Abstract
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.
Highlights
Polyploidization is considered one of the main mechanisms of plant genome evolution
Three-dimensional pools of the Minimum Tiling Path (MTP) comprising 3,827 clones were prepared and screened using twelve markers derived from ESTs that were mapped previously to a completely sequenced and annotated 3 Mb region of chromosome 3B [10]
The MTP of these contigs consisted of 24 BAC clones (Table 1) that were sequenced by 454 GSFX titanium technology
Summary
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. Some whole-genome duplication events occurred tens or even hundreds of million years ago (MYA). Some plant species such as bread wheat (Triticum aestivum L.) experienced genome duplication more recently. In this case, intact homoeologous chromosomes persist without apparent structural changes except for some interchromosomal rearrangements [4]. The first took place 0.2 – 0.5 MYA [5] and involved a diploid wild species T. urartu (AA genome) and a diploid species related to Aegilops speltoides (SS genome) This event gave rise to the allotetraploid T. dicoccoides, the ancestor of the cultivated durum wheat T. turgidum with the AABB genome. About 10,000 years ago, a diploid donor of the D genome (Ae. tauschii) hybridized with T. dicoccoides to produce the ancestor of cultivated Triticum aestivum L. with the AABBDD genome [6]
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