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

BMC Plant Biology

Research Article

Jan Bartoš¹  Hana Šimková¹  Jaroslav Doležel¹  Jan Šafář¹  Kateřina Cviková¹  Catherine Feuillet²  Frédéric Choulet²  Pierre Sourdille²  Hélène Bergès³  Jan Pačes⁴  Hynek Strnad⁴  Čestmír Vlček⁴  Mária Džunková⁴  Federica Cattonaro⁵ 

[1] Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, CZ-77200, Olomouc, Czech Republic;INRA University Blaise Pascal UMR 1095 Genetics Diversity Ecophysiology of Cereals, F-63100, Clermont-Ferrand, France;INRA, National Resources Centre for Plant Genomics, F-31326, Castanet Tolosan Cedex, France;Institute of Molecular Genetics, Vídeňská 1083, CZ-14220, Praha, Czech Republic;Instituto di Genomica Applicata, Via J. Linussio 51, 33100, Udine, Italy;

关键词: Wheat;    BAC sequencing;    Homoeologous genomes;    Gene duplication;    Non-collinear genes;    Allopolyploidy;   

DOI  :  10.1186/1471-2229-12-155

 received in 2012-03-17, accepted in 2012-08-15,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundPolyploidization 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.ResultsWe 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.ConclusionDirect 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.

【 授权许可】

CC BY   
© Bartoš et al.; licensee BioMed Central Ltd. 2012