Tags

Type your tag names separated by a space and hit enter

LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species.
Genetica. 2015 Jun; 143(3):343-52.G

Abstract

LTR-retrotransposons are ubiquitous and highly abundant in plant genomes. Moreover, LTR-retrotransposons can often cause genome obesity in plants. Although Lilium species have been known carrying large genomes among flowering plants, reports on the LTR-retrotransposons in Lilium species are rather limited. We isolated a novel Ty3/gypsy-like retrotransposon, LIRE-del, and two Ty1/copia-like retrotransposons, a LIRE-del and an unclassified, from a fosmid clone of Lilium longiflorum. Decayed internal ORF sequences indicated that they were non-autonomous elements. IRAP protocol was developed based on the LTR sequences of the isolated LTR-retrotransposons. Fourteen primer combinations showed clear distinctive PCR amplification bands that were highly informative in the analysis of species relationship among Lilium species. The phylogenetic relationship based on the IRAP profile revealed some discordant with phylogenetic studies based on the ITS sequences of 45S ribosomal gene and matK gene variations in a few species. Thus, the phylogenetic relationship among Lilium species may need to be re-evaluated with other tools such as cross compatibility and selectively neutral genetic markers.

Authors+Show Affiliations

Department of Molecular Bioscience, Kangwon National University, Chuncheon, 200-701, Korea.No 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

25787319

Citation

Lee, Sung-Il, et al. "LTR-retrotransposons and Inter-retrotransposon Amplified Polymorphism (IRAP) Analysis in Lilium Species." Genetica, vol. 143, no. 3, 2015, pp. 343-52.
Lee SI, Kim JH, Park KC, et al. LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species. Genetica. 2015;143(3):343-52.
Lee, S. I., Kim, J. H., Park, K. C., & Kim, N. S. (2015). LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species. Genetica, 143(3), 343-52. https://doi.org/10.1007/s10709-015-9833-6
Lee SI, et al. LTR-retrotransposons and Inter-retrotransposon Amplified Polymorphism (IRAP) Analysis in Lilium Species. Genetica. 2015;143(3):343-52. PubMed PMID: 25787319.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - LTR-retrotransposons and inter-retrotransposon amplified polymorphism (IRAP) analysis in Lilium species. AU - Lee,Sung-Il, AU - Kim,Jong-Hwa, AU - Park,Kyong-Cheul, AU - Kim,Nam-Soo, Y1 - 2015/03/19/ PY - 2014/09/01/received PY - 2015/03/16/accepted PY - 2015/3/20/entrez PY - 2015/3/20/pubmed PY - 2015/10/1/medline SP - 343 EP - 52 JF - Genetica JO - Genetica VL - 143 IS - 3 N2 - LTR-retrotransposons are ubiquitous and highly abundant in plant genomes. Moreover, LTR-retrotransposons can often cause genome obesity in plants. Although Lilium species have been known carrying large genomes among flowering plants, reports on the LTR-retrotransposons in Lilium species are rather limited. We isolated a novel Ty3/gypsy-like retrotransposon, LIRE-del, and two Ty1/copia-like retrotransposons, a LIRE-del and an unclassified, from a fosmid clone of Lilium longiflorum. Decayed internal ORF sequences indicated that they were non-autonomous elements. IRAP protocol was developed based on the LTR sequences of the isolated LTR-retrotransposons. Fourteen primer combinations showed clear distinctive PCR amplification bands that were highly informative in the analysis of species relationship among Lilium species. The phylogenetic relationship based on the IRAP profile revealed some discordant with phylogenetic studies based on the ITS sequences of 45S ribosomal gene and matK gene variations in a few species. Thus, the phylogenetic relationship among Lilium species may need to be re-evaluated with other tools such as cross compatibility and selectively neutral genetic markers. SN - 1573-6857 UR - https://www.unboundmedicine.com/medline/citation/25787319/LTR_retrotransposons_and_inter_retrotransposon_amplified_polymorphism__IRAP__analysis_in_Lilium_species_ L2 - https://doi.org/10.1007/s10709-015-9833-6 DB - PRIME DP - Unbound Medicine ER -