Sequence composition, organization, and evolution of the core Triticeae genome

Abstract

SummaryWe investigated the composition and the basis of genome expansion in the core Triticeae genome using Aegilops tauschii, the D-genome donor of bread wheat. We sequenced an unfiltered genomic shotgun (trs) and a methylation-filtration (tmf) library of A. tauschii, and analyzed wheat expressed sequence tags (ESTs) to estimate the expression of genes and transposable elements (TEs). The sampled D-genome sequences consisted of 91.6% repetitive elements, 2.5% known genes, and 5.9% low-copy sequences of unknown function. TEs constituted 68.2% of the D-genome compared with 50% in maize and 14% in rice. The DNA transposons constituted 13% of the D-genome compared with 2% in maize. TEs were methylated unevenly within and among elements and families, and most were transcribed which contributed to genome expansion in the core Triticeae genome. The copy number of a majority of repeat families increased gradually following polyploidization. Certain TE families occupied discrete chromosome territories. Nested insertions and illegitimate recombination occurred extensively between the TE families, and a majority of the TEs contained internal deletions. The GC content varied significantly among the three sequence sets examined ranging from 42% in tmf to 46% in trs and 52% in the EST. Based on enrichment of genic sequences, methylation-filtration offers one option, although not as efficient as in maize, for isolating gene-rich regions from the large genome of wheat.

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

“…Bread wheat has one of the largest plant genomes (17 Gb), containing about 90% repetitive sequences, 70% of which are transposable elements and a large fraction of microsatellites and tandem repeats (Li et al 2004). BAC-FISH in wheat painted either all chromosomes over their entire length, produced a genome-specific painting, or painted clusters of tandem repeats depending on the content of repetitive sequences in a BAC clone .…”

Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat

“…Sample sequence analysis of a few thousand randomly selected clones with inserts from Aegilops tauschii, the D genome donor of bread wheat, has shown that its nuclear DNA contains Ϸ91.6% repetitive sequences (16). How these repeats are associated with each other and with genes is not well understood.…”

Recurrent Deletions of Puroindoline Genes at the GrainHardnessLocus in Four Independent Lineages of Polyploid Wheat

“…The rate of DNA sequence divergence is much higher in polyploid wheat compared to diploid relatives (for review, see Dubcovsky and Dvorak, 2007). The great abundance of repetitive sequences, especially retroelements, in the wheat genome (Li et al, 2004;Devos et al, 2005) seems to promote gene deletion/duplication events. Chantret et al (2005) reported that the loss of a block of genes, including the Pina and Pinb genes from A and B genomes of tetraploid T. turgidum, occurred independently by illegitimate recombination among retroelements bordering the Ha locus.…”