Ancient paralogy in the cpDNA trnL‐F region in Annonaceae: implications for plant molecular systematics

Abstract

The plastid trnL-F region has proved useful in molecular phylogenetic studies addressing diverse evolutionary questions from biogeographic history to character evolution in a broad range of plant groups. An important assumption for phylogenetic reconstruction is that data used in combined analyses contain the same phylogenetic signal. The trnL-F region is often used in combined analyses of multiple chloroplast markers. These markers are assumed to contain congruent phylogenetic signal due to lack of recombination. Here we show that trnL-F sequences display a phylogenetic signal conflicting with that of other chloroplast markers in Annonaceae, and we demonstrate that this conflict results from ancient paralogy. TrnL-F copy 2 diverged from trnL-F copy 1 (as used in family-wide phylogenetic analyses) in a direct ancestor of the Annonaceae. Although this divergence dates back 88 million years or more, the exons of both copies appear to be intact. In this case, assuming that (putative) chloroplast markers contain the same phylogenetic signal results in an incorrect topology and an incorrect estimate of ages. Our study demonstrates that researchers should be cautious when interpreting gene phylogenies, irrespective of the genome from which they are presumed to have been sampled.

Development of molecular markers for determining continental origin of wood from white oaks (QuercusL. sect.Quercus)

“…Similarly, differentiation within the genus Populus failed using trnLF [38]. Nevertheless, there are other examples for successful use of this marker in molecular systematics [39,40] and citations therein) and for unraveling of the phylogeny of different plant species [41]. Similarly, trnCD and trnDT have been used in comprehensive studies of chloroplast DNA diversity in European white oaks [42][43][44][45][46][47][48][49][50][51].…”

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

“…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.…”

Genetic diversity in tetraploid switchgrass revealed by AFLP marker polymorphisms

“…Missaoui et al (2006) also found polymorphism for the trnL (UAA) chloroplastic marker associated with upland and lowland ecotypes. The trnL UAA intron region is in the chloroplasts of all plants (Pirie et al, 2007). It is part of the chloroplast DNA and is transferred through the maternal parent (Martinez-Reyna et al, 2001).…”