Fig. 5: Pangenome analysis of RPE-1 in comparison to HPRC and other human reference assemblies.
From: The reference genome of the human diploid cell line RPE-1
a Cartoon of comparison and dendrogram of the RPE-1 genome and HPRC samples based on whole-genome (all chromosomes) pangenome analysis. The tree shows the genomic relationships between RPE-1 haplotypes (green), individual HPRC genomes (red), CHM13 (blue), and GRCh38 (purple). Created in BioRender. Giunta, S. (2025) https://BioRender.com/nozlc3z. b Principal Component Analysis (PCA) of the whole pangenome. The plot shows the first two principal components, with the percentage of explained variance indicated on each axis. HPRC samples are represented by red dots, RPE-1 by green triangles, CHM13 by a blue square and GRCh38 by a purple cross. Given that the centromeric sequences of GRCh38 are masked, we interpret the first principal component (PC1) as representing the centromeric diversity of the assemblies. Furthermore, the distinct positioning of RPE-1 haplotype 1 (RPE-1#1) on PC2 highlights its divergence in chromosome X due to the t(X;10)(Xq28;10q21.2) translocation. AFR African, AMR American, EAS East Asian, SAS South Asian.
