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.
Highlights
Integrating data from multiple different sources is a task which is becoming more prevalent with the increased availability of systems biology data from high-throughput ‘omics technologies and phenotyping strategies (Gomez-Cabrero et al, 2014)
We investigate potential co-evolution signatures between the centromeric histone CENH3 and the newly identified centromeric regions through the calculation of Single Nucleotide Polymorphisms (SNPs) correlations across the population, and find evidence supporting the hypothesis of the co-evolution of putative P. trichocarpa CENH3 genes with the centromere sequences in P. trichocarpa
Populus trichocarpa (Tuskan et al, 2006) variant data was obtained from https://doi.ccs.ornl. 434gov/ui/doi/55. This dataset consists of SNP 28,342,758 SNPs called across 882 P. trichocarpa genotypes and is derived the whole genome resequencing of a Genome Wide Association Study (GWAS) population clonally replicated in common gardens (Tuskan et al, 2011)
Summary
Integrating data from multiple different sources is a task which is becoming more prevalent with the increased availability of systems biology data from high-throughput ‘omics technologies and phenotyping strategies (Gomez-Cabrero et al, 2014). The full genome sequence is available and is currently in its third version (Tuskan et al, 2006). A large collection of ∼28,000,000 Single Nucleotide Polymorphisms (SNPs) called across 882 genotypes are publicly available 434gov/ui/doi/55), which were derived from the resequenced genomes of ∼1,000 P. trichocarpa genotypes propagated in common gardens (Tuskan et al, 2011; Slavov et al, 2012; Evans et al, 2014). Methyl-DNA immunoprecipitation (MEDIP)-seq DNA methylation data is available for 10 different P. trichocarpa tissues (Vining et al, 2012). A gene expression atlas for P. trichocarpa is available on Phytozome (Goodstein et al, 2012)
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