Free-roaming dogs have been present in the Galápagos Islands since the 1830s, but their population significantly increased in the 1900s, posing a threat to wildlife and spreading diseases. Efforts to manage the dog population began in 1981; however, large populations still exist on Isabela and Santa Cruz Islands, with their genetic backgrounds not thoroughly investigated until now. A comprehensive genomic analysis was conducted on 187 modern Galápagos dogs, six historical samples between 1969 and 2003, and data from over 2,000 purebred and village dogs. Findings reveal that contemporary Galápagos dogs are a recent mix of purebred breeds without evidence of a population bottleneck from past culling efforts. Furthermore, historical dogs showed signs of shared ancestry with shepherd dogs. Overall, the study suggests that 1980s culling did not effectively control dog populations and indicates a need for improved population management strategies on the islands to protect endangered species.

The chromosomal theory of inheritance explains that genes on the same chromosome segregate together, while those on different chromosomes assort independently. In cancer, extrachromosomal DNAs (ecDNAs) contribute to oncogene amplification and gene expression dysregulation. Distinct ecDNA sequences can coexist, promoting cooperation among cancer cells. This study reveals that these cooperative ecDNA species are inherited through mitotic co-segregation. Multiple ecDNAs encoding different oncogenes are often found together and correlate in copy number within human cancer cells. During mitosis, these ecDNA species segregate asymmetrically, leading to simultaneous copy-number gains in daughter cells. Active transcription and proximity at mitosis’ onset enhance this co-segregation while inhibiting transcription disrupts it. Computational models elucidate the principles of ecDNA co-segregation, predicting their patterns in cancer cells. This coordinated inheritance supports the co-amplification of ecDNAs, informs therapeutic strategies to target oncogenes, and maintains stability in oncogene interactions and gene regulation across generations.

A new hybridization capture kit has been developed to enhance genomic sequencing for the Annonaceae plant family, targeting 799 low-copy genes. This kit combines 469 genes from the original Annonaceae probe with 334 genes from the universal Angiosperms353 kit. The study compares results from the original Angiosperms353 kit with the custom approach using various specimens. Findings show that the Annonaceae799 kit achieves high recovery rates, and while off-target reads were noted, the genes from the Angiosperms353 panel significantly outperformed those from the original Annonaceae kit in terms of size, on- and off-target regions, and the number of parsimony-informative sites. This integration not only improves the utility of the probe kit for species-level phylogenomics and within-species analysis but also broadens access to new genes for future phylogenetic and population studies.

Snake venoms are complex mixtures of toxic proteins with important medical and pharmacological relevance. To explore the genetic diversity of these venoms, VenomCap was created—an exon-capture probe set targeting toxin-coding genes in various elapid snakes, especially the Hydrophiinae subfamily. Testing on 24 species showed VenomCap’s success in recovering exons from about 1500 target markers, covering 24 known venom gene families. The results were particularly robust among hydrophiines, demonstrating its effectiveness as a cost-efficient alternative to full genome sequencing. VenomCap facilitates the study of venom gene diversity and evolution, with potential applications across other venomous snake families.

Phylogenomic data are enhancing insect phylogenetics, particularly through target enrichment methods. This study introduces an Orthoptera-specific target enrichment (OR-TE) probe set developed from 80 transcriptomes, targeting 1828 loci with diverse evolutionary rates. The probe set was validated by generating phylogenomic data from 36 previously unstudied orthopteran species, capturing an average of 1037 loci and clarifying phylogenetic relationships. Documentation of the probe design and bioinformatics process aims to promote broader adoption of this tool.

Antarctic krill (Euphausia superba) is a crucial species in the Southern Ocean, significant for both its ecological role and commercial value. With climate change posing a threat to its survival, there is an urgent need to explore its adaptive capacity. Historical krill samples from the early 20th century offer a unique opportunity to examine changes in krill populations over time due to various pressures. This study evaluates two cost-effective genomic methods—low-coverage shotgun sequencing and exome capture—on 20 historical krill samples. The results included generating mitochondrial and nuclear ribosomal sequences, revealing genetic variability but no distinct population structure. Exome capture enhanced sequencing efficiency, enabling a deeper genetic analysis. This research aims to leverage historical collections for a better understanding of the biodiversity and adaptability of krill in the face of climate change.

Posterior fossa group A (PFA) ependymoma is a lethal brain cancer diagnosed in infants and young children. The lack of driver events in the PFA linear genome led us to search its 3D genome for characteristic features. Here, we reconstructed 3D genomes from diverse childhood tumor types and uncovered a global topology in PFA that is highly reminiscent of stem and progenitor cells in a variety of human tissues. A remarkable feature exclusively present in PFA are type B ultra long-range interactions in PFAs (TULIPs), regions separated by great distances along the linear genome that interact with each other in the 3D nuclear space with surprising strength. TULIPs occur in all PFA samples and recur at predictable genomic coordinates, and their formation is induced by expression of EZHIP. The universality of TULIPs across PFA samples suggests a conservation of molecular principles that could be exploited therapeutically.

Hybridization is essential for biodiversity and improving crop traits. Recent advances have successfully overcome the hybridization barrier between wheat and rice, two major cereals. Researchers produced allopolyploid hybrid zygotes in vitro, leading to mature plants with a unique genomic composition: wheat nuclear and cytoplasmic DNA paired with variable amounts (11%-47%) of rice mitochondrial DNA. This hybrid, termed OryzaWheat, can pass on rice mtDNA to future generations. Furthermore, a chromosome translocation was noted, where rice chromosome 1 integrated into wheat chromosome 6A. OryzaWheat opens new avenues for genetic resource utilization between the distinct subfamilies of wheat and rice.

Bacteriophages are promising alternatives to traditional antimicrobial treatment of bacterial infections. To further increase the potential of phages, efficient engineering methods are needed. This study investigates an approach to phage engineering based on phage rebooting and compares selected methods of assembly and rebooting of phage genomes. GG assembly of phage genomes and subsequent rebooting by cell-free transcription-translation reactions yielded the most efficient phage engineering and allowed production of a proof-of-concept T7 phage library of 1.8 × 107 phages. We obtained 7.5 × 106 different phages, demonstrating generation of large and diverse libraries suitable for high-throughput screening of mutant phenotypes. Implementing versatile and high-throughput phage engineering methods allows vastly accelerated and improved phage engineering, bringing us closer to applying effective phages to treat infections in the clinic.

Integral and interacting membrane proteins (IIMPs) are crucial biomolecules involved in various life processes, yet their characterization has been hindered by difficulties in purifying and labeling them. This study introduces a novel approach combining cell-free transcription-translation with quartz crystal microbalance with dissipation (TXTL-QCMD). This technique allows for the dynamic characterization of IIMP interactions with lipid bilayers without the need for purification or labeling. The method successfully reconstitutes known IIMP-membrane interactions, including the behavior of E. coli division proteins MinCDE. Additionally, it was applied to the Zorya anti-phage system, revealing specific interactions of the proteins ZorA and ZorB with bacterial membranes, while ZorE exhibited free diffusion. Overall, TXTL-QCMD demonstrates significant potential for exploring the diverse roles of IIMPs in biological systems.