Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat

Jan Bartos (1) , Cestmir Vlcek (2) , Frédéric Choulet (3) , Maria Dzunkova (2) , Katerina Cvikova , Jan Safar (1) , Hana Simkova (1) , Jan Paces (2) , Hynek Strnad (2) , Pierre Sourdille (3) , Helene Berges (4) , Federica Cattonaro (5) , Catherine Feuillet (3) , Jaroslav Dolezel (1)

1 Ctr Reg Hana Biotechnol & Agr Res
2 Institute of Molecular Genetics ASCR
3 GDEC - Génétique Diversité et Ecophysiologie des Céréales
4 CNRGV - Centre National de Ressources Génomiques Végétales
5 Inst Genom Applicata

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.

Mots clés: Wheat; BAC sequencing; Homoeologous genomes; Gene duplication; Non-collinear genes; Allopolyploidy; TRITICUM-AESTIVUM L.; AEGILOPS-TAUSCHII; BRACHYPODIUM-DISTACHYON; POLYPLOWHEAT; CHROMOSOME 3B; PLANT GENOMES; MAIZE GENOME; EVOLUTION; ANNOTATION; EXPRESSION

Domaines: Sciences du Vivant [q-bio]

Jan Bartos, Cestmir Vlcek, Frédéric Choulet, Maria Dzunkova, Katerina Cvikova, et al.. Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat. BMC Plant Biology, 2012, 12, ⟨10.1186/1471-2229-12-155⟩. ⟨hal-01190732⟩