A 3-way hybrid approach to generate a new high quality chimpanzee reference genome (Pan_tro_3.0)

The chimpanzee is arguably the most important species for the study of human origins. A key resource for these studies is a high quality reference genome assembly, however, as most mammalian genomes, the current iteration of the chimpanzee reference genome assembly it is highly fragmented. In the current iteration of the chimpanzees reference genome assembly (Pan_tro_2.1.4), the sequence is scattered across more then 183,000 contigs and incorporating over 159,000 gaps, with a genome wide contig N50 of 51 Kbp. Findings: In this work we produce an extensive and diverse array of sequencing datasets to rapidly assemble a new chimpanzee reference that surpasses previous iterations in bases represented and organized in large scaffolds. To this end, we show substantial improvements over the current release of the chimpanzee genome (Pan_tro_2.1.4) by several metrics, such as: increased contiguity by >750% and 300% on contigs and scaffolds, respectively; closure of 77% of gaps in the Pan_tro_2.1.4 assembly gaps spanning >850 Kbp of novel coding sequence based on RNASeq data. We furthermore report over 2,700 genes that had putatively erroneous frame-shift predictions to human in Pan_tro_2.1.4 and show a substantial increase in the annotation of repetitive elements. Conclusions: We apply a simple 3-way hybrid approach to considerably improve the reference genome assembly for the chimpanzee, providing a valuable resource to study human origins. We furthermore produced extensive sequencing datasets that are all derived from the same cell line, generating a broad non-human benchmark dataset.