Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement

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dc.contributor.author Liu, Sanzhen Z.
dc.contributor.author Zheng, J.
dc.contributor.author Migeon, P.
dc.contributor.author Ren, J.
dc.contributor.author Hu, Y.
dc.contributor.author He, C.
dc.contributor.author Liu, H. J.
dc.contributor.author Fu, J. J.
dc.contributor.author White, F. F.
dc.contributor.author Toomajian, Christopher
dc.contributor.author Wang, G. Y.
dc.date.accessioned 2017-11-30T21:53:39Z
dc.date.available 2017-11-30T21:53:39Z
dc.date.issued 2017-02-10
dc.identifier.uri http://hdl.handle.net/2097/38400
dc.description Citation: Liu, S. Z., Zheng, J., Migeon, P., Ren, J., Hu, Y., He, C., . . . Wang, G. Y. (2017). Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement. Scientific Reports, 7, 15. https://doi.org/10.1038/srep42444
dc.description.abstract The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allelespecific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.
dc.relation.uri https://doi.org/10.1038/srep42444
dc.rights This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
dc.rights.uri https://creativecommons.org/licenses/by/4.0/
dc.subject Zea-Mays
dc.subject Genome Complexity
dc.subject 5S Rdna
dc.subject Dna
dc.subject Identification
dc.subject Diversity
dc.title Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement
dc.type Text
dc.date.published 2017
dc.citation.doi 10.1038/srep42444
dc.citation.issn 2045-2322
dc.citation.issue 1
dc.citation.jtitle Scientific Reports
dc.citation.spage 15
dc.citation.volume 7
dc.citation Liu, S. Z., Zheng, J., Migeon, P., Ren, J., Hu, Y., He, C., . . . Wang, G. Y. (2017). Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement. Scientific Reports, 7, 15. https://doi.org/10.1038/srep42444
dc.contributor.authoreid liu3zhen
dc.contributor.authoreid toomajia
dc.description.version Article: Version of Record
dc.contributor.kstate Liu, Sanzhen
dc.contributor.kstate Toomajian, Christopher


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This work is licensed under a Creative Commons Attribution 4.0 International License. The images
or other third party material in this article are included in the article’s Creative Commons license,
unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license,
users will need to obtain permission from the license holder to reproduce the material. To view a copy of this
license, visit http://creativecommons.org/licenses/by/4.0/ Except where otherwise noted, the use of this item is bound by the following: This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

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