title: Identification and characterization of plastid trnF(GAA) pseudogenes in four species of Solanum (Solanaceae).
abstract: Non-functional trnF pseudogenes that rarely occur in embryophytes have been found in Solanaceae. We have sequenced the trnL-F intergenic spacer of four species of Solanum, and found duplicated regions of the original trnF gene. These repeats were 94-260 bp long causing large length variation in the trnL-F intergenic spacer resulting from differences in pseudogene copy number (2-4). The duplicated trnF regions are comprised of several highly structured motifs, which were partial residues, or entire parts of the Anticodon, T- and D-domains of the original gene, but all lacked the acceptor stems at the 5'- or 3'-end. Pseudogenes included several transitions and transversions in their sequences compared to the original trnF gene. Among pseudogene copies, T-domains were more frequent and fragmented than D-domain elements. Our results demonstrate that although chloroplast evolution is uniform such structural duplications in the sequences used for phylogenetic reconstructions should be treated with great caution.
authors.affiliation: Department of Plant Biology, University of Helsinki, Helsinki, Finland. peter.poczai@gmail.com
authors.forename: Péter
authors.initials: P
authors.lastname: Poczai
authors.forename: Jaakko
authors.initials: J
authors.lastname: Hyvönen
mesh_terms: D018742:DNA, Chloroplast / Q000737:chemistry / Q000235:genetics; D021901:DNA, Intergenic; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D018628:Gene Dosage; D008969:Molecular Sequence Data; D009154:Mutation; D018087:Plastids / Q000235:genetics*; D011544:Pseudogenes; D017422:Sequence Analysis, DNA; D032322:Solanum / Q000235:genetics*
chemical_list: D018742:DNA, Chloroplast; D021901:DNA, Intergenic; D018744:DNA, Plant