Inter-chromosomal insertions into wild-type chromosomes induced by SCRaMbLE

Genomic rearrangements play a crucial role in shaping biological phenotypic diversity and driving species evolution. Synthetic chromosome rearrangement and modification by LoxP-mediated evolution (SCRaMbLE) has been applied to explore large-scale genomic rearrangements, yet it has been observed that these rearrangements occur exclusively in genomic regions containing loxPsym sites. Here, we found that SCRaMbLE of synthetic yeast harboring synthetic chromosome V and X can generate a variety of synthetic segment insertions into wild-type chromosomes, ranging from 1 to 300 kb. Furthermore, it was revealed that the novel insertions impacted the transcriptional level of neighboring regions and affected the production of exemplar pathway of zeaxanthin. Collectively, our results improve the understanding of the ability of SCRaMbLE to generate complex structural variations in nonsynthetic regions and provide a potential model to explore genomic transposable events.