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The Dark Matter of Large Cereal Genomes: Long Tandem Repeats
Reference genomes of important cereals, including barley, emmer wheat and bread wheat, were released recently. Their comparison with genome size estimates obtained by flow cytometry indicated that the assemblies represent not more than 88–98% of the complete genome. This work is aimed at identifying...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6567227/ https://www.ncbi.nlm.nih.gov/pubmed/31137466 http://dx.doi.org/10.3390/ijms20102483 |
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author | Kapustová, Veronika Tulpová, Zuzana Toegelová, Helena Novák, Petr Macas, Jiří Karafiátová, Miroslava Hřibová, Eva Doležel, Jaroslav Šimková, Hana |
author_facet | Kapustová, Veronika Tulpová, Zuzana Toegelová, Helena Novák, Petr Macas, Jiří Karafiátová, Miroslava Hřibová, Eva Doležel, Jaroslav Šimková, Hana |
author_sort | Kapustová, Veronika |
collection | PubMed |
description | Reference genomes of important cereals, including barley, emmer wheat and bread wheat, were released recently. Their comparison with genome size estimates obtained by flow cytometry indicated that the assemblies represent not more than 88–98% of the complete genome. This work is aimed at identifying the missing parts in two cereal genomes and proposing techniques to make the assemblies more complete. We focused on tandemly organised repetitive sequences, known to be underrepresented in genome assemblies generated from short-read sequence data. Our study found arrays of three tandem repeats with unit sizes of 1242 to 2726 bp present in the bread wheat reference genome generated from short reads. However, this and another wheat genome assembly employing long PacBio reads failed in integrating correctly the 2726-bp repeat in the pseudomolecule context. This suggests that tandem repeats of this size, frequently incorporated in unassigned scaffolds, may contribute to shrinking of pseudomolecules without reducing size of the entire assembly. We demonstrate how this missing information may be added to the pseudomolecules with the aid of nanopore sequencing of individual BAC clones and optical mapping. Using the latter technique, we identified and localised a 470-kb long array of 45S ribosomal DNA absent from the reference genome of barley. |
format | Online Article Text |
id | pubmed-6567227 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-65672272019-06-17 The Dark Matter of Large Cereal Genomes: Long Tandem Repeats Kapustová, Veronika Tulpová, Zuzana Toegelová, Helena Novák, Petr Macas, Jiří Karafiátová, Miroslava Hřibová, Eva Doležel, Jaroslav Šimková, Hana Int J Mol Sci Article Reference genomes of important cereals, including barley, emmer wheat and bread wheat, were released recently. Their comparison with genome size estimates obtained by flow cytometry indicated that the assemblies represent not more than 88–98% of the complete genome. This work is aimed at identifying the missing parts in two cereal genomes and proposing techniques to make the assemblies more complete. We focused on tandemly organised repetitive sequences, known to be underrepresented in genome assemblies generated from short-read sequence data. Our study found arrays of three tandem repeats with unit sizes of 1242 to 2726 bp present in the bread wheat reference genome generated from short reads. However, this and another wheat genome assembly employing long PacBio reads failed in integrating correctly the 2726-bp repeat in the pseudomolecule context. This suggests that tandem repeats of this size, frequently incorporated in unassigned scaffolds, may contribute to shrinking of pseudomolecules without reducing size of the entire assembly. We demonstrate how this missing information may be added to the pseudomolecules with the aid of nanopore sequencing of individual BAC clones and optical mapping. Using the latter technique, we identified and localised a 470-kb long array of 45S ribosomal DNA absent from the reference genome of barley. MDPI 2019-05-20 /pmc/articles/PMC6567227/ /pubmed/31137466 http://dx.doi.org/10.3390/ijms20102483 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Kapustová, Veronika Tulpová, Zuzana Toegelová, Helena Novák, Petr Macas, Jiří Karafiátová, Miroslava Hřibová, Eva Doležel, Jaroslav Šimková, Hana The Dark Matter of Large Cereal Genomes: Long Tandem Repeats |
title | The Dark Matter of Large Cereal Genomes: Long Tandem Repeats |
title_full | The Dark Matter of Large Cereal Genomes: Long Tandem Repeats |
title_fullStr | The Dark Matter of Large Cereal Genomes: Long Tandem Repeats |
title_full_unstemmed | The Dark Matter of Large Cereal Genomes: Long Tandem Repeats |
title_short | The Dark Matter of Large Cereal Genomes: Long Tandem Repeats |
title_sort | dark matter of large cereal genomes: long tandem repeats |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6567227/ https://www.ncbi.nlm.nih.gov/pubmed/31137466 http://dx.doi.org/10.3390/ijms20102483 |
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