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Lee SI, Park KC, Son JH, Hwang YJ, Lim KB, Song YS, Kim JH, Kim NS. Isolation and characterization of novel Ty1-copia-like retrotransposons from lily. Genome 2013; 56:495-503. [DOI: 10.1139/gen-2013-0088] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Species of the genus Lilium are well known for their large genomes. Although expansion of noncoding repeated DNA is believed to account for this genome size, retroelement del Ty3-gypsy is the only one described so far in the genus Lilium. We isolated Ty1-copia elements from Lilium longiflorum and named them LIREs (lily retrotransposons). The long terminal repeats, primer binding site, and polypurine tract sequences are highly similar among the LIRE elements, indicating that they are in the same lineage. Although the protein-coding regions were highly decayed, the sequence motifs of the integrase, reverse transcriptase, and RNase H domains were identifiable as belonging to the order of Ty1-copia elements. Phylogenetic analysis and primer binding site sequences revealed that these elements belonged to the Ale lineage among the six lineages of plant Ty1-copia elements. Base substitutions in the long terminal repeats estimated that the integration times of the LIRE Ty1-copia elements were between 0.7 and 5.5 mya. In situ hybridization showed that the LIRE elements were present in all the chromosomes of L. longiflorum and L. lancifolium, but absent in centromeres, telomeres, and 45S rRNA sites in both species. The LIRE elements were present very abundantly in species of the genus Lilium, but absent in other genera of the family Liliaceae, implying that the LIRE elements might have contributed to the expansion of the genome in the genus Lilium.
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Affiliation(s)
- Sung-Il Lee
- BK21 Training Program, Department of Molecular Bioscience, Kangwon National University, Chuncheon, 200-701, Korea
- Department of Molecular Bioscience, Kangwon National University, Chuncheon, 200-701, Korea
| | - Kyong-Cheul Park
- Institute of Biosciences and Biotechnology, Kangwon National University, Chuncheon, 200-701, Korea
| | - Jae-Han Son
- BK21 Training Program, Department of Molecular Bioscience, Kangwon National University, Chuncheon, 200-701, Korea
- Department of Molecular Bioscience, Kangwon National University, Chuncheon, 200-701, Korea
| | - Youn-Jung Hwang
- Department of Horticulture, Kyungbook National University, Daegu, Korea
| | - Ki-Byung Lim
- Department of Horticulture, Kyungbook National University, Daegu, Korea
| | - Ye-Su Song
- Department of Horticulture, Kangwon National University, Chuncheon, 200-701, Korea
| | - Jong-Hwa Kim
- Department of Horticulture, Kangwon National University, Chuncheon, 200-701, Korea
| | - Nam-Soo Kim
- BK21 Training Program, Department of Molecular Bioscience, Kangwon National University, Chuncheon, 200-701, Korea
- Institute of Biosciences and Biotechnology, Kangwon National University, Chuncheon, 200-701, Korea
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