Volpe Emilia, Colantoni Alessio, Corda Luca, Di Tommaso Elena, Pelliccia Franca, Ottalevi Riccardo, Guarracino Andrea, Licastro Danilo, Faino Luigi, Capulli Mattia, Formenti Giulio, Tassone Evelyne, Giunta Simona
Giunta Laboratory of Genome Evolution, Department of Biology and Biotechnologies "Charles Darwin", University of Rome "Sapienza", Rome, Italy.
Department of Bioinformatic, Dante Genomics Corp Inc., New York, NY, USA.
Nat Commun. 2025 Sep 12;16(1):7751. doi: 10.1038/s41467-025-62428-z.
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.
近期的技术进步推动了端粒到端粒（T2T）基因组的组装。当前的T2T CHM13展示了人类基因组的完整架构，但其在功能实验中的应用受到与所研究特定生物系统实际基因组差异的限制。因此，获取与实验相关细胞系的参考组装对于推进基于测序的分析和精确操作至关重要，特别是在着丝粒等高度可变区域。在此，我们展示了RPE1v1.1，这是hTERT RPE - 1细胞系的近乎完整的二倍体基因组组装，hTERT RPE - 1细胞系是一种具有稳定核型的非癌性人类视网膜上皮模型。利用高覆盖率的太平洋生物科学公司和牛津纳米孔技术的长读长测序，我们生成了高质量的从头组装，通过多种方法对其进行验证，并通过整合高通量染色体构象捕获（Hi - C）数据进行定相。我们的组装包括跨越所有染色体着丝粒的染色体水平支架。将两个单倍型与CHM13基因组进行比较，我们检测到单倍型特异性的基因组变异，包括RPE - 1细胞特有的10号染色体与X染色体之间的易位t(X;10)(Xq28;10q21.2)，以及着丝粒处的差异峰值。总之，RPE1v1.1基因组提供了一个广泛使用的细胞系的参考质量二倍体组装，支持在该模型系统中进行高精度的遗传和表观遗传研究。
