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 and Jiří FAJKUS

Basic information

Original name

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

Authors

PEŠKA, Vratislav (203 Czech Republic), Terezie MANDÁKOVÁ (203 Czech Republic, belonging to the institution), Veronika IHRADSKÁ (703 Slovakia, belonging to the institution) and Jiří FAJKUS (203 Czech Republic, guarantor, belonging to the institution)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10611 Plant sciences, botany

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 4.556

RIV identification code

RIV/00216224:14740/19:00107672

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.3390/ijms20030733

UT WoS

000462412500277

Keywords in English

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

Abstract

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.

Links

GA17-09644S, research and development project

Name: Molekulární podstata evolučních přeměn telomer u rostlin řádu Asparagales

Investor: Czech Science Foundation

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

PEŠKA, Vratislav, Terezie MANDÁKOVÁ, Veronika IHRADSKÁ and 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, vol. 20, No 3, p. 1-25. ISSN 1422-0067. Available from: https://dx.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 = {http://dx.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 and 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, vol.~20, No~3, p.~1-25. ISSN~1422-0067. Available from: https://dx.doi.org/10.3390/ijms20030733.

Detailed Information on Publication Record