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Genome Biol. 2015 Sep 9;16:188. doi: 10.1186/s13059-015-0754-6.

Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B.

Author information

1
INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039, Clermont-Ferrand, France.
2
University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039, Clermont-Ferrand, France.
3
Present address: Bayer CropScience NV, Technologiepark 38, 9052, Ghent, Belgium.
4
Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Technologiepark 927, 9052, Ghent, Belgium.
5
Present address: Bayer CropScience, 3500 Paramount Parkway, Morrisville, NC, 27560, USA.
6
INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039, Clermont-Ferrand, France. frederic.choulet@clermont.inra.fr.
7
University Blaise Pascal UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, 63039, Clermont-Ferrand, France. frederic.choulet@clermont.inra.fr.

Abstract

BACKGROUND:

Bread 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.

RESULTS:

We 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.

CONCLUSION:

Our 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.

PMID:
26353816
PMCID:
PMC4563886
DOI:
10.1186/s13059-015-0754-6
[Indexed for MEDLINE]
Free PMC Article

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