Plastidic trnF_UUC Pseudogenes in North American Genus Boechera (Brassicaceae): Mechanistic Aspects of Evolution

Abstract

The origin and maintenance of a plastidic tandem repeat next to the TRNF (UUC) gene were analyzed in the genus BOECHERA in a phylogenetic context and were compared to published analogous examples that emerged in parallel in the Asteraceae and Juncaceae, respectively. Although we identified some features common to these taxonomic groups with respect to structure and origin of the region, obvious differences were encountered, which argue against a specific mechanism or evolutionary principle underlying the parallel origin and maintenance of the TRNF-tandem repeats in those families. In contrast to the situation in the Asteraceae, no reciprocal recombinant repeat types have been observed in the Brassicaceae. Forty copy types, classified into three groups, were isolated from 103 chloroplast haplotypes of BOECHERA and it was demonstrated that they are composed of four subregions of various origins. We discuss various mutation mechanisms such as DNA replication slippage, and inter- and intrachromosomal recombination which were reported to mediate variation in copy numbers and other types of observed sequence length polymorphism. It is shown that the observed molecular structure of the tandem repeat region did not fully fit the particular patterns expected under a scenario of evolution including any of the known mechanisms. Nevertheless, it appeared that intermolecular unequal crossing-over is most likely the driving force in the evolution of this tandem repeat. However, it remains to be explained, why no reciprocal recombinant copy types have been observed. The reconstructed phylogenetic relationships among copies reflected different evolutionary scenarios as follows: (1) A single and ancient origin of copies pre-dates the radiation of BOECHERA. (2) Parallel expansion and shortening of the tandem repeat within different BOECHERA lineages. (3) Conservation of the first copy, as it was the only one present in all chloroplast haplotypes.

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

“…This leads to the assumption of complex or at least different molecular read mechanism driven development and evolution. It has been previously concluded that tandemly repeated trnF (GAA) pseudogenes are undergoing parallel independent changes which are mediated by complex processes of illegitimate recombination (see Dobeš et al 2007). Ansell et al (2007) studying trnF (GAA) pseudogenes in Arabidopsis lyrata (L.) O'Kane and Al-Shehbaz populations found that disperse repeats which share similar secondary structure patterns interact and facilitate reciprocal exchange of structural motifs between copies through intra-and intermolecular recombinations.…”

Using Chloroplast trnF Pseudogenes for Phylogeography in Arabidopsis Lyrata

“…Recombination by this method could act to increase pseudogene variation through uneven crossing over [8,9] (Appendix 1).…”

“…Since the development of universal primers [10] the non-coding trnL (UAA)-trnF(GAA) intergenic spacer region (trnL-F IGS) of the chloroplast genome has been extensively utilized for plant evolutionary analysis [9,[11][12][13][14] (Appendix 2). In the Brassicaceae, the trnL-F region from at least 20 genera has been documented to contain multiple copies of a duplicated trnF pseudogene [11,13,14].…”

DNA Based Techniques for Studying Genetic Diversity

“…It has been suggested that this will be mediated by short repeats formed by slip-strand mispairing (Ogihara et al, 1988), and intermolecular recombination between two genome copies of the plastids because the plastid contains a large number of copies of the chloroplast genome. Recombination by this method could act to increase pseudogene variation through uneven crossing over (Dobes, 2007). The difference in copy number of pseudogenes can be used in genetic diversify studies as well as classification.…”