Molecular evolution of the trnTUGU-trnFGAA region in Bryophytes.

Abstract

Structure, variability, and molecular evolution of the trnT-F region in the Bryophyta (mosses and liverworts) is analyzed based on about 200 sequences of the trnT-L spacer and trnL 5' exon, 1000 sequences of the trnL intron, and 800 sequences of the trnL 3' exon and trnL-F spacer, including comparisons of lengths, GC contents, sequence similarities, and functional elements. Mutations occurring in the trnL 5' and 3' exons, including compensatory base pair changes, and a transition in the trnL anticodon in Takakia lepidozioides, are discussed. All three non-coding regions display a mosaic structure of highly variable elements (V1 - V3 in the trnT-L spacer, V4/V5 corresponding to stem-loop regions P6/P8 in the trnL intron, and V6/V7 in the trnL-F spacer) and more conserved elements. In the trnL intron this structure is a consequence of the defined secondary structure necessary for correct splicing, whereas in both spacers conserved regions are restricted to promoter elements. At least the highly variable regions in the trnT-L spacer and stem-loop region P8 of the trnL intron seem to evolve independently in the major bryophyte lineages and are therefore not suitable for high taxonomic level phylogenetic reconstructions. In mosses, a trend of length reduction towards the more derived lineages is observed in all three non-coding regions. GC contents are mostly linked to sequence variability, with the conserved regions being more GC rich and the more variable AT rich. The lowest GC values (< 10 %) are found in the trnT-L spacer of mosses. In addition to two putative sigma (70)-type promoters in the trnT-L spacer, a third putative promoter is present in the trnL-F spacer, although trnL and trnF are assumed to be co-transcribed. Consensus sequences are provided for the -35 and -10 sequences of the major bryophyte lineages. The third promoter is part of a hairpin secondary structure, whose loop region is highly homoplastic in mosses due to an inversion occurring independently in non-related taxa, even at the intraspecific level.