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Open Access Short report

Discovery of novel plastid phenylalanine (trnF) pseudogenes defines a distinctive clade in Solanaceae

Péter Poczai* and Jaakko Hyvönen

Author Affiliations

Plant Biology, Department of Biosciences, University of Helsinki, PO Box 65, Helsinki, FIN-00014, Finland

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SpringerPlus 2013, 2:459  doi:10.1186/2193-1801-2-459

Published: 12 September 2013

Abstract

Background

The plastome of embryophytes is known for its high degree of conservation in size, structure, gene content and linear order of genes. The duplication of entire tRNA genes or their arrangement in a tandem array composed by multiple pseudogene copies is extremely rare in the plastome. Pseudogene repeats of the trnF gene have rarely been described from the chloroplast genome of angiosperms.

Findings

We report the discovery of duplicated copies of the original phenylalanine (trnFGAA) gene in Solanaceae that are specific to a larger clade within the Solanoideae subfamily. The pseudogene copies are composed of several highly structured motifs that are partial residues or entire parts of the anticodon, T- and D-domains of the original trnF gene.

Conclusions

The Pseudosolanoid clade consists of 29 genera and includes many economically important plants such as potato, tomato, eggplant and pepper.

Keywords:
Chloroplast DNA (cpDNA); Gene duplications; Phylogeny; Plastome evolution; Tandem repeats; trnL-trnF; Solanaceae