Dario Copetti1, 2, Rod A. Wing1, 2, ,
1 Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
2 International Rice Research Institute, T.T. Chang Genetic Resources Center, Los BaĂ±os, Laguna, Philippines
Received 10 June 2016, Revised 12 September 2016, Accepted 22 September 2016, Available online 28 September 2016
The majority of genome assemblies to date fail to represent the true structure of native genomes. This lack of completeness is largely due to the inability to assemble the variable (often significant) fraction of nuclear genomes that is composed primarily of repeated sequences (with either a structural function such as satellite DNA and simple sequence repeats or â€śselfish DNAâ€ť such as high-copy transposable elements â€“ TEs) â€“ herein defined at the â€śdark side of the genomeâ€ť. To address this problem, we developed a method to detect and quantify the dark side of the genome and used it to infer the genomic composition and dynamic evolution of the majority of native repeats and TEs present within several test eukaryotic genomes.