Dynamics of the evolution of orthologous and paralogous portions of a complex locus region in two genomes of allopolyploid wheat

Kong, Xiuying; Gu, Yong; You, Frank M.; Dubcovsky, Jorge; Anderson, Olin D.

doi:10.1023/b:plan.0000028768.21587.dc

Cited by 67 publications

(67 citation statements)

References 59 publications

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“…It is hypothesized that Gsp gene after the splitting of the wheat rice lineage was duplicated in the wheat lineage and gave rise to the puroindoline genes (33). A similar scenario has been proposed for the evolution of gluten genes that control bread-making properties in wheat and are missing in rice, but both lineages share related globulin genes (34).…”

Section: Random Vs Localized Genome Evolutionmentioning

confidence: 81%

Gene evolution at the ends of wheat chromosomes

See

Brooks

Nelson

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Wheat ESTs mapped to deletion bins in the distal 42% of the long arm of chromosome 4B (4BL) were ordered in silico based on blastn homology against rice pseudochromosome 3. The ESTs spanned 29 cM on the short arm of rice chromosome 3, which is known to be syntenic to long arms of group-4 chromosomes of wheat. Fine-scale deletion-bin and genetic mapping revealed that 83% of ESTs were syntenic between wheat and rice, a far higher level of synteny than previously reported, and 6% were nonsyntenic (not located on rice chromosome 3). One inversion spanning a 5-cM region in rice and three deletion bins in wheat was identified. The remaining 11% of wheat ESTs showed no sequence homology in rice and mapped to the terminal 5% of the wheat chromosome 4BL. In this region, 27% of ESTs were duplicated, and it accounted for 70% of the recombination in the 4BL arm. Globally in wheat, no sequence homology ESTs mapped to the terminal bins, and ESTs rarely mapped to interstitial chromosomal regions known to be recombination hot spots. The wheat–rice comparative genomics analysis indicated that gene evolution occurs preferentially at the ends of chromosomes, driven by duplication and divergence associated with high rates of recombination.

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Section: Random Vs Localized Genome Evolutionmentioning

confidence: 81%

Gene evolution at the ends of wheat chromosomes

See

Brooks

Nelson

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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“…This suggests that at least two waves of retrotransposon insertions have occurred during the evolution of the A ancestral wheat genome. It is very rare to find conserved sequences of transposable elements in colinear regions of cereal species, and so far, only partial sequences of conserved elements have been reported (Wicker et al 2003a;Gu et al 2004;Kong et al 2004). The halflife of LTR retrotransposons was recently estimated to be ∼6 million years in rice .…”

Section: Common Themes Of Evolution In Both Haplotypesmentioning

confidence: 99%

“…Langdon (AABB, Cenci et al 2003), and the donor of the D genome Aegilops tauschii (Moullet et al 1999) has allowed the isolation and sequencing of large wheat genomic fragments. Recent studies have compared orthologous loci in the three A, B, and D homoeologous wheat genomes Kong et al 2004), which diverged 2.5-4 Mya (Huang et al 2002). Rapid genome evolution was observed that was mostly due to insertion of retroelements after the divergence of the three subgenomes.…”

mentioning

confidence: 99%

Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels

Isidore¹,

Scherrer²,

Chalhoub³

et al. 2005

Genome Res.

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Plant genomes, in particular grass genomes, evolve very rapidly. The closely related A genomes of diploid, tetraploid, and hexaploid wheat are derived from a common ancestor that lived <3 million years ago and represent a good model to study molecular mechanisms involved in such rapid evolution. We have sequenced and compared physical contigs at the Lr10 locus on chromosome 1AS from diploid (211 kb), tetraploid (187 kb), and hexaploid wheat (154 kb). A maximum of 33% of the sequences were conserved between two species. The sequences from diploid and tetraploid wheat shared all of the genes, including Lr10 and RGA2 and define a first haplotype (H1). The 130-kb intergenic region between Lr10 and RGA2 was conserved in size despite its activity as a hot spot for transposon insertion, which resulted in >70% of sequence divergence. The hexaploid wheat sequence lacks both Lr10 and RGA2 genes and defines a second haplotype, H2, which originated from ancient and extensive rearrangements. These rearrangements included insertions of retroelements and transposons deletions, as well as unequal recombination within elements. Gene disruption in haplotype H2 was caused by a deletion and subsequent large inversion. Gene conservation between H1 haplotypes, as well as conservation of rearrangements at the origin of the H2 haplotype at three different ploidy levels indicate that the two haplotypes are ancient and had a stable gene content during evolution, whereas the intergenic regions evolved rapidly. Polyploidization during wheat evolution had no detectable consequences on the structure and evolution of the two haplotypes.

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“…More recently, comparisons have been performed between the homoeologous genomes of wheat that have radiated 2.5 to 4.5 Mya (Huang et al, 2002). Large sequences were compared at orthologous storage protein loci in the homoeologous A and A m genomes of T. monococcum and T. durum (Wicker et al, 2003) and in the A, B, and D genomes of T. durum and Aegilops tauschii Kong et al, 2004). In both cases, conservation was mainly restricted to the gene space, and rearrangements, including gene duplications and rapid divergence of intergenic regions through the movement of retroelements, were observed.…”

Section: Introductionmentioning

confidence: 99%

Large Intraspecific Haplotype Variability at theRph7Locus Results from Rapid and Recent Divergence in the Barley Genome

et al. 2005

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To study genome evolution and diversity in barley (Hordeum vulgare), we have sequenced and compared more than 300 kb of sequence spanning the Rph7 leaf rust disease resistance gene in two barley cultivars. Colinearity was restricted to five genic and two intergenic regions representing <35% of the two sequences. In each interval separating the seven conserved regions, the number and type of repetitive elements were completely different between the two homologous sequences, and a single gene was absent in one cultivar. In both cultivars, the nonconserved regions consisted of ;53% repetitive sequences mainly represented by long-terminal repeat retrotransposons that have inserted <1 million years ago. PCR-based analysis of intergenic regions at the Rph7 locus and at three other independent loci in 41 H. vulgare lines indicated large haplotype variability in the cultivated barley gene pool. Together, our data indicate rapid and recent divergence at homologous loci in the genome of H. vulgare, possibly providing the molecular mechanism for the generation of high diversity in the barley gene pool. Finally, comparative analysis of the gene composition in barley, wheat (Triticum aestivum), rice (Oryza sativa), and sorghum (Sorghum bicolor) suggested massive gene movements at the Rph7 locus in the Triticeae lineage.

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Dynamics of the evolution of orthologous and paralogous portions of a complex locus region in two genomes of allopolyploid wheat

Cited by 67 publications

References 59 publications

Gene evolution at the ends of wheat chromosomes

Gene evolution at the ends of wheat chromosomes

Ancient haplotypes resulting from extensive molecular rearrangements in the wheat A genome have been maintained in species of three different ploidy levels

Large Intraspecific Haplotype Variability at theRph7Locus Results from Rapid and Recent Divergence in the Barley Genome

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