The intergenic region between the Vicia faba chloroplast tRNACAA Leu and tRNAUAA Leu genes contains a partial copy of the split tRNAUAA Leu gene

Abstract

A cluster of three tRNA genes located on fragment Bam6a from Vicia faba chloroplast DNA has been sequenced: it contains the genes for tRNA(CAALeu), tRNA(UAALeu) and tRNA(Phe). The two tRNA(Leu) genes are separated by 443 bp and are transcribed divergently from different DNA strands. The intergenic region contains a series of short repeats and a partial copy of the split tRNA(UAALeu) gene which includes 100 bp of the 5' flanking region, 35 bp of the 5'exon and the first 42 bp of the intron. It is possible that some of these duplications occurred upon the rearrangement of the two tRNA(Leu) genes in broad bean (and in pea) or upon the deletion of one copy of the inverted repeat, since in all other higher plant chloroplast genomes studied so far these two tRNA(Leu) genes are located far apart on the genome, one being in the inverted repeat region, the other one in the large single copy region. The tRNA(Phe) and tRNA(UAALeu) are encoded by the same DNA strand, and separated by 110 bp.

Chloroplast DNA variation and reticulate evolution in sexual and apomictic sections of dandelions

“…The duplications and deletions of the pseudogene copies were here an obstacle for reconstructing the phylogeny. Partially duplicated tRNA genes have occasionally been reported in chloroplast genomes and may be associated with major genetic rearrangements, such as inversions (Bonnard et al 1985; Howe et al 1988; Hiratsuka et al 1989). Once duplicated, the partial tRNA gene may give rise to genetic instability and produce a variable number of short repeats (Hipkins et al 1995).…”

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

“…Reports of short (4mers to 20mers) tandem repeats within the trnL-trnF IGS were given by Isoda et al (2000), Bellstedt et al (2001), and Kamiya et al (2002), but in these cases the repeated motifs did not show any significant similarities to tRNA genes. Full or partial duplicates of some other transfer RNA genes, including trnT GGU , trnT GUA , trnS GCU , trnL UAA , trnL CAA , trnG, trnP, and trnY GUA , are reviewed in Vijverberg and Bachmann (1999) and Bonnard et al (1985), but these copies were not necessarily arranged in tandem repeats. One out of 10 000 most parsimonious trees reconstructed from the alignment of Boechera copies shown in Fig.…”

Molecular evolution of a tandemly repeated trnF(GAA) gene in the chloroplast genomes of Microseris (Asteraceae) and the use of structural mutations in phylogenetic analyses

“…Dispersed and partially duplicated tRNA (pseudo)genes are more often reported. Apart from the conifers and grasses mentioned, they concern mostly cpDNA of legumes (Mubumbila, Crouse, and Weil 1984;Bonnard, Weil, and Steinmetz 1985). The cpDNAs of these taxa are known for complex rearrangements (see Introduction), and tRNA (pseudo)genes have been associated with several of these rearrangements (e.g., Wolfe 1988;Shimada and Sugiura 1989), particularly with inversion endpoints Tsai and Strauss 1989).…”