title: Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: GaTe lab, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo Departamento de Botânica, São Paulo, SP Brasil. maria_manetti@hotmail.com <maria_manetti@hotmail.com>
authors.forename: Maria E
authors.initials: ME
authors.lastname: Manetti
authors.forename: Magdalena
authors.initials: M
authors.lastname: Rossi
authors.forename: Ana P P
authors.initials: AP
authors.lastname: Costa
authors.forename: Andrea M
authors.initials: AM
authors.lastname: Clausen
authors.forename: Marie-Anne
authors.initials: MA
authors.lastname: Van Sluys
mesh_terms: D001483:Base Sequence; D019143:Evolution, Molecular; D017343:Genes, Plant; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D020537:RNA, Small Nucleolar / Q000235:genetics; D018626:Retroelements; D016914:Ribonuclease H / Q000235:genetics; D016415:Sequence Alignment; D032322:Solanum / Q000235:genetics*; D013045:Species Specificity; D020079:Terminal Repeat Sequences / Q000235:genetics
chemical_list: D020537:RNA, Small Nucleolar; C117378:RNA, U3 small nucleolar; D018626:Retroelements; D016914:Ribonuclease H