A NEW CHROMOSOME SPECIFIC SUBTELOMERIC TANDEM REPEAT IN ALLIUM FISTULOSUM (L.)
Evaluation and function of tandem repeats (TRs) are poorly understood. TRs are associated with important chromosomal landmarks such as centromeres, telomeres, subtelomeric and other heterochromatic regions. The genomes of Alliums remain poorly investigated because of their large size, the high frequency of duplications, and increased heterozygosity. Using the next generation sequencing data we found a new tandem repeat (CL26) that occupied 0.2% of A. fistulosum genome. Polymerase chain reaction (PCR) with designed primers on known CL26 sequence and genomic DNA of A. fistulosum as a matrix DNA resulted in a 400 bp band. Fluorescent in situ hybridization (FISH) with the 400 bp PCR product showed that CL26 was located in the subtelomeric region on the short arm of chromosome 6. FISH with CL26 on close related species showed hybridization signal also in the subtelomeric region on the short arm of chromosome 6 of A. cepa and no hybridization signals were observed on chromosomes of A. porrum and A. schoenoprasum. Using FISH in combination with BAC (Bacterial Artificial Chromosome) clones has been an effective approach for genome study, physical mapping, identification repeats elements and their organization in genome. Previously in our group, a total of 1100 BAC clones were constructed from the A. fistulosum genomic DNA. Screening of the A. fistulosum genomic DNA BAC library revealed a single BAC clone possessing the CL26 TRs. We proved that the BAC clone consists, along with CL26 TRs, a 378 bp subtelomeric tandem repeat. Multi-color FISH showed that CL26 was located more proximal on the chromosome 6 as compared to the 378 bp subtelomeric repeat location. The structural organization of the CL26 as well as their application as chromosome marker is discussed.