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Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum
Knowledge of the fascinating world of DNA repeats is continuously being enriched by newly identified elements and their hypothetical or well-established biological relevance. Genomic approaches can be used for comparative studies of major repeats in any group of genomes, regardless of their size and...
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/PMC6387171/ https://www.ncbi.nlm.nih.gov/pubmed/30744119 http://dx.doi.org/10.3390/ijms20030733 |
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author | Peška, Vratislav Mandáková, Terezie Ihradská, Veronika Fajkus, Jiří |
author_facet | Peška, Vratislav Mandáková, Terezie Ihradská, Veronika Fajkus, Jiří |
author_sort | Peška, Vratislav |
collection | PubMed |
description | Knowledge of the fascinating world of DNA repeats is continuously being enriched by newly identified elements and their hypothetical or well-established biological relevance. Genomic approaches can be used for comparative studies of major repeats in any group of genomes, regardless of their size and complexity. Such studies are particularly fruitful in large genomes, and useful mainly in crop plants where they provide a rich source of molecular markers or information on indispensable genomic components (e.g., telomeres, centromeres, or ribosomal RNA genes). Surprisingly, in Allium species, a comprehensive comparative study of repeats is lacking. Here we provide such a study of two economically important species, Allium cepa (onion), and A. sativum (garlic), and their distantly related A. ursinum (wild garlic). We present an overview and classification of major repeats in these species and have paid specific attention to sequence conservation and copy numbers of major representatives in each type of repeat, including retrotransposons, rDNA, or newly identified satellite sequences. Prevailing repeats in all three studied species belonged to Ty3/gypsy elements, however they significantly diverged and we did not detect them in common clusters in comparative analysis. Actually, only a low number of clusters was shared by all three species. Such conserved repeats were for example 5S and 45S rDNA genes and surprisingly a specific and quite rare Ty1/copia lineage. Species-specific long satellites were found mainly in A. cepa and A. sativum. We also show in situ localization of selected repeats that could potentially be applicable as chromosomal markers, e.g., in interspecific breeding. |
format | Online Article Text |
id | pubmed-6387171 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-63871712019-02-27 Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum Peška, Vratislav Mandáková, Terezie Ihradská, Veronika Fajkus, Jiří Int J Mol Sci Article Knowledge of the fascinating world of DNA repeats is continuously being enriched by newly identified elements and their hypothetical or well-established biological relevance. Genomic approaches can be used for comparative studies of major repeats in any group of genomes, regardless of their size and complexity. Such studies are particularly fruitful in large genomes, and useful mainly in crop plants where they provide a rich source of molecular markers or information on indispensable genomic components (e.g., telomeres, centromeres, or ribosomal RNA genes). Surprisingly, in Allium species, a comprehensive comparative study of repeats is lacking. Here we provide such a study of two economically important species, Allium cepa (onion), and A. sativum (garlic), and their distantly related A. ursinum (wild garlic). We present an overview and classification of major repeats in these species and have paid specific attention to sequence conservation and copy numbers of major representatives in each type of repeat, including retrotransposons, rDNA, or newly identified satellite sequences. Prevailing repeats in all three studied species belonged to Ty3/gypsy elements, however they significantly diverged and we did not detect them in common clusters in comparative analysis. Actually, only a low number of clusters was shared by all three species. Such conserved repeats were for example 5S and 45S rDNA genes and surprisingly a specific and quite rare Ty1/copia lineage. Species-specific long satellites were found mainly in A. cepa and A. sativum. We also show in situ localization of selected repeats that could potentially be applicable as chromosomal markers, e.g., in interspecific breeding. MDPI 2019-02-09 /pmc/articles/PMC6387171/ /pubmed/30744119 http://dx.doi.org/10.3390/ijms20030733 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 Peška, Vratislav Mandáková, Terezie Ihradská, Veronika Fajkus, Jiří Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum |
title | Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum |
title_full | Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum |
title_fullStr | Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum |
title_full_unstemmed | Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum |
title_short | Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum |
title_sort | comparative dissection of three giant genomes: allium cepa, allium sativum, and allium ursinum |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6387171/ https://www.ncbi.nlm.nih.gov/pubmed/30744119 http://dx.doi.org/10.3390/ijms20030733 |
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