Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

Abstract

To improve our understanding of the organization and evolution of the wheat (Triticum aestivum) genome, we sequenced and annotated 13-Mb contigs (18.2 Mb) originating from different regions of its largest chromosome, 3B (1 Gb), and produced a 2x chromosome survey by shotgun Illumina/Solexa sequencing. All regions carried genes irrespective of their chromosomal location. However, gene distribution was not random, with 75% of them clustered into small islands containing three genes on average. A twofold increase of gene density was observed toward the telomeres likely due to high tandem and interchromosomal duplication events. A total of 3222 transposable elements were identified, including 800 new families. Most of them are complete but showed a highly nested structure spread over distances as large as 200 kb. A succession of amplification waves involving different transposable element families led to contrasted sequence compositions between the proximal and distal regions. Finally, with an estimate of 50,000 genes per diploid genome, our data suggest that wheat may have a higher gene number than other cereals. Indeed, comparisons with rice (Oryza sativa) and Brachypodium revealed that a high number of additional noncollinear genes are interspersed within a highly conserved ancestral grass gene backbone, supporting the idea of an accelerated evolution in the Triticeae lineages.

Draft genome of the wheat A-genome progenitor Triticum urartu

“…About 66.88% of the T. urartu assembly was identified as repetitive elements, including long terminal repeat retrotransposons (49.07%), DNA transposons (9.77%) and unclassified elements (8.04%) (Supplementary Information). The proportion of repetitive DNA was lower than the roughly 80% previously reported 16 , which is probably due to a decreased incorporation of repeat sequence reads into the assemblies.…”

Unlocking the Barley Genome by Chromosomal and Comparative Genomics

“…An estimate of 50,000 genes was given for a diploid wheat genome on the basis of megabase-sized BAC contig sequencing of chromosome 3B and short-read (Illumina/Solexa) survey sequencing of sorted 3B chromosomes (Choulet et al, 2010). Since the approaches used and the underlying sequence data differ, our analysis is not directly comparable to that of wheat 3B.…”

“…In this study, onethird of all genes (6788 genes) in the genome zippers are located within 10-cM intervals that encompass each genetic centromere (6.4% of the entire barley genetic map). In wheat, sequencing megabase-sized BAC contigs selected from distributed regions of the chromosome 3B physical map revealed the presence of genes throughout the physical length of the chromosome, with a twofold higher concentration toward the telomeres (Choulet et al, 2010). Since regions with low recombination frequency per physical unit (hence, the regions around genetic centromeres) may extend in barley over as much as half a barley chromosome (Kü nzel et al, 2000), it can be expected that gene distribution in barley will follow a similar pattern as observed for wheat chromosome 3B.…”

Flow Sorting and Sequencing Meadow Fescue Chromosome 4F

“…Assuming the estimated size of chromosome 4F at 543 Mb and the 4F gene density representative for the entire genus Festuca genome (Kopecký et al, 2010), the total genus Festuca genome contains about 35,000 genes. This is a slightly higher number that the estimation for barley (32,000 or more genes; Mayer et al, 2011) and less than that for the B genome of wheat (38,000 genes; Choulet et al, 2010). The recent estimate for the A genome of wheat is below that for Festuca spp.…”