A second look at the chimpanzee genome

Trabajo presentado en la Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2016), celebrada en Gold Coast (Queensland, Australia) del 3 al 7 de julio de 2016.The initial sequencing of the chimpanzee genome and its comparison to our own constituted a major leap in the understanding of the evolutionary trajectories of our species. Nevertheless, the proper characterization of some complex regions are far from complete as even the most current iteration of the chimpanzee assembly (Pantro_2.1.4) is still a draft a decade after its initial release. In this work, we will present a complete de-novo assembly for the common Chimpanzee, incorporating several different novel technologies such as Illumina 2x250 bp overlapping paired end reads, PacBio single molecule sequencing long reads, Illumina Moleculo and Dovetail HiC-chromosomal contact maps for scaffolding. We produce a high quality assembly derived from a single male individual (Clint), boosting contiguity by over 300% on the scaffold level, and by over 750% on the contig level, additionally resolving around 230Mbps of the genome. We are able to characterize more complexity in this version of the chimpanzee genome and explore the genome wide diversity of tandem repeats and copy number variation at population level.N