Molecular evolution of a tandemly repeated trnF(GAA) gene in the chloroplast genomes of Microseris (Asteraceae) and the use of structural mutations in phylogenetic analyses

Abstract

We sequenced the first ca. 900 bp of the 5Ј-trnL(UAA)-trnV(UAC)/ndhJ region of the chloroplast DNA of different Microseris accessions in order to resolve homoplasious length variation detected in the trnL(UAA)-trnF(GAA) region. We found two to four tandemly repeated trnF genes in the species of Microseris (Asteraceae, Lactuceae) and two in their sister genus Uropappus. Sequences indicated nonhomologous transitions between two, three, and four trnF genes in different Microseris taxa. Independent origins of similar trnF copy numbers were inferred from a chloroplast phylogeny of Microseris. The taxa involved grow on separate continents, supporting parallel origins of similar length variants. The changes in trnF copy numbers were best explained by interchromosomal recombination with unequal crossing over. The 5Ј copies of the repeats showed the highest sequence conservation, suggesting that these copies are likely to be functional trnF genes, whereas the other ones probably represent pseudogenes. Our results show that length polymorphisms accumulate once a duplicated sequence has become incorporated. Due to parallel gains of similar trnF copy numbers, homoplasious length variation was introduced into the data matrix. The data demonstrate that length polymorphisms cannot be used as indicators for phylogenetic distance unless they can be analyzed at the sequence level.

Identification and characterization of plastid trnF(GAA) pseudogenes in four species of Solanum (Solanaceae)

“…Therefore, the overall structure of the chloroplast genome, at least in embryophytes, is considered to be generally conserved (Ansell et al 2007), and interspersed by short structural changes (\10 bp) that are frequently detected. However, it seems that cpDNA pseudogenes behave differently since all the reported pseudogenes from different plant families were structurally variable (Vijverberg and Bachmann 1999;Drábkova et al 2004;Koch et al 2007). This leads to the assumption of complex or at least different molecular read mechanism driven development and evolution.…”

“…Borsch et al 2003); otherwise conflicting phylogenies could be inferred (e.g. Vijverberg and Bachmann 1999). These inconsistencies may be due to specific recombination mechanisms which are accompanied by high mutational rates and trigger the parallel generation of particular molecular changes, like the integration of tandem repeats or the formation of pseudogenic copies ).…”

“…The occurrence of plastid trnF pseudogenes in seed plants is extremely rare (Schmickl et al 2009). They have been only described from a few plant genera in Asteraceae (Vijverberg and Bachmann 1999), Annonaceae (Pirie et al 2007), Brassicaceae ) and Juncaceae (Drábkova et al 2004), but they have not been reported in Solanaceae.…”

Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data

“…Most structural mutations in cpDNA are small indels, from 1 to 10 bp (reviewed by Vijverberg and Bachmann 1999), however, a general feature of trnT-L-F region is the occurrence of large indels. Juncus trifidus is unique among the other Juncus species by a 322-bp deletion in the trnL intron and an 84-bp insertion in the trnL-F spacer.…”

Análises filogenéticas no gênero Anacardium

“…Esse único resultado foi bastante surpreendente, uma vez que foi obtido para uma região que não é a mais indicada para estudos desse tipo (VIJVERBERG; BACHMANN, 1999;VARGAS;JURY, 1999), a não ser que haja variação interespecífica suficiente, que foi a proposta desse trabalho. de Mitchell e Mori (1987), com muito menos informações disponíveis para análise.…”