Dynamics of Tandem Repetitive Afa-Family Sequences in Triticeae, Wheat-Related Species

Abstract

The Afa-family sequences in wheat-related species, Triticeae, are tandem repetitive sequences of 340 bp. All the analyzed Triticeae species carried the sequences in their genomes, though the copy numbers varied about 100-fold among the species. The nucleotide fragments amplified by PCR were cloned and sequenced, and their behavior in the evolution of Triticeae was analyzed by the neighbor-joining (NJ) method. The sequences in genomes with many copies of this family clustered at independent branches of the phylogenic tree, whereas the sequences in genomes with a few copies did not. This may suggest that Afa-family sequences had amplified several times in the evolution of Triticeae, each using a limited number of different master copies. In addition, the sequences of the A and B genomes of hexaploid common wheat indicated that the Afa-family sequences had not evolved in a concerted manner between the genomes. Furthermore, the sequences of each chromosome of the D genome of this species indicated that the sequences had amplified on all over the D-genome chromosomes in a short period.

CACTA Transposons in Triticeae. A Diverse Family of High-Copy Repetitive Elements

“…This "transposon hypothesis" explains three properties of this repeat family as they were described by Nagaki et al (1998a). First, it was reported that the copy number of Afa repeats is highly variable in different Triticeae spp.…”

“…A surprising finding was that eight Caspar elements contain the previously described Afa repeats (Rayburn and Gill, 1986;Nagaki et al, 1998a). Afa repeats are a class of tandem repeats of approximately 340 bp in size that are believed to be present in all Triticeae spp.…”

“…Afa repeats are a class of tandem repeats of approximately 340 bp in size that are believed to be present in all Triticeae spp. Their copy number, however, was shown to vary up to 100-fold in different Triticeae spp., and they were found in various, genome-specific locations in Triticeae genomes (Nagaki et al, 1998a).…”

“…Second, the mobility of a transposon explains why no chromosome specificity within one species was observed. Third, Nagaki et al (1998a) suggested the presence of a specific mechanism to remove Afa repeats from the genome. The transposon hypothesis can provide this specific mechanism.…”

Single-copy gene fluorescence in situ hybridization and genome analysis: Acc-2 loci mark evolutionary chromosomal rearrangements in wheat

“…2a). Sequences of the D-genome-specific Afa-family repeat pAs1 (Nagaki et al 1995;Nagaki et al 1998) were used to design several oligonucleotide probes. Two of them showed D-genome-specific labeling and were combined ( Table 2).…”