Abstract
BackgroundBread wheat is not only an important crop, but its large (17 Gb), highly repetitive, and hexaploid genome makes it a good model to study the organization and evolution of complex genomes. Recently, we produced a high quality reference sequence of wheat chromosome 3B (774 Mb), which provides an excellent opportunity to study the evolutionary dynamics of a large and polyploid genome, specifically the impact of single gene duplications.ResultsWe find that 27 % of the 3B predicted genes are non-syntenic with the orthologous chromosomes of Brachypodium distachyon, Oryza sativa, and Sorghum bicolor, whereas, by applying the same criteria, non-syntenic genes represent on average only 10 % of the predicted genes in these three model grasses. These non-syntenic genes on 3B have high sequence similarity to at least one other gene in the wheat genome, indicating that hexaploid wheat has undergone massive small-scale interchromosomal gene duplications compared to other grasses. Insertions of non-syntenic genes occurred at a similar rate along the chromosome, but these genes tend to be retained at a higher frequency in the distal, recombinogenic regions. The ratio of non-synonymous to synonymous substitution rates showed a more relaxed selection pressure for non-syntenic genes compared to syntenic genes, and gene ontology analysis indicated that non-syntenic genes may be enriched in functions involved in disease resistance.ConclusionOur results highlight the major impact of single gene duplications on the wheat gene complement and confirm the accelerated evolution of the Triticeae lineage among grasses.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0754-6) contains supplementary material, which is available to authorized users.
Highlights
Bread wheat is an important crop, but its large (17 Gb), highly repetitive, and hexaploid genome makes it a good model to study the organization and evolution of complex genomes
We verified the syntenic relationships between wheat chromosome 3 (Ta3B), rice chromosome 1 (Os1), sorghum chromosome 3 (Sb3), and the distal regions of Brachypodium chromosome 2 (Bd2) [12, 15, 27,28,29] and delineated their exact borders using EnsemblPlants Synteny viewer [30] (Additional file 1: Figures S1-S4)
We found barley chromosome 3H to have a similar percentage of non-syntenic genes (31 %) and fixation rate (8.1 × 10−3 locus−1 MY−1) (Additional file 1: Table S3) as wheat 3B, suggesting that the high rate of interchromosomal duplication is a feature of the Triticeae lineage
Summary
Bread wheat is an important crop, but its large (17 Gb), highly repetitive, and hexaploid genome makes it a good model to study the organization and evolution of complex genomes. We produced a high quality reference sequence of wheat chromosome 3B (774 Mb), which provides an excellent opportunity to study the evolutionary dynamics of a large and polyploid genome, the impact of single gene duplications. Hexaploid bread wheat (Triticum aestivum L.; 2n = 6x = 42; AABBDD) originated from two recent hybridizations between three diploid progenitors, donors of the A, B, and D subgenomes, which diverged an estimated 6.5 MYA [13]. The first hybridization occurred
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