Polyploidy is considered one of the main driving forces of plant evolution and speciation. Whole genome duplication (WGD) provides a substrate for plant genome evolution, diversification and adaptation. The presence of two or more copies of the same gene reduces selection pressure and enables sub-functionalization and neo-functionalization. The analysis of whole-genome sequences revealed a frequent and often repeated occurrence of genome doubling during the evolution of higher plants. Even plants with relatively small genomes such as Arabidopsis thalianaBrachypodium distachyon
and Malus domestica
have experienced polyploidization events during their evolution [1
Some whole-genome duplication events occurred tens or even hundreds of million years ago (MYA). These paleoploidization events are not easy to detect by cytogenetic methods, but can be identified at the sequence level. In addition to paleoploidy, 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 genome of hexaploid bread wheat (2n
17Gb) was formed by two distinct hybridization events. 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. Only 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
In addition to WGD, tandem and dispersed duplications of individual genes and gene clusters are involved in genome evolution. These events disrupt collinearity between genomes of related species and limit the potential of model species with small genomes as surrogates for gene mapping and cloning in crops with complex genomes. The mechanisms leading to gene duplication are still not well understood, but transposable elements (TEs) which account for more than 85% of the wheat genome may play a critical role. TE activity can result in gene duplication through at least two mechanisms. First, a gene can be captured by a TE and copied together with the transposable element to a new location. The ability of TEs to capture genes and gene fragments has been well documented in plants [2
]. Another mechanism of gene duplication coupled with TE activity is based on double-strand break repair through synthesis-dependent strand annealing (SDSA) which can accompany TE insertion [9
]. In this case the sequence fragment containing a gene is used as filler DNA to repair the double strand-break, which occurs during filling of target site duplications. TE-mediated gene movements result in the insertion of genes at non collinear positions. Recent studies indicate that collinearity of wheat chromosomes to syntenic regions in two related grass species Brachypodium
and rice is lower than estimated previously [10
]. It has been suggested that the higher number of non-collinear genes results from TE activity [10
]. However, Choulet et al.
] and Wicker et al.
] differ in the estimated rate of non-collinear gene insertion. While Choulet et al.
] suggest the same fraction of non-collinear genes in the three genomes of bread wheat and in barley, Wicker et al.
] found significant differences in the gene insertion rate among the wheat group 1 chromosomes.
Gene loss is another mechanism leading to the observation of apparently non-collinear genes. Massive gene loss may accompany chromosome re-arrangements as documented in Arabidopsis
]. The loss can be significant as shown by [13
] who observed 50% gene loss from the two progenitors of maize within about 5 million years after polyploidization. In Arabidopsis, almost half of the genome was lost during the last 10 million years of evolution [12
]. Loss of genes from one of the homoeologous segments was also described in more recent allotetraploids such as Arabidopsis suecica
and Tragopogon mirus
]. Thus, gene loss in Brachypodium
and rice after paleopolyploidization could be responsible for the apparent increase in the number of non-collinear genes in wheat, even if the genes remain in their ancestral positions in wheat.
While previous reports identified major mechanisms driving the evolution of plant genomes, additional large-scale genomic sequences are needed to investigate non-collinear gene frequency, duplication mechanisms and non collinear gene function in more details. Due to its recent evolutionary history, hexaploid wheat is a good model to study these processes. As the sequencing of the wheat genome has been hampered by polyploidy and genome size (17Gb), the international wheat genome sequencing consortium (IWGSC) has adopted a chromosome based approach that relies on the construction of physical maps from isolated chromosomes and chromosome arms [16
]. In wheat, chromosome arms represent 1.3 to 3.4% of the whole genome and thus chromosome genomics offers a great reduction in sample complexity. The methods for chromosome isolation and flow cytometric sorting are well established in wheat [17
] and BAC libraries, which are being constructed from all chromosome arms [19
], were shown suitable to construct sequence-ready physical maps [20
The aim of the study was to examine whether homoeologous genomes of hexaploid wheat are characterized by the same rate of non-collinear gene insertion and if orthologous genes retain the same activity. We used the available chromosome arm-specific BAC library of bread wheat and sequenced a locus on chromosome 3D orthologous to contig ctg0954b on chromosome 3B. Contig ctg0954b (~ 3.1
Mb) contained 53 coding sequences and displayed high degree of non-collinearity with Brachypodium
and rice (62% of CDS are non-collinear) [10
]. Due to its character, the locus appears a suitable candidate for comparison of non-collinear gene insertions among homoeologous genomes of hexaploid wheat. We have identified and sequenced 1.6
Mb region on chromosome arm 3DS corresponding to part of the contig ctg0954b and compared gene content, gene by gene. This first ever comparison of Mb-sized orthologous regions of hexaploid wheat revealed similar rates of non-collinear gene insertion in the B- and D-genome loci. About two thirds of gene insertions are shared between the two loci, while the remaining gene movements took place after the divergence from common ancestor. Moreover, our results indicate a reduction of gene expression along the B locus as compared to the D locus.