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

Abstract

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.

Authors:
ORCiD logo [1];  [2];  [2]; ORCiD logo [3];  [3];  [4];  [5]; ORCiD logo [3]; ORCiD logo [1]
  1. Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  2. West Virginia Univ., Morgantown, WV (United States)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
  5. HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1542248
Alternate Identifier(s):
OSTI ID: 1616075
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Genetics
Additional Journal Information:
Journal Volume: 10; Journal Issue: N/a; Journal ID: ISSN 1664-8021
Publisher:
Frontiers
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Populus trichocarpacentromeres; wavelet transform; DNA methylation; SNP density; CENH3; co-evolution; data integration

Citation Formats

Weighill, Deborah, Macaya-Sanz, David, DiFazio, Stephen Paul, Joubert, Wayne, Shah, Manesh B., Schmutz, Jeremy, Sreedasyam, Avinash, Tuskan, Gerald A., and Jacobson, Daniel A. Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation. United States: N. p., 2019. Web. doi:10.3389/fgene.2019.00487.
Weighill, Deborah, Macaya-Sanz, David, DiFazio, Stephen Paul, Joubert, Wayne, Shah, Manesh B., Schmutz, Jeremy, Sreedasyam, Avinash, Tuskan, Gerald A., & Jacobson, Daniel A. Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation. United States. doi:10.3389/fgene.2019.00487.
Weighill, Deborah, Macaya-Sanz, David, DiFazio, Stephen Paul, Joubert, Wayne, Shah, Manesh B., Schmutz, Jeremy, Sreedasyam, Avinash, Tuskan, Gerald A., and Jacobson, Daniel A. Fri . "Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation". United States. doi:10.3389/fgene.2019.00487. https://www.osti.gov/servlets/purl/1542248.
@article{osti_1542248,
title = {Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation},
author = {Weighill, Deborah and Macaya-Sanz, David and DiFazio, Stephen Paul and Joubert, Wayne and Shah, Manesh B. and Schmutz, Jeremy and Sreedasyam, Avinash and Tuskan, Gerald A. and Jacobson, Daniel A.},
abstractNote = {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.},
doi = {10.3389/fgene.2019.00487},
journal = {Frontiers in Genetics},
number = N/a,
volume = 10,
place = {United States},
year = {2019},
month = {5}
}

Journal Article:
Free Publicly Available Full Text
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Cited by: 1 work
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Figures / Tables:

Figure 1 Figure 1: Ricker Wavelet. The Ricker wavelet shown for different values of scale s and translation $τ$ in Equation (1) (Leavey et al., 2003; Machado et al., 2011).

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