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1. High levels of intra-strain structural variation in Drosophila simulans X pericentric heterochromatin

   https://doi.org/10.1093/genetics/iyad176  

   Courret, Cécile; Larracuente, Amanda M (September 2023, GENETICS)

   Bateman, J (Ed.)

   Abstract Large genome structural variations can impact genome regulation and integrity. Repeat-rich regions like pericentric heterochromatin are vulnerable to structural rearrangements although we know little about how often these rearrangements occur over evolutionary time. Repetitive genome regions are particularly difficult to study with genomic approaches, as they are missing from most genome assemblies. However, cytogenetic approaches offer a direct way to detect large rearrangements involving pericentric heterochromatin. Here, we use a cytogenetic approach to reveal large structural rearrangements associated with the X pericentromeric region of Drosophila simulans. These rearrangements involve large blocks of satellite DNA—the 500-bp and Rsp-like satellites—which colocalize in the X pericentromeric heterochromatin. We find that this region is polymorphic not only among different strains, but between isolates of the same strain from different labs, and even within individual isolates. On the one hand, our observations raise questions regarding the potential impact of such variation at the phenotypic level and our ability to control for such genetic variability. On the other hand, this highlights the very rapid turnover of the pericentric heterochromatin most likely associated with genomic instability of the X pericentromere. It represents a unique opportunity to study the dynamics of pericentric heterochromatin, the evolution of associated satellites on a very short time scale, and to better understand how structural variation arises. 

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2. Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion

   https://doi.org/10.1128/mbio.01046-25  

   Sanath-Kumar, Ram; Rahman, Arafat; Ren, Zhongqing; Reynolds, Ian P; Augusta, Lauren; Fuqua, Clay; Weisberg, Alexandra J; Wang, Xindan (June 2025, mBio)

   Komeili, Arash (Ed.)

   ABSTRACT Multipartite bacterial genome organization can confer advantages, including coordinated gene regulation and faster genome replication, but is challenging to maintain.Agrobacterium tumefacienslineages often contain a circular chromosome (Ch1), a linear chromosome (Ch2), and multiple plasmids. We previously observed that in some stocks of the C58 lab model, Ch1 and Ch2 were fused into a linear dicentric chromosome. Here we analyzedAgrobacteriumnatural isolates from the French Collection for Plant-Associated Bacteria and identified two strains distinct from C58 with fused chromosomes. Chromosome conformation capture identified integration junctions that were different from the C58 fusion strain. Genome-wide DNA replication profiling showed that both replication origins remained active. Transposon sequencing revealed that partitioning systems of both chromosome centromeres were essential. Importantly, the site-specific recombinase XerCD is required for the survival of the strains containing the fusion chromosome. Our findings show that replicon fusion occurs in natural environments and that balanced replication arm sizes and proper resolution systems enable the survival of such strains. IMPORTANCEMost bacterial genomes are monopartite with a single, circular chromosome. However, some species, likeAgrobacterium tumefaciens, carry multiple chromosomes. Emergence of multipartite genomes is often related to adaptation to specific niches, including pathogenesis or symbiosis. Multipartite genomes confer certain advantages; however, maintaining this complex structure can present significant challenges. We previously reported a laboratory-propagated lineage ofA. tumefaciensstrain C58 in which the circular and linear chromosomes fused to form a single dicentric chromosome. Here we discovered two geographically separated environmental isolates ofA. tumefacienscontaining fused chromosomes with integration junctions different from the C58 fusion chromosome, revealing the constraints and diversification of this process. We found that balanced replication arm sizes and the repurposing of multimer resolution systems enable the survival and stable maintenance of dicentric chromosomes. These findings reveal how multipartite genomes function across different bacterial species and the role of genomic plasticity in bacterial genetic diversification. 

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3. Construction and iterative redesign of synXVI a 903 kb synthetic Saccharomyces cerevisiae chromosome

   https://doi.org/10.1038/s41467-024-55318-3  

   Goold, Hugh D; Kroukamp, Heinrich; Erpf, Paige E; Zhao, Yu; Kelso, Philip; Calame, Julie; Timmins, John_J B; Wightman, Elizabeth_L I; Peng, Kai; Carpenter, Alexander C; et al (December 2025, Nature Communications)

   Abstract The Sc2.0 global consortium to design and construct a synthetic genome based on theSaccharomyces cerevisiaegenome commenced in 2006, comprising 16 synthetic chromosomes and a new-to-nature tRNA neochromosome. In this paper we describe assembly and debugging of the 902,994-bp syntheticSaccharomyces cerevisiaechromosomesynXVIof the Sc2.0 project. Application of the CRISPR D-BUGS protocol identified defective loci, which were modified to improve sporulation and recover wild-type like growth when grown on glycerol as a sole carbon source when grown at 37˚C. LoxPsym sites inserted downstream of dubious open reading frames impacted the 5’ UTR of genes required for optimal growth and were identified as a systematic cause of defective growth. Based on lessons learned from analysis of Sc2.0 defects andsynXVI, anin-silicoredesign of thesynXVIchromosome was performed, which can be used as a blueprint for future synthetic yeast genome designs. Thein-silicoredesign ofsynXVIincludes reduced PCR tag frequency, modified chunk and megachunk termini, and adjustments to allocation of loxPsym sites and TAA stop codons to dubious ORFs. This redesign provides a roadmap into applications of Sc2.0 strategies in non-yeast organisms. 

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4. The complete sequence and comparative analysis of ape sex chromosomes

   https://doi.org/10.1038/s41586-024-07473-2  

   Makova, Kateryna D; Pickett, Brandon D; Harris, Robert S; Hartley, Gabrielle A; Cechova, Monika; Pal, Karol; Nurk, Sergey; Yoo, DongAhn; Li, Qiuhui; Hebbar, Prajna; et al (June 2024, Nature)

   Apes possess two sex chromosomes—the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked to infertility¹. The X chromosome is vital for reproduction and cognition². Variation in mating patterns and brain function among apes suggests corresponding differences in their sex chromosomes. However, owing to their repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (bonobo (Pan paniscus), chimpanzee (Pan troglodytes), western lowland gorilla (Gorilla gorilla gorilla), Bornean orangutan (Pongo pygmaeus) and Sumatran orangutan (Pongo abelii)) and a lesser ape (the siamang gibbon (Symphalangus syndactylus)), and untangled the intricacies of their evolution. Compared with the X chromosomes, the ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements—owing to the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements and satellites. Many Y chromosome genes expand in multi-copy families and some evolve under purifying selection. Thus, the Y chromosome exhibits dynamic evolution, whereas the X chromosome is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of more than 100 individual great apes. These reference assemblies are expected to inform human evolution and conservation genetics of non-human apes, all of which are endangered species. 

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5. High‐quality chromosome‐level genome assembly and multi‐omics analysis of rosemary ( Salvia rosmarinus ) reveals new insights into the environmental and genome adaptation

   https://doi.org/10.1111/pbi.14305  

   Lai, Yong; Ma, Jinghua; Zhang, Xuebin; Xuan, Xiaobo; Zhu, Fengyun; Ding, Shen; Shang, Fude; Chen, Yuanyuan; Zhao, Bing; Lan, Chen; et al (July 2024, Plant Biotechnology Journal)

   Summary High‐quality genome of rosemary (Salvia rosmarinus) represents a valuable resource and tool for understanding genome evolution and environmental adaptation as well as its genetic improvement. However, the existing rosemary genome did not provide insights into the relationship between antioxidant components and environmental adaptability. In this study, by employing Nanopore sequencing and Hi‐C technologies, a total of 1.17 Gb (97.96%) genome sequences were mapped to 12 chromosomes with 46 121 protein‐coding genes and 1265 non‐coding RNA genes. Comparative genome analysis reveals that rosemary had a closely genetic relationship withSalvia splendensandSalvia miltiorrhiza, and it diverged from them approximately 33.7 million years ago (MYA), and one whole‐genome duplication occurred around 28.3 MYA in rosemary genome. Among all identified rosemary genes, 1918 gene families were expanded, 35 of which are involved in the biosynthesis of antioxidant components. These expanded gene families enhance the ability of rosemary adaptation to adverse environments. Multi‐omics (integrated transcriptome and metabolome) analysis showed the tissue‐specific distribution of antioxidant components related to environmental adaptation. During the drought, heat and salt stress treatments, 36 genes in the biosynthesis pathways of carnosic acid, rosmarinic acid and flavonoids were up‐regulated, illustrating the important role of these antioxidant components in responding to abiotic stresses by adjusting ROS homeostasis. Moreover, cooperating with the photosynthesis, substance and energy metabolism, protein and ion balance, the collaborative system maintained cell stability and improved the ability of rosemary against harsh environment. This study provides a genomic data platform for gene discovery and precision breeding in rosemary. Our results also provide new insights into the adaptive evolution of rosemary and the contribution of antioxidant components in resistance to harsh environments. 

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