title: Plastid trnF pseudogenes are present in Jaltomata, the sister genus of Solanum (Solanaceae): molecular evolution of tandemly repeated structural mutations.
abstract: Extensive gene duplication arranged in a tandem array is rare in the plastome of embryophytes. Interestingly, we found pseudogene copies of the trnF gene in the genus Jaltomata, the sister genus of Solanum where such gene duplication has been previously reported. In each Jaltomata sequence available we found two pseudogene copies in close 5'-proximity to the original functional gene. The size of each pseudogene copy ranged between 17 and 48 bp and the anticodon domain was identified as the most conserved element. A common ATT(G)n motif is particularly interesting and its modifications were found to border the 3' of the duplicated regions. Other motifs were partial residues, or entire parts of the T- and D-domains, and both domains proved to be variable in length among the pseudogenes identified. The residues of the 3' and 5' acceptor stem were not found among the copies. We further compared the newly discovered copies of Jaltomata with those ones previously described from Solanum and inferred phylogenetic relationships of the copies aligned. The evolution of Solanum copies, in contrast to Jaltomata, is hard to explain as resulting only in parsimonious changes since reticulate evolutionary patterns were detected among the copies. The dynamic evolutionary patterns of Solanum might be explained by possible inter- or intrachromosomal recombination.
authors: Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, FIN-00014 Helsinki, Finland. Electronic address: peter.poczai@gmail.com.
authors: Péter
authors: P
authors: Poczai
authors: Jaakko
authors: J
authors: Hyvönen
mesh_terms: D018742:DNA, Chloroplast / Q000235:genetics; D019143:Evolution, Molecular; D009154:Mutation; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D018087:Plastids / Q000235:genetics; D011544:Pseudogenes / Q000235:genetics*; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D019657:Solanaceae / Q000235:genetics*; D020080:Tandem Repeat Sequences / Q000235:genetics*
chemical_list: D018742:DNA, Chloroplast; D010940:Plant Proteins
keywords: Chloroplast DNA; EPT; Gene duplications; IGS; MCP; Molecular recombination; NNet; PSC; Solanaceae; Tandem repeats; equally parsimonious tree; intergenic spacer; multiple change point model; neighbor net; pseudogene copy; tRNA; transfer RNA; transfer RNA for leucine; transfer RNA for phenylalanine; transfer RNA for threonine; trnF; trnL; trnT