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

Synthetic biology is advancing that enable the assembly of biomolecular components for rewiring and reprogramming organisms. Synthetic chromosome recombination and modification by LoxP-mediated evolution (SCRaMbLE) technology in the synthetic yeast genome project can induce a high frequency of chromosomal rearrangement events. Current research on the SCRaMbLE system has focused on structural variations in synthetic chromosomes themselves. Here, we demonstrate that SCRaMbLE can be employed as a transposable model that synthetic DNA segments can be inserted into wild-type chromosomes. Using next- and third-generation sequencing, we observed that SCRaMbLE can produce transposable insertion into wild-type chromosomes. Furthermore, it was revealed that novel insertions impacted the transcriptional level of neighboring regions and affected the production 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.