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Isolation and characterization of novel Ty1-copia-like retrotransposons from lily.
Genome. 2013 Sep; 56(9):495-503.G

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.

Authors+Show Affiliations

a BK21 Training Program, Department of Molecular Bioscience, Kangwon National University, Chuncheon, 200-701, Korea.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24168670

Citation

Lee, Sung-Il, et al. "Isolation and Characterization of Novel Ty1-copia-like Retrotransposons From Lily." Genome, vol. 56, no. 9, 2013, pp. 495-503.
Lee SI, Park KC, Son JH, et al. Isolation and characterization of novel Ty1-copia-like retrotransposons from lily. Genome. 2013;56(9):495-503.
Lee, S. I., Park, K. C., Son, J. H., Hwang, Y. J., Lim, K. B., Song, Y. S., Kim, J. H., & Kim, N. S. (2013). Isolation and characterization of novel Ty1-copia-like retrotransposons from lily. Genome, 56(9), 495-503. https://doi.org/10.1139/gen-2013-0088
Lee SI, et al. Isolation and Characterization of Novel Ty1-copia-like Retrotransposons From Lily. Genome. 2013;56(9):495-503. PubMed PMID: 24168670.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Isolation and characterization of novel Ty1-copia-like retrotransposons from lily. AU - Lee,Sung-Il, AU - Park,Kyong-Cheul, AU - Son,Jae-Han, AU - Hwang,Youn-Jung, AU - Lim,Ki-Byung, AU - Song,Ye-Su, AU - Kim,Jong-Hwa, AU - Kim,Nam-Soo, Y1 - 2013/09/05/ PY - 2013/10/31/entrez PY - 2013/10/31/pubmed PY - 2014/5/3/medline SP - 495 EP - 503 JF - Genome JO - Genome VL - 56 IS - 9 N2 - 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. SN - 1480-3321 UR - https://www.unboundmedicine.com/medline/citation/24168670/Isolation_and_characterization_of_novel_Ty1_copia_like_retrotransposons_from_lily_ L2 - https://nrc-prod.literatumonline.com/doi/10.1139/gen-2013-0088?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub=www.ncbi.nlm.nih.gov DB - PRIME DP - Unbound Medicine ER -