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Rapid evolution and complex structural organization in genomic regions harboring multiple prolamin genes in the polyploid wheat genome

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Abstract

Genes encoding wheat prolamins belong to complicated multi-gene families in the wheat genome. To understand the structural complexity of storage protein loci, we sequenced and analyzed orthologous regions containing both gliadin and LMW-glutenin genes from the A and B genomes of a tetraploid wheat species, Triticum turgidum ssp. durum. Despite their physical proximity to one another, the gliadin genes and LMW-glutenin genes are organized quite differently. The gliadin genes are found to be more clustered than the LMW-glutenin genes which are separated from each other by much larger distances. The separation of the LMW-glutenin genes is the result of both the insertion of large blocks of repetitive DNA owing to the rapid amplification of retrotransposons and the presence of genetic loci interspersed between them. Sequence comparisons of the orthologous regions reveal that gene movement could be one of the major factors contributing to the violation of microcolinearity between the homoeologous A and B genomes in wheat. The rapid sequence rearrangements and differential insertion of repetitive DNA has caused the gene islands to be not conserved in compared regions. In addition, we demonstrated that the i-type LMW-glutenin originated from a deletion of 33-bps in the 5′ coding region of the m-type gene. Our results show that multiple rounds of segmental duplication of prolamin genes have driven the amplification of the ω-gliadin genes in the region; such segmental duplication could greatly increase the repetitive DNA content in the genome depending on the amount of repetitive DNA present in the original duplicate region.

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Acknowledgements

We thank Mingcheng Luo for the assistance in BAC fingerprinting and Gerald Lazo for bioinformatics support. This work was partially supported by grants from National Basic Research Program of China (2002CB111301) and National Natural Science Foundation of China (30571158). Work at WRRC is supported by US, Department of Agriculture-Agriculture Research Service Grant CRIS 5325022100-011.

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Correspondence to Yong Qiang Gu or Xiuying Kong.

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Shuangcheng Gao and Yong Qiang Gu contributed equally to the work.

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11103_2007_9208_MOESM1_ESM.pdf

Nested insertion of retroelements and subsequent deletion in the intergenic region between two LMW-glutenin genes. Two LMW-glutenin genes are represented by black boxes. The start position of each LMW-glutenin gene in the contiguous 265-kb region is provided. Retroelements were annotated based on BLAST searches against the TREP database (http://wheat.pw.usda.gov/ITMI/Repeats/). A repetitive DNA with “s” stands for a solo retroelement and “p” for a partial retroelement. Deletion(s) has occurred in the region. The putative deleted portion from each retroelement is indicated with a blue region. The exact sequencelength deleted is difficult to determine. However, It can be expected that without the deletion event, the two LMW-glutenin genes could be separated by a much larger distance. Insertion of Glabra2-like gene into a Fatimah retroelement is indicated. (PDF 19 kb)

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Gao, S., Gu, Y.Q., Wu, J. et al. Rapid evolution and complex structural organization in genomic regions harboring multiple prolamin genes in the polyploid wheat genome. Plant Mol Biol 65, 189–203 (2007). https://doi.org/10.1007/s11103-007-9208-1

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