Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution

Abstract

SummaryIn plant species with large genomes such as wheat or barley, genome organization at the level of DNA sequence is largely unknown. The largest sequences that are publicly accessible so far from Triticeae genomes are two 60 kb and 66 kb intervals from barley. Here, we report on the analysis of a 211 kb contiguous DNA sequence from diploid wheat (Triticum monococcum L.). Five putative genes were identi®ed, two of which show similarity to disease resistance genes. Three of the ®ve genes are clustered in a 31 kb gene-enriched island while the two others are separated from the cluster and from each other by large stretches of repetitive DNA. About 70% of the contig is comprised of several classes of transposable elements. Ten different types of retrotransposons were identi®ed, most of them forming a pattern of nested insertions similar to those found in maize and barley. Evidence was found for major deletion, insertion and duplication events within the analysed region, suggesting multiple mechanisms of genome evolution in addition to retrotransposon ampli®cation. Seven types of foldback transposons, an element class previously not described for wheat genomes, were characterized. One such element was found to be closely associated with genes in several Triticeae species and may therefore be of use for the identi®cation of gene-rich regions in these species.

Rapid Genome Divergence at Orthologous Low Molecular Weight Glutenin Loci of the A and Am Genomes of Wheat[W]

“…Three hypothetical genes were predicted in a 16-kb region between TdGlu-A3-1 and TdRGL-1 ( Figure 3B). Finally, a pseudogene of 111 bp that has 70% homology with the protein sequence encoded by the last exon of a gene that encodes a Glabra2-like1 protein, TdHbox-1 ( Figure 3B, gene 8), was found inside a gypsy retrotransposon, Fatima_107G22-2 (Wicker et al, 2001). It is likely that it has been acquired by Fatima_107G22-2.…”

“…Illegitimate recombination and double-strand break repair mechanisms that introduce filler sequences into chromosomes might be responsible for genome restructuring and the formation of truncated genes (Ramakrishna et al, 2002b). The large genome size of wheat is attributable partially to the presence of a large amount of nested long terminal repeat (LTR) retrotransposons, very similar to the situation in maize (SanMiguel et al, 1996;Wicker et al, 2001;Ramakrishna et al, 2002a). The increase of genome size caused by retrotransposons as well as transposons (Wicker et al, 2003) is counteracted by mechanisms that reduce genome size.…”

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

“…Along with polyploidization, accumulation of repetitive DNA, particularly long terminal repeat retrotransposons (LTR-RTs), is the primary mechanism driving plant genome expansion . In large-genome species such as maize, barley, and wheat, LTR-RTs make up more than 60%-80% of their genomes, and the majority of these elements have amplified within the last few million years (SanMiguel et al 1996(SanMiguel et al , 1998Vicient et al 1999;Wicker et al 2001;Bruggmann et al 2006). A particularly striking study shows that Oryza australiensis, a wild species of rice, has accumulated more than 90,000 copies of LTR-RTs during the last three million years, leading to a twofold increase in genome size without polyploidization (Piegu et al 2006).…”

Identification and Preliminary Analysis of Several Centromere‐associated Bacterial Artificial Chromosome Clones from a Diploid Wheat Library

“…That is, the 28 positive clones identified in the present study were obtained from an approximate 319 Mb region, equal to 5.6% of the haploid genome of T. boeoticum (1C=5 700 Mb; Wicker et al 2001), containing at least 32 copies of RCS1. Therefore, the total number of RCS1 sequences in the haploid genome of T. boeoticum was estimated to be 572, at least approximately 82 copies per chromosome, which was similar to that reported for Ae.…”