Comparative Dissection of Three Giant Genomes: Allium cepa,
Allium sativum, and Allium ursinum

J 2019

Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum

PEŠKA, Vratislav; Terezie MANDÁKOVÁ; Veronika IHRADSKÁ a Jiří FAJKUS

Základní údaje

Originální název

Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum

Autoři

PEŠKA, Vratislav; Terezie MANDÁKOVÁ; Veronika IHRADSKÁ a Jiří FAJKUS

Vydání

International Journal of Molecular Sciences, Basel, Multidisciplinary Digital Publishing Institute, 2019, 1422-0067

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10611 Plant sciences, botany

Stát vydavatele

Švýcarsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/19:00107672

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

Allium; plant genome; repeats; retrotransposon; satellite; telomere; rDNA;RepeatExplorer; TAREAN

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 29. 4. 2020 11:43, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

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.

Návaznosti

GA17-09644S, projekt VaV

Název: Molekulární podstata evolučních přeměn telomer u rostlin řádu Asparagales

Investor: Grantová agentura ČR, Molekulární podstata evolučních přeměn telomer u rostlin řádu Asparagales

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

PEŠKA, Vratislav; Terezie MANDÁKOVÁ; Veronika IHRADSKÁ a Jiří FAJKUS. Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum. International Journal of Molecular Sciences. Basel: Multidisciplinary Digital Publishing Institute, 2019, roč. 20, č. 3, s. 1-25. ISSN 1422-0067. Dostupné z: https://doi.org/10.3390/ijms20030733.

@article{1561217,
   author = {Peška, Vratislav and Mandáková, Terezie and Ihradská, Veronika and Fajkus, Jiří},
   article_location = {Basel},
   article_number = {3},
   doi = {https://doi.org/10.3390/ijms20030733},
   keywords = {Allium; plant genome; repeats; retrotransposon; satellite; telomere; rDNA;RepeatExplorer; TAREAN},
   language = {eng},
   issn = {1422-0067},
   journal = {International Journal of Molecular Sciences},
   title = {Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum},
   url = {https://www.mdpi.com/1422-0067/20/3/733},
   volume = {20},
   year = {2019}
}

TY  - JOUR
ID  - 1561217
AU  - Peška, Vratislav - Mandáková, Terezie - Ihradská, Veronika - Fajkus, Jiří
PY  - 2019
TI  - Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum
JF  - International Journal of Molecular Sciences
VL  - 20
IS  - 3
SP  - 1-25
EP  - 1-25
PB  - Multidisciplinary Digital Publishing Institute
SN  - 14220067
KW  - Allium
KW  - plant genome
KW  - repeats
KW  - retrotransposon
KW  - satellite
KW  - telomere
KW  - rDNA;RepeatExplorer
KW  - TAREAN
UR  - https://www.mdpi.com/1422-0067/20/3/733
L2  - https://www.mdpi.com/1422-0067/20/3/733
N2  - 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.
ER  -

PEŠKA, Vratislav; Terezie MANDÁKOVÁ; Veronika IHRADSKÁ a Jiří FAJKUS. Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum. \textit{International Journal of Molecular Sciences}. Basel: Multidisciplinary Digital Publishing Institute, 2019, roč.~20, č.~3, s.~1-25. ISSN~1422-0067. Dostupné z: https://doi.org/10.3390/ijms20030733.

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