Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation

Weighill, Deborah; Macaya-Sanz, David; DiFazio, Stephen Paul; Joubert, Wayne; Shah, Manesh B.; Schmutz, Jeremy; Sreedasyam, Avinash; Tuskan, Gerald A.; Jacobson, Daniel A.

doi:10.3389/fgene.2019.00487

Title: Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation

Journal Article · 31 May 2019 · Frontiers in Genetics

DOI: https://doi.org/10.3389/fgene.2019.00487 · OSTI ID:1542248

^[1]; Macaya-Sanz, David ^[2]; DiFazio, Stephen Paul ^[2];

^[3]; Shah, Manesh B. ^[3]; Schmutz, Jeremy ^[4]; Sreedasyam, Avinash ^[5];

^[3];

^[1]

Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
West Virginia Univ., Morgantown, WV (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)

Various ‘omics data types have been generated for Populus trichocarpa, each providing a layer of information which can be represented as a density signal across a chromosome. We make use of genome sequence data, variants data across a population as well as methylation data across 10 different tissues, combined with wavelet-based signal processing to perform a comprehensive analysis of the signature of the centromere in these different data signals, and successfully identify putative centromeric regions in P. trichocarpa from these signals. Furthermore, using SNP (single nucleotide polymorphism) correlations across a natural population of P. trichocarpa, we find evidence for the co-evolution of the centromeric histone CENH3 with the sequence of the newly identified centromeric regions, and identify a new CENH3 candidate in P. trichocarpa.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725; AC02-05CH11231

OSTI ID:: 1542248

Journal Information:: Frontiers in Genetics, Journal Name: Frontiers in Genetics Journal Issue: N/a Vol. 10; ISSN 1664-8021

Publisher:: FrontiersCopyright Statement

Country of Publication:: United States

Language:: English

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Characterization of two CENH3 genes and their roles in wheat evolution Yuan, Jing; Guo, Xiang; Hu, Jing New Phytologist, Vol. 206, Issue 2 https://doi.org/10.1111/nph.13235	journal	December 2014
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The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) Tuskan, G. A.; DiFazio, S.; Jansson, S. Science, Vol. 313, Issue 5793, p. 1596-1604 https://doi.org/10.1126/science.1128691	journal	September 2006
The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana Ossowski, S.; Schneeberger, K.; Lucas-Lledo, J. I. Science, Vol. 327, Issue 5961 https://doi.org/10.1126/science.1180677	journal	December 2009
Genetic Definition and Sequence Analysis of Arabidopsis Centromeres Copenhaver, G. P. Science, Vol. 286, Issue 5449 https://doi.org/10.1126/science.286.5449.2468	journal	December 1999
Single-base-resolution methylomes of populus trichocarpa reveal the association between DNA methylation and drought stress Liang, Dan; Zhang, Zhoujia; Wu, Honglong BMC Genetics, Vol. 15, Issue Suppl 1 https://doi.org/10.1186/1471-2156-15-S1-S9	journal	January 2014
Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression Vining, Kelly J.; Pomraning, Kyle R.; Wilhelm, Larry J. BMC Genomics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2164-13-27	journal	January 2012
Data integration in the era of omics: current and future challenges Gomez-Cabrero, David; Abugessaisa, Imad; Maier, Dieter BMC Systems Biology, Vol. 8, Issue Suppl 2 https://doi.org/10.1186/1752-0509-8-S2-I1	journal	January 2014
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Data Integration in Poplar: ‘Omics Layers and Integration Strategies Weighill, Deborah; Tschaplinski, Timothy J.; Tuskan, Gerald A. Frontiers in Genetics, Vol. 10 https://doi.org/10.3389/fgene.2019.00874	journal	September 2019

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59 BASIC BIOLOGICAL SCIENCES
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co-evolution
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Title: Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation

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