The reference genome of the human diploid cell line RPE-1

Emilia Volpe, Alessio Colantoni, Luca Corda, Elena Di Tommaso, Franca Pelliccia, Riccardo Ottalevi, Andrea Guarracino, Danilo Licastro, Luigi Faino, Mattia Capulli, Giulio Formenti, Evelyne Tassone and Simona Giunta ()
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Emilia Volpe: University of Rome “Sapienza”
Alessio Colantoni: University of Rome “Sapienza”
Luca Corda: University of Rome “Sapienza”
Elena Di Tommaso: University of Rome “Sapienza”
Franca Pelliccia: University of Rome “Sapienza”
Riccardo Ottalevi: Dante Genomics Corp Inc.
Andrea Guarracino: University of Tennessee Health Science Center
Danilo Licastro: Area Science Park
Luigi Faino: University of Rome “Sapienza”
Mattia Capulli: University of L’Aquila
Giulio Formenti: The Rockefeller University
Evelyne Tassone: University of Rome “Sapienza”
Simona Giunta: University of Rome “Sapienza”

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Recent technological advances have facilitated the assembly of telomere-to-telomere (T2T) genomes. The current T2T CHM13 showcases the complete architecture of the human genome, yet its use in functional experiments is limited by discrepancies with the actual genome of the specific biological system under study. Access to reference assemblies for experimentally relevant cell lines is therefore essential in advancing sequencing-based analyses and precise manipulation, particularly in highly variable regions such as centromeres. Here, we present RPE1v1.1, the near-complete diploid genome assembly of the hTERT RPE-1 cell line, a non-cancerous human retinal epithelial model with a stable karyotype. Using high-coverage Pacific Biosciences and Oxford Nanopore Technologies long-read sequencing, we generate a high-quality de novo assembly, validate it through multiple methods, and phase it by integrating high-throughput chromosome conformation capture (Hi-C) data. Our assembly includes chromosome-level scaffolds that span centromeres for all chromosomes. Comparing both haplotypes with the CHM13 genome, we detect haplotype-specific genomic variations, including the translocation between chromosome 10 and chromosome X t(X;10)(Xq28;10q21.2) characteristic of RPE-1 cells, and divergence peaking at centromeres. Altogether, the RPE1v1.1 genome provides a reference-quality diploid assembly of a widely used cell line, supporting high-precision genetic and epigenetic studies in this model system.

Date: 2025
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DOI: 10.1038/s41467-025-62428-z

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