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

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; Solanaceae; Tandem repeats; trnL-trnF.

Figure 1

Phylogeny of Solanaceae and the distribution and schematic structure oftrnF pseudogene copies. a) Suprageneric groups recognized are indicted to the right on the tree, while major clades are collapsed at the base node and their names follow Olmstead et al. (2008). The new Pseudosolanoid clade united by the presence of pseudogenic trnF gene duplication is marked with ‘ψ’ in the Solanoideae subfamily. b) The schematic representation of the plastidic trnL-F spacer region in Solanaceae and the intercalated pseudogene copies (PSC) in the intergenic spacer region close to 5′ of the trnF gene. Pseudogene repeats are variable in number and structure and are found after the putative promoter motifs that are also variable among species. The spacer region between the first PSC and promoter motifs consists of intergenic repeats of variable length. Each PSC is separated by a common bordering motif (ATTG) at the 5′end.