Vol. 12; no. 6; p. e0177896 |
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Main Authors: | , , , , , , , |
Format: | Journal Article |
Language: | English |
Published: |
United States
Public Library of Science
01-06-2017
Public Library of Science (PLoS) |
Subjects: | |
Online Access: | Get full text |
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Summary: | 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. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Current address: Research Group for Ancient Genomics and Evolution, Dept. of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany Conceptualization: PB MBH JJ JRI.Data curation: PB AL.Formal analysis: PB.Funding acquisition: PB JJ JRI.Investigation: PB AL YH PZ MCE.Methodology: PB MBH AL YH PZ JJ JRI.Writing – original draft: PB JRI.Writing – review & editing: PB JJ JRI. Competing Interests: The authors have declared that no competing interests exist. |
ISSN: | 1932-6203 1932-6203 |
DOI: | 10.1371/journal.pone.0177896 |