Molecular Evolution of the trn T UGU ‐ trn F GAA Region in Bryophytes

Structure, variability, and molecular evolution of the trn T‐F region in the Bryophyta (mosses and liverworts) is analyzed based on about 200 sequences of the trn T‐L spacer and trn L 5′ exon, 1000 sequences of the trn L intron, and 800 sequences of the trn L 3′ exon and trn L‐F spacer, including comparisons of lengths, GC contents, sequence similarities, and functional elements. Mutations occurring in the trn L 5′ and 3′ exons, including compensatory base pair changes, and a transition in the trn L anticodon in Takakia lepidozioides, are discussed. All three non‐coding regions display a mosaic structure of highly variable elements (V1 ‐ V3 in the trn T‐L spacer, V4/V5 corresponding to stem‐loop regions P6/P8 in the trn L intron, and V6/V7 in the trn L‐F spacer) and more conserved elements. In the trn L 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 trn T‐L spacer and stem‐loop region P8 of the trn L 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 trn T‐L spacer of mosses. In addition to two putative sigma 70 ‐type promoters in the trn T‐L spacer, a third putative promoter is present in the trn L‐F spacer, although trn L and trn F 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.