AUTHOR=Weighill Deborah , Macaya-Sanz David , DiFazio Stephen Paul , Joubert Wayne , Shah Manesh , Schmutz Jeremy , Sreedasyam Avinash , Tuskan Gerald , Jacobson Daniel 

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

JOURNAL=Frontiers in Genetics

VOLUME=10

YEAR=2019

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2019.00487

DOI=10.3389/fgene.2019.00487

ISSN=1664-8021

ABSTRACT=<p>Various ‘omics data types have been generated for <italic>Populus trichocarpa</italic>, 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 <italic>P. trichocarpa</italic> from these signals. Furthermore, using SNP (single nucleotide polymorphism) correlations across a natural population of <italic>P. trichocarpa</italic>, 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 <italic>P. trichocarpa</italic>.</p>