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BMC Plant Biol. 2012; 12: 155.
Published online Aug 30, 2012. doi:  10.1186/1471-2229-12-155
PMCID: PMC3445842
Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat
Jan Bartoš,corresponding author1 Čestmír Vlček,2 Frédéric Choulet,3 Mária Džunková,2 Kateřina Cviková,1 Jan Šafář,1 Hana Šimková,1 Jan Pačes,2 Hynek Strnad,2 Pierre Sourdille,3 Hélène Bergès,4 Federica Cattonaro,5 Catherine Feuillet,3 and Jaroslav Doležel1
1Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc, CZ-77200, Czech Republic
2Institute of Molecular Genetics, Vídeňská 1083, Praha, CZ-14220, Czech Republic
3INRA University Blaise Pascal UMR 1095 Genetics Diversity Ecophysiology of Cereals, Clermont-Ferrand, F-63100, France
4INRA, National Resources Centre for Plant Genomics, Castanet Tolosan Cedex, F-31326, France
5Instituto di Genomica Applicata, Via J. Linussio 51, Udine, 33100, Italy
corresponding authorCorresponding author.
Jan Bartoš: bartos/at/ueb.cas.cz; Čestmír Vlček: vlcek/at/img.cas.cz; Frédéric Choulet: frederic.choulet/at/clermont.inra.fr; Mária Džunková: maria.dzunkova/at/seznam.cz; Kateřina Cviková: cvikova/at/ueb.cas.cz; Jan Šafář: safar/at/ueb.cas.cz; Hana Šimková: simkovah/at/ueb.cas.cz; Jan Pačes: hpaces/at/img.cas.cz; Hynek Strnad: strnad/at/img.cas.cz; Pierre Sourdille: pierre.sourdille/at/clermont.inra.fr; Hélène Bergès: helene.berges/at/toulouse.inra.fr; Federica Cattonaro: cattonaro/at/appliedgenomics.org; Catherine Feuillet: catherine.feuillet/at/clermont.inra.fr; Jaroslav Doležel: dolezel/at/ueb.cas.cz
Received March 17, 2012; Accepted August 15, 2012.
Abstract
Background
Polyploidization is considered one of the main mechanisms of plant genome evolution. The presence of multiple copies of the same gene reduces selection pressure and permits sub-functionalization and neo-functionalization leading to plant diversification, adaptation and speciation. In bread wheat, polyploidization and the prevalence of transposable elements resulted in massive gene duplication and movement. As a result, the number of genes which are non-collinear to genomes of related species seems markedly increased in wheat.
Results
We used new-generation sequencing (NGS) to generate sequence of a Mb-sized region from wheat chromosome arm 3DS. Sequence assembly of 24 BAC clones resulted in two scaffolds of 1,264,820 and 333,768 bases. The sequence was annotated and compared to the homoeologous region on wheat chromosome 3B and orthologous loci of Brachypodium distachyon and rice. Among 39 coding sequences in the 3DS scaffolds, 32 have a homoeolog on chromosome 3B. In contrast, only fifteen and fourteen orthologs were identified in the corresponding regions in rice and Brachypodium, respectively. Interestingly, five pseudogenes were identified among the non-collinear coding sequences at the 3B locus, while none was found at the 3DS locus.
Conclusion
Direct comparison of two Mb-sized regions of the B and D genomes of bread wheat revealed similar rates of non-collinear gene insertion in both genomes with a majority of gene duplications occurring before their divergence. Relatively low proportion of pseudogenes was identified among non-collinear coding sequences. Our data suggest that the pseudogenes did not originate from insertion of non-functional copies, but were formed later during the evolution of hexaploid wheat. Some evidence was found for gene erosion along the B genome locus.
Keywords: Wheat, BAC sequencing, Homoeologous genomes, Gene duplication, Non-collinear genes, Allopolyploidy
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