International Journal of Molecular Sciences Article Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum Vratislav Peška 1,* , Terezie Mandáková 2 , Veronika Ihradská 1,2,† and Jiˇrí Fajkus 1,2,* 1 Institute of Biophysics, The Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic;
[email protected] 2 Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic;
[email protected] * Correspondence:
[email protected] (V.P.);
[email protected] (J.F.); Tel.: +420-541-517-199 (V.P.); +420-549-494-003 (J.F.) † Current address: Institute of Plant Genetics and Biotechnology, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Akademická 2, P.O. Box 39A, 950 07 Nitra, Slovakia. Received: 4 January 2019; Accepted: 2 February 2019; Published: 9 February 2019 Abstract: 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.