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

被引:28
作者
Peska, Vratislav [1 ]
Mandakova, Terezie [2 ]
Ihradska, Veronika [1 ,2 ,3 ]
Fajkus, Jiri [1 ,2 ]
机构
[1] Czech Acad Sci, Inst Biophys, Kralovopolska 135, Brno 61265, Czech Republic
[2] Masaryk Univ, CEITEC, Mendel Ctr Plant Genom & Prote, Kamenice 5, CZ-62500 Brno, Czech Republic
[3] Slovak Acad Sci, Inst Plant Genet & Biotechnol, Plant Sci & Biodivers Ctr, Akad 2,POB 39A, Nitra 95007, Slovakia
来源
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES | 2019年 / 20卷 / 03期
关键词
Allium; plant genome; repeats; retrotransposon; satellite; telomere; rDNA; RepeatExplorer; TAREAN; NUCLEAR-DNA AMOUNTS; TERMINAL HETEROCHROMATIN; CHROMOSOMAL LOCALIZATION; NUCLEOTIDE-SEQUENCE; LENGTH REGULATION; TANDEM REPEATS; 5S; ORGANIZATION; RDNA; RETROTRANSPOSONS;
D O I
10.3390/ijms20030733
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
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页数:25
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