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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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Autores principales: Bilinski, Paul, Han, Yonghua, Hufford, Matthew B., Lorant, Anne, Zhang, Pingdong, Estep, Matt C., Jiang, Jiming, Ross-Ibarra, Jeffrey
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453492/
https://www.ncbi.nlm.nih.gov/pubmed/28570674
http://dx.doi.org/10.1371/journal.pone.0177896
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author Bilinski, Paul
Han, Yonghua
Hufford, Matthew B.
Lorant, Anne
Zhang, Pingdong
Estep, Matt C.
Jiang, Jiming
Ross-Ibarra, Jeffrey
author_facet Bilinski, Paul
Han, Yonghua
Hufford, Matthew B.
Lorant, Anne
Zhang, Pingdong
Estep, Matt C.
Jiang, Jiming
Ross-Ibarra, Jeffrey
author_sort Bilinski, Paul
collection PubMed
description 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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spelling pubmed-54534922017-06-12 Genomic abundance is not predictive of tandem repeat localization in grass genomes Bilinski, Paul Han, Yonghua Hufford, Matthew B. Lorant, Anne Zhang, Pingdong Estep, Matt C. Jiang, Jiming Ross-Ibarra, Jeffrey PLoS One Research Article 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. Public Library of Science 2017-06-01 /pmc/articles/PMC5453492/ /pubmed/28570674 http://dx.doi.org/10.1371/journal.pone.0177896 Text en © 2017 Bilinski et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Bilinski, Paul
Han, Yonghua
Hufford, Matthew B.
Lorant, Anne
Zhang, Pingdong
Estep, Matt C.
Jiang, Jiming
Ross-Ibarra, Jeffrey
Genomic abundance is not predictive of tandem repeat localization in grass genomes
title Genomic abundance is not predictive of tandem repeat localization in grass genomes
title_full Genomic abundance is not predictive of tandem repeat localization in grass genomes
title_fullStr Genomic abundance is not predictive of tandem repeat localization in grass genomes
title_full_unstemmed Genomic abundance is not predictive of tandem repeat localization in grass genomes
title_short Genomic abundance is not predictive of tandem repeat localization in grass genomes
title_sort genomic abundance is not predictive of tandem repeat localization in grass genomes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453492/
https://www.ncbi.nlm.nih.gov/pubmed/28570674
http://dx.doi.org/10.1371/journal.pone.0177896
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