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TARE1, a mutated Copia-like LTR retrotransposon followed by recent massive amplification in tomato.
PLoS One. 2013; 8(7):e68587.Plos

Abstract

Long terminal repeat retrotransposons (LTR-RTs) are the major DNA components in flowering plants. Most LTR-RTs contain dinucleotides 'TG' and 'CA' at the ends of the two LTRs. Here we report the structure, evolution, and propensity of a tomato atypical retrotransposon element (TARE1) with both LTRs starting as 'TA'. This family is also characterized by high copy numbers (354 copies), short LTR size (194 bp), extremely low ratio of solo LTRs to intact elements (0.05∶1), recent insertion (most within 0.75∼1.75 million years, Mys), and enrichment in pericentromeric region. The majority (83%) of the TARE1 elements are shared between S. lycopersicum and its wild relative S. pimpinellifolium, but none of them are found in potato. In the present study, we used shared LTR-RTs as molecular markers and estimated the divergence time between S. lycopersicum and S. pimpinellifolium to be <0.5 Mys. Phylogenetic analysis showed that the TARE1 elements, together with two closely related families, TARE2 and TGRE1, have formed a sub-lineage belonging to a Copia-like Ale lineage. Although TARE1 and TARE2 shared similar structural characteristics, the timing, scale, and activity of their amplification were found to be substantially different. We further propose a model wherein a single mutation from 'G' to 'A' in 3' LTR followed by amplification is responsible for the origin of TARE1, thus providing evidence that the proliferation of a spontaneous mutation can be mediated by the amplification of LTR-RTs at the level of RNA.

Authors+Show Affiliations

Bioinformatics Group, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China.No 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

23861922

Citation

Yin, Hao, et al. "TARE1, a Mutated Copia-like LTR Retrotransposon Followed By Recent Massive Amplification in Tomato." PloS One, vol. 8, no. 7, 2013, pp. e68587.
Yin H, Liu J, Xu Y, et al. TARE1, a mutated Copia-like LTR retrotransposon followed by recent massive amplification in tomato. PLoS One. 2013;8(7):e68587.
Yin, H., Liu, J., Xu, Y., Liu, X., Zhang, S., Ma, J., & Du, J. (2013). TARE1, a mutated Copia-like LTR retrotransposon followed by recent massive amplification in tomato. PloS One, 8(7), e68587. https://doi.org/10.1371/journal.pone.0068587
Yin H, et al. TARE1, a Mutated Copia-like LTR Retrotransposon Followed By Recent Massive Amplification in Tomato. PLoS One. 2013;8(7):e68587. PubMed PMID: 23861922.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - TARE1, a mutated Copia-like LTR retrotransposon followed by recent massive amplification in tomato. AU - Yin,Hao, AU - Liu,Jing, AU - Xu,Yingxiu, AU - Liu,Xing, AU - Zhang,Shaoling, AU - Ma,Jianxin, AU - Du,Jianchang, Y1 - 2013/07/04/ PY - 2013/03/20/received PY - 2013/06/05/accepted PY - 2013/7/18/entrez PY - 2013/7/19/pubmed PY - 2014/2/4/medline SP - e68587 EP - e68587 JF - PloS one JO - PLoS One VL - 8 IS - 7 N2 - Long terminal repeat retrotransposons (LTR-RTs) are the major DNA components in flowering plants. Most LTR-RTs contain dinucleotides 'TG' and 'CA' at the ends of the two LTRs. Here we report the structure, evolution, and propensity of a tomato atypical retrotransposon element (TARE1) with both LTRs starting as 'TA'. This family is also characterized by high copy numbers (354 copies), short LTR size (194 bp), extremely low ratio of solo LTRs to intact elements (0.05∶1), recent insertion (most within 0.75∼1.75 million years, Mys), and enrichment in pericentromeric region. The majority (83%) of the TARE1 elements are shared between S. lycopersicum and its wild relative S. pimpinellifolium, but none of them are found in potato. In the present study, we used shared LTR-RTs as molecular markers and estimated the divergence time between S. lycopersicum and S. pimpinellifolium to be <0.5 Mys. Phylogenetic analysis showed that the TARE1 elements, together with two closely related families, TARE2 and TGRE1, have formed a sub-lineage belonging to a Copia-like Ale lineage. Although TARE1 and TARE2 shared similar structural characteristics, the timing, scale, and activity of their amplification were found to be substantially different. We further propose a model wherein a single mutation from 'G' to 'A' in 3' LTR followed by amplification is responsible for the origin of TARE1, thus providing evidence that the proliferation of a spontaneous mutation can be mediated by the amplification of LTR-RTs at the level of RNA. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/23861922/TARE1_a_mutated_Copia_like_LTR_retrotransposon_followed_by_recent_massive_amplification_in_tomato_ L2 - https://dx.plos.org/10.1371/journal.pone.0068587 DB - PRIME DP - Unbound Medicine ER -