Abstract
We identified 15 regions of >1 Mb in the human genome composed of large ancient local duplications corresponding to gene deserts. We detected these intrachromosomal duplications in mouse and dog but not in chicken; they present as patches of similarity as low as 60%. These findings suggest that some human gene deserts originated from duplications of segments lacking genes in a mammalian common ancestor.
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Acknowledgements
We thank K. Murakami, Y. Hayakawa and technical staff of RIKEN Genomic Sciences Center for technical assistance; H. Watanabe, T. Kojima and T. Taniguchi for discussions and comments on the manuscript; and the providers of the dog genome sequencing project (The Broad Institute and Agencourt Bioscience) for use of the genomic data in public databases before publication. This work was supported in part by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan.
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Supplementary information
Supplementary Fig. 1
Dot-matrix analysis for the comparison of human gene deserts containing LADs with mouse, dog and chicken sequences. (PDF 536 kb)
Supplementary Table 1
Genes flanking LADs or the gene deserts containing LADs are listed from the Ensembl dataset. (PDF 87 kb)
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Itoh, T., Toyoda, A., Taylor, T. et al. Identification of large ancient duplications associated with human gene deserts. Nat Genet 37, 1041–1043 (2005). https://doi.org/10.1038/ng1648
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DOI: https://doi.org/10.1038/ng1648
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