Single-cell template strand sequencing reveals culture-induced chromosomal instability in a gibbon cell line

Cell lines are invaluable tools for biomedical and evolutionary studies, but their genomic stability over time is often assumed rather than systematically assessed. In this study, we investigate the dynamics of genomic instability and structural rearrangements across multiple batches of a Nomascus siki cell line using a combination of single-cell template strand sequencing (Strand-seq), whole-genome sequencing (WGS), and fluorescence in situ hybridization (FISH). We identify 22 shared inversions in all the Strand-sequenced batches, confirming a common clonal origin. However, we detect additional large-scale rearrangements in all the batches, including trisomy of Chromosome 14 and the formation of isochromosomes of the same chromosome (iso-q and iso-p), leading to the rise of distinct subclonal populations. These rearrangements show evidence of clonal expansion, suggesting a proliferative advantage under in vitro conditions. From an evolutionary perspective, the gibbon genome is known for its exceptional level of chromosomal reshuffling, and this inherent plasticity may have contributed to the cell line's sensitivity to culture-induced structural changes. Despite extensive structural variation, the cell line remains stable at the nucleotide level, with ∼99% of SNPs shared across all batches. Our results illustrate how cell culture can recapitulate aspects of karyotypic evolution and underscore the need for regular genomic surveillance, particularly in long-term cultures. Furthermore, this study demonstrates the power of combining Strand-seq and cytogenetic approaches to detect both balanced and unbalanced rearrangements, especially those present in subclonal populations that would be missed by standard WGS.