Molecular evolution of noncoding regions of the chloroplast genome in the Crassulaceae and related species

Abstract

Universal primers were used for PCR amplification of three noncoding regions of chloroplast DNA (cpDNA) in order to study sequence-length variation in the Crassulaceae and in related species. Several length mutations were observed that are of diagnostic value for evolutionary relationships in the Crassulaceae and the Saxifragaceae. Length variation and sequence divergence in the intergenic spacer between the trnL (UAA) 3' exon and the trnF (GAA) gene among 15 species were studied in detail by nucleotide-sequence analysis. A total of 50 insertion/deletion mutations were observed, accounting for a spacer-length variation in the range of 228-360 bp. Eighteen short direct repeat motifs (4-11 bp) and two inverted repeat motifs (7-11 bp) were found to be associated with length variation. Phylogenetic analysis of the sequence data indicated a pattern of relationships that was largely consistent with a previous analysis of cpDNA restriction-site variation. Evaluation of the level of homoplasy in insertion/deletion mutations within a phylogenetic framework revealed that only 1 out of 34 length mutations longer than 2 bp must have had multiple origins. The feasibility of the noncoding chloroplast DNA regions for molecular evolutionary studies is discussed.

A phylogeny of the flowering plant family Apiaceae based on chloroplast DNA rpl16 and rpoC1 intron sequences: towards a suprageneric classification of subfamily Apioideae

“…The resultant topology was then compared to the one inferred when gaps were omitted as additional characters. Previous investigations of cpDNA rpoC1 intron and other noncoding sequences (e.g., van Ham et al, 1994) have revealed that indels contain much phylogenetic information and, indeed, may provide particularly clear indications of relationship.…”

Chloroplast Phylogeny of Asplenioid Ferns based on rbcL and trnL-F Spacer Sequences (Polypodiidae, Aspleniaceae) and its Implications for Biogeography

“…: Rendering all genera of the German flora monophyletic ters (Kadereit & al. 1997 Crassulaceae (J. T. Klein) Sedum L. has repeatedly been shown to be highly polyphyletic (van Ham & al. 1994;van Ham & 't Hart 1998;Mort & al.…”

The Chloroplast trnT–trnF Region in the Seed Plant Lineage Gnetales

“…Other tRNA genes, however, lack prokaryote-type promoter elements and instead have internal promoter elements that are highly conserved (Galli et al 1981;Gruissem et al 1986;Cheng et al 1997). Putative promoter elements upstream of trnT as well as trnF (Steinmetz et al 1983;Kanno and Hirai 1993;van Ham et al 1994) suggest that these genes can be expressed independently, although no experimental study has been done. Independent expression is also indicated by the opposite orientation of the tRNA Thr (UGU) gene relative to the tRNA Leu (UAA) and tRNA Phe (GAA) genes (Figs.…”