Aneuploidy compromises genomic stability, often leading to embryo inviability, and is frequently associated with tumorigenesis and aging. Different aneuploid chromosome stoichiometries lead to distinct transcriptomic and phenotypic changes, making it helpful to study aneuploidy in tightly controlled genetic backgrounds. By deploying the engineered SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) system to the newly synthesized megabase Sc2.0 chromosome VII (synVII), we constructed a synthetic disomic yeast and screened hundreds of SCRaMbLEd derivatives with diverse chromosomal rearrangements. Phenotypic characterization and multi-omics analysis revealed that fitness defects associated with aneuploidy could be restored by (1) removing most of the chromosome content or (2) modifying specific regions in the duplicated chromosome. These findings indicate that both chromosome copy number and specific chromosomal regions contribute to the aneuploidy-related phenotypes, and the synthetic chromosome resource opens new paradigms in studying aneuploidy.

Recent advances in synthetic genomics launched the ambitious goal of generating the first synthetic designer eukaryote, based on the model organism Saccharomyces cerevisiae (Sc2.0). Excitingly, the Sc2.0 project is now nearing its completion and SCRaMbLE, an accelerated evolution tool implemented by the integration of symmetrical loxP sites (loxPSym) downstream of almost every non-essential gene, is arguably the most applicable synthetic genome-wide alteration to date. The SCRaMbLE system offers the capability to perform rapid genome diversification, providing huge potential for targeted strain improvement. Here we describe how SCRaMbLE can evolve a semi-synthetic yeast strain housing the synthetic chromosome II (synII) to generate hygromycin B resistant genotypes. Exploiting long-read nanopore sequencing, we show that all structural variations are due to recombination between loxP sites, with no off-target effects. We also highlight a phenomenon imposed on SCRaMbLE termed “essential raft”, where a fragment flanked by a pair of loxPSym sites can move within the genome but cannot be removed due to essentiality restrictions. Despite this, SCRaMbLE was able to explore the genomic space and produce alternative structural compositions that resulted in an increased hygromycin B resistance in the synII strain. We show that among the rearrangements generated via SCRaMbLE, deletions of YBR219C and YBR220C contribute to hygromycin B resistance phenotypes. However, the hygromycin B resistance provided by SCRaMbLEd genomes showed significant improvement when compared to corresponding single deletions, demonstrating the importance of the complex structural variations generated by SCRaMbLE to improve hygromycin B resistance. We anticipate that SCRaMbLE and its successors will be an invaluable tool to predict and evaluate the emergence of antibiotic resistance in yeast.

Here we report the design, construction and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae . Intending to address one of the central design principles of the Sc2.0 project, the ∼190 kb tRNA neochromosome houses all 275 relocated nuclear tRNA genes. To maximize stability, the design incorporated orthogonal genetic elements from non- S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enable an orthogonal SCRaMbLE system capable of adjusting tRNA abundance. Following construction, we obtained evidence of a potent selective force once the neochromosome was introduced into yeast cells, manifesting as a spontaneous doubling in cell ploidy. Furthermore, tRNA sequencing, transcriptomics, proteomics, nucleosome mapping, replication profiling, FISH and Hi-C were undertaken to investigate questions of tRNA neochromosome behavior and function. Its construction demonstrates the remarkable tractability of the yeast model and opens up new opportunities to directly test hypotheses surrounding these essential non-coding RNAs. Highlights: De novo design, construction and functional characterization of a neochromosome containing all 275 nuclear tRNA genes of Saccharomyces cerevisiae . Increasing the copy number of the 275 highly expressed tRNA genes causes cellular burden, which the host cell likely buffers either by selecting for partial tRNA neochromosome deletions or by increasing its ploidy. The tRNA neochromosome can be chemically extracted and transformed into new strain backgrounds, enabling its transplantation into multi-synthetic chromosome strains to finalize the Sc2.0 strain. Comprehensive functional characterization does not pinpoint a singular cause for the cellular burden caused by the tRNA neochromosome, but does reveal novel insights into its tRNA and structural chromosome biology.

The protocol for Extraction and Analysis of Small Yeast-Chromosomes (EASY-C) is a transformative, rapid, cost-effective, and user-friendly method designed for the efficient isolation of artificial synthetic mini-chromosomes (~42–52 kb) and large plasmids (~12 kb) from Saccharomyces cerevisiae wild-type and synthetic yeast strains (Sc2.0), and a range of nonconventional yeast (NCY) species. In this two-step workflow, the DNA from yeast is first extracted and transferred into bacteria, and then the circular DNA is recovered from the bacteria and subjected to downstream analysis, including long-read sequencing. The EASY-C protocol operates at small volumes (~1 mL) and requires less than 2.5 hours, allowing the use of standard commercial plasmid purification kits for bacterial plasmids. Under the tested conditions, the EASY-C methodology yielded clean DNA that could be digested and linearized prior to sequencing, resulting in a higher number of high-quality reads (~2000). The EASY-C protocol worked successfully for the extraction of a variety of constructs, including low-copy centromeric vectors (CEN/ARS), high-copy plasmids (pan/ARS), and artificial mini-chromosomes harbouring (CEN/ARS). It is also applicable to a variety of yeast species, including NCY such as Starmerella sp., Maudiozyma sp., and Kazachstania sp. Thanks to its precision, robustness, and simplicity, EASY-C equips researchers with a powerful, time-saving tool and cost-effective approach to accelerate the validation of a wide array of synthetic genetic and metabolic constructs engineered in vivo across diverse yeast species.

: Large-scale genome minimisation in eukaryotes remains a major challenge due to essential genes embedded within deletion-refractory regions and pervasive synthetic lethal interactions. Here, we address these limitations by engineering an essential neo–chromosome III that relocates all 14 essential genes from synthetic chromosome III onto a separate chromosome, thereby enabling further minimisation of synIII. To further expand design space, we created highly synthetic neo-chromosome variants with sequences absent from natural genomes. We refactored essential gene expression using both native and orthogonal promoter–terminator pairs from Saccharomyces paradoxus and S. eubayanus . Reporter assays showed that orthogonal regulatory elements largely recapitulate S. cerevisiae activity. Both architectures restored viability in essential gene deletion libraries, demonstrating robust cross-species complementation. Engineered linear and circular forms of essential neo-chromosomes were highly stable over 100 generations and supported a near wild-type phenotype. Relocating essential functions enabled SCRaMbLE-mediated deletion of previously inaccessible regions, substantially expanding the deletion landscape. To improve the screening efficiency of SCRaMbLEd strains, we developed a SCRaMbLE reporter, ERICA (Elementary Random Integration Cassette), a loxPsym-flanked URA3 cassette that integrates randomly and enables iterative selection. Nanopore sequencing confirmed complex rearrangements, including deletions of up to ∼40 kb and loss of essential loci. Together, this work establishes a modular and extensible platform for orthogonal essential gene engineering and SCRaMbLE-enabled genome reduction, providing key design principles for next-generation synthetic eukaryotic genomes. These findings have broad implications beyond yeast, providing transferable design principles for genome minimisation in more complex eukaryotic systems, including mammalian and human cells.

Efficient DNA delivery remains one of the greatest barriers to engineering non-conventional yeasts, limiting their genetic domestication and exploitation as next-generation microbial cell factories. Here, we present BRIDGE (Bacteria-to-yeast Rapid Interkingdom DNA Gene Exchange), an integrated synthetic biology platform for broad-host interkingdom DNA delivery. BRIDGE is centred on a compact 6-kb Pan/ARS–oriT broad-host BRIDGE vector, enabled by a super conjugative helper plasmid (pSC5). Using BRIDGE, we expanded interkingdom DNA transfer from representatives of four genera accessible using pSC5 alone to ten phylogenetically diverse yeast genera, including Saccharomyces, Maudiozyma, Starmerella, Kazachstania, Yarrowia, Zygosaccharomyces, Lachancea, Kluyveromyces, Pichia and Komagataella . To demonstrate the versatility of BRIDGE, we engineered a 16-kb visual reporter carrying a synthetic five-gene violacein biosynthetic pathway from Chromobacterium violaceum . Individual transcriptional units were first constructed using the YeastFab modular cloning system and subsequently assembled into the complete pathway by single-step in vivo homologous recombination in Saccharomyces cerevisiae , followed by rapid plasmid recovery using the EASY-C platform. The reporter was successfully delivered to all ten yeast genera, demonstrating efficient BRIDGE transfer of complete multigene synthetic pathways. Robust violacein production was observed across all six Saccharomyces species tested, providing a rapid visual marker for transformant identification, while modest functional pathway expression was also detected in Kazachstania and Kluyveromyces . Successful pathway transfer, albeit without visible pigmentation, was achieved in the remaining genera indicating that regulatory compatibility, rather than DNA transfer, is the principal determinant of heterologous pathway expression in distantly related yeasts. Collectively, BRIDGE establishes an integrated Design–Build–Recover–Deliver workflow that combines modular in vitro construction of transcriptional units, single-step in vivo assembly of multigene pathways, rapid plasmid recovery using the EASY-C platform and broad-host interkingdom DNA delivery. This versatile framework enables the rapid genetic modification of previously intractable microorganisms, expanding the synthetic biology toolbox for sustainable biomanufacturing and industrial biotechnology. Abstract Figure: Abstract Figure. Overview of the BRIDGE technology: BRIDGE (Bacteria-to-yeast Rapid Interkingdom DNA Gene Exchange) is a broad-host platform for conjugation-mediated DNA transfer from bacteria to phylogenetically diverse yeasts. An Escherichia coli donor cell (left) harbours a ~60 kb super conjugative helper plasmid encoding the conjugative machinery together with a Pan/ARS-based BRIDGE delivery vector capable of stable replication across diverse yeast species. The vector carries an oriT sequence that mediates interkingdom DNA transfer and a five-gene violacein ( vioA–E ) biosynthetic pathway that serves as a visual reporter of successful DNA delivery. Following transfer, recipient yeast cells (right) acquire the delivery vector and develop varying intensities of purple pigmentation, enabling rapid identification of positive colonies. BRIDGE was successfully evaluated across 12 phylogenetically diverse yeast species representing 10 genera, including Saccharomyces cerevisiae, Maudiozyma bulderi 39, Starmerella batistae, Starmerella bombicola, Kazachstania naganishii, Kazachstania aerobia, Yarrowia lipolytica, Zygosaccharomyces bailii, Lachancea thermotolerans, Kluyveromyces aestuarii, Pichia manshurica , and Komagataella phaffii .