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Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera

BACKGROUND: Tnt1 was the first active plant retrotransposon identified in tobacco after nitrate reductase gene disruption. The Tnt1 superfamily comprises elements from Nicotiana (Tnt1 and Tto1) and Lycopersicon (Retrolyc1 and Tlc1) species. The study presented here was conducted to characterise Tnt1...

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Autores principales: Manetti, Maria E, Rossi, Magdalena, Costa, Ana PP, Clausen, Andrea M, Van Sluys, Marie-Anne
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1838419/
https://www.ncbi.nlm.nih.gov/pubmed/17343755
http://dx.doi.org/10.1186/1471-2148-7-34
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author Manetti, Maria E
Rossi, Magdalena
Costa, Ana PP
Clausen, Andrea M
Van Sluys, Marie-Anne
author_facet Manetti, Maria E
Rossi, Magdalena
Costa, Ana PP
Clausen, Andrea M
Van Sluys, Marie-Anne
author_sort Manetti, Maria E
collection PubMed
description BACKGROUND: Tnt1 was the first active plant retrotransposon identified in tobacco after nitrate reductase gene disruption. The Tnt1 superfamily comprises elements from Nicotiana (Tnt1 and Tto1) and Lycopersicon (Retrolyc1 and Tlc1) species. The study presented here was conducted to characterise Tnt1-related sequences in 20 wild species of Solanum and five cultivars of Solanum tuberosum. RESULTS: Tnt1-related sequences were amplified from total genomic DNA using a PCR-based approach. Purified fragments were cloned and sequenced, and clustering analysis revealed three groups that differ in their U3 region. Using a network approach with a total of 453 non-redundant sequences isolated from Solanum (197), Nicotiana (140) and Lycopersicon (116) species, it is demonstrated that the Tnt1 superfamily can be treated as a population to resolve previous phylogenetic multifurcations. The resulting RNAseH network revealed that sequences group according to the Solanaceae genus, supporting a strong association with the host genome, whereas tracing the U3 region sequence association characterises the modular evolutionary pattern within the Tnt1 superfamily. Within each genus, and irrespective of species, nearly 20% of Tnt1 sequences analysed are identical, indicative of being part of an active copy. The network approach enabled the identification of putative "master" sequences and provided evidence that within a genus these master sequences are associated with distinct U3 regions. CONCLUSION: The results presented here support the hypothesis that the Tnt1 superfamily was present early in the evolution of Solanaceae. The evidence also suggests that the RNAseH region of Tnt1 became fixed at the host genus level whereas, within each genus, propagation was ensured by the diversification of the U3 region. Different selection pressures seemed to have acted on the U3 and RNAseH modules of ancestral Tnt1 elements, probably due to the distinct functions of these regions in the retrotransposon life cycle, resulting in both co evolution and adaptation of the element population with its host.
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spelling pubmed-18384192007-03-28 Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera Manetti, Maria E Rossi, Magdalena Costa, Ana PP Clausen, Andrea M Van Sluys, Marie-Anne BMC Evol Biol Research Article BACKGROUND: Tnt1 was the first active plant retrotransposon identified in tobacco after nitrate reductase gene disruption. The Tnt1 superfamily comprises elements from Nicotiana (Tnt1 and Tto1) and Lycopersicon (Retrolyc1 and Tlc1) species. The study presented here was conducted to characterise Tnt1-related sequences in 20 wild species of Solanum and five cultivars of Solanum tuberosum. RESULTS: Tnt1-related sequences were amplified from total genomic DNA using a PCR-based approach. Purified fragments were cloned and sequenced, and clustering analysis revealed three groups that differ in their U3 region. Using a network approach with a total of 453 non-redundant sequences isolated from Solanum (197), Nicotiana (140) and Lycopersicon (116) species, it is demonstrated that the Tnt1 superfamily can be treated as a population to resolve previous phylogenetic multifurcations. The resulting RNAseH network revealed that sequences group according to the Solanaceae genus, supporting a strong association with the host genome, whereas tracing the U3 region sequence association characterises the modular evolutionary pattern within the Tnt1 superfamily. Within each genus, and irrespective of species, nearly 20% of Tnt1 sequences analysed are identical, indicative of being part of an active copy. The network approach enabled the identification of putative "master" sequences and provided evidence that within a genus these master sequences are associated with distinct U3 regions. CONCLUSION: The results presented here support the hypothesis that the Tnt1 superfamily was present early in the evolution of Solanaceae. The evidence also suggests that the RNAseH region of Tnt1 became fixed at the host genus level whereas, within each genus, propagation was ensured by the diversification of the U3 region. Different selection pressures seemed to have acted on the U3 and RNAseH modules of ancestral Tnt1 elements, probably due to the distinct functions of these regions in the retrotransposon life cycle, resulting in both co evolution and adaptation of the element population with its host. BioMed Central 2007-03-07 /pmc/articles/PMC1838419/ /pubmed/17343755 http://dx.doi.org/10.1186/1471-2148-7-34 Text en Copyright © 2007 Manetti et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Manetti, Maria E
Rossi, Magdalena
Costa, Ana PP
Clausen, Andrea M
Van Sluys, Marie-Anne
Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera
title Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera
title_full Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera
title_fullStr Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera
title_full_unstemmed Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera
title_short Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera
title_sort radiation of the tnt1 retrotransposon superfamily in three solanaceae genera
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1838419/
https://www.ncbi.nlm.nih.gov/pubmed/17343755
http://dx.doi.org/10.1186/1471-2148-7-34
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