High quality chimpanzee reference genome (Pan_tro_3.0) from hybrid assembly approach

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. The current iteration of the chimpanzee reference genome assembly (Pan_tro_2.1.4) is highly fragmented, with more than 183,000 contigs and incorporating over 159,000 gaps, with a genome wide contig N50 of 51 Kbp. <br> 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. We show substantial improvements over the Pan_tro_2.1.4 version by several metrics: increased contiguity by &gt;750% and 300% on contigs and scaffolds, respectively; closure of 77% of gaps in the Pan_tro_2.1.4 assembly gaps spanning &gt;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. <br> 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.