A high-quality rhesus macaque genome: Genome technology has improved substantially since the first full organismal genomes were generated. Applying new technology, Warren et al. refined the genome of the rhesus macaque, a model nonhuman primate. Long-read technology and other recent advances in sequencing technology were applied to generate a genome with far fewer gaps and helped to refine the locations and numbers of repetitive elements. Furthermore, the authors performed resequencing among populations to identify the genetic variability of the rhesus macaque. Thus, a previously incomplete and inaccurate set of sequence information is now fully resolved, improving gene mapping for biomedical and comparative genetic studies. Science , this issue p. eabc6617

Adaptive archaic hominin genes: As they migrated out of Africa and into Europe and Asia, anatomically modern humans interbred with archaic hominins, such as Neanderthals and Denisovans. The result of this genetic introgression on the recipient populations has been of considerable interest, especially in cases of selection for specific archaic genetic variants. Hsieh et al. characterized adaptive structural variants and copy number variants that are likely targets of positive selection in Melanesians. Focusing on population-specific regions of the genome that carry duplicated genes and show an excess of amino acid replacements provides evidence for one of the mechanisms by which genetic novelty can arise and result in differentiation between human genomes. Science , this issue p. eaax2083

Postharvest spoilage fungi, such as Botrytis cinerea, are considered the main cause of losses of fresh fruit quality and vegetables during storage, distribution, and consumption. The current control strategy is the use of SO₂ generator pads whose application is now largely under observation. A high quantity of SO₂ can be deleterious for fresh fruits and vegetables and it is not allowed in organic agriculture. For this reason, great attention has been recently focused on identifying Biological Control Agents (BCA) to implement biological approaches devoid of chemicals. In this direction, we carried out our study in isolating five different non-Saccharomyces yeast strains from local vineyards in the South of Italy as possible BCA. We performed both in vitro and in vivo assays in semi-commercial conditions on detached grape berries stored at 0 °C, simulating the temperature normally used during cold storage, and obtained relevant results. We isolated three M. pulcherrima strains and one L. thermotolerans strain able to largely antagonize the development of the B. cinerea, at both in vitro and in vivo conditions. In particular, we detected the ability of the three isolates of M. pulcherrima strains Ale4, N20/006, and Pr7 and the L. thermotolerans strain N10 to completely inhibit (100% in reduction) the mycelial growth of B. cinerea by producing fungistatic compounds. We found, using an extracellular lytic enzymes activity assay, that such activity could be related to lipid hydrolyzation, β-1,3-glucanase and pectinase activity, and pectinase and protease activity, depending on the yeasts used. Results from our in vitro assays allowed us to hypothesize for M. pulcherrima strains Ale4 and N20/006 a possible combination of both the production of soluble metabolites and volatile organic compounds to antagonize against B. cinerea growth. Moreover, in semi-commercial conditions, the M. pulcherrima strain N20/006 and L. thermotolerans strain N10 showed relevant antagonistic effect also at low concentrations (with a significantly reduction of ‘slip skin’ incidence of 86.4% and 72.7%, respectively), thus highlighting a peculiar property to use in commercial development for organic agriculture and the handling process.

Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and is an important animal model for human disease studies. A deep understanding of its genetics is therefore required for both biomedical and evolutionary studies. Among structural variants, inversions represent a driving force in speciation and play an important role in disease predisposition. Here we generated a genome-wide map of inversions between human and macaque, combining single-cell strand sequencing with cytogenetics. We identified 375 total inversions between 859 bp and 92 Mbp, increasing by eightfold the number of previously reported inversions. Among these, 19 inversions flanked by segmental duplications overlap with recurrent copy number variants associated with neurocognitive disorders. Evolutionary analyses show that in 17 out of 19 cases, the Hominidae orientation of these disease-associated regions is always derived. This suggests that duplicated sequences likely played a fundamental role in generating inversions in humans and great apes, creating architectures that nowadays predispose these regions to disease-associated genetic instability. Finally, we identified 861 genes mapping at 156 inversions breakpoints, with some showing evidence of differential expression in human and macaque cell lines, thus highlighting candidates that might have contributed to the evolution of species-specific features. This study depicts the most accurate fine-scale map of inversions between human and macaque using a two-pronged integrative approach, such as single-cell strand sequencing and cytogenetics, and represents a valuable resource toward understanding of the biology and evolution of primate species.

Human chromosome 15q25 is involved in several disease-associated structural rearrangements, including microdeletions and chromosomal markers with inverted duplications. Using comparative fluorescence in situ hybridization, strand-sequencing, single-molecule, real-time sequencing and Bionano optical mapping analyses, we investigated the organization of the 15q25 region in human and nonhuman primates. We found that two independent inversions occurred in this region after the fission event that gave rise to phylogenetic chromosomes XIV and XV in humans and great apes. One of these inversions is still polymorphic in the human population today and may confer differential susceptibility to 15q25 microdeletions and inverted duplications. The inversion breakpoints map within segmental duplications containing core duplicons of the GOLGA gene family and correspond to the site of an ancestral centromere, which became inactivated about 25 million years ago. The inactivation of this centromere likely released segmental duplications from recombination repression typical of centromeric regions. We hypothesize that this increased the frequency of ectopic recombination creating a hotspot of hominid inversions where dispersed GOLGA core elements now predispose this region to recurrent genomic rearrangements associated with disease. Human chromosome 15 derived from a fission event that occurred in the ancestor of great apes. Following inactivation of the ancestral centromere at 15q25 a dispersal of segmental duplications took place, providing templates for ectopic recombination and predisposing the region to genomic instability. Different disease-associated microdeletions and chromosomal markers have been described with breakpoints mapping within these segmental duplications. To gain insight into the instability at 15q25, we sought to analyze this region in human and nonhuman primates using multiple genomics techniques and demonstrated the presence of two independent inversion events that occurred during great apes evolution. One of these inversions is still polymorphic in humans and may cause, in conjunction with a GOLGA core duplicon—a ~14 kbp chromosome 15 repeat, susceptibility to non-allelic homologous recombination leading to pathogenic recurrent rearrangements. Our results support the existence of a strong relationship between inversions and core duplicons and reinforce the hypothesis that GOLGA repeats play a fundamental role both in disease and evolution.

Grapevine (Vitis vinifera L.), a globally significant crop, is highly susceptible to Botrytis cinerea, the causative agent of gray mold disease. This study investigates transcriptomic responses to B. cinerea in tolerant and susceptible grapevine genotypes using RNA sequencing (RNA-seq). Differentially expressed genes (DEGs) were identified at three time points (T1, T2, T3), highlighting both genotype-independent and genotype-specific responses. Early-stage infection (T1) revealed rapid and robust activation of defense pathways in both genotypes, though the tolerant genotype showed enhanced modulation of metabolic processes by T2, prioritizing secondary metabolism and stress adaptation over growth. In contrast, the susceptible genotype exhibited less coordinated metabolic reprogramming, with delayed or weaker activation of key defense mechanisms. Gene Ontology and KEGG analyses identified critical pathways, including phenylpropanoid biosynthesis-like lignin metabolism, MAPK signaling, as well as candidate genes such as WRKY transcription factors and enzymes involved in cell wall fortification and antifungal compound biosynthesis. Genotype-specific responses emphasized metabolic flexibility as a determinant of resistance, with the tolerant genotype exhibiting superior resource allocation to defense pathways. These findings provide insights into the molecular basis of grapevine resistance to B. cinerea, offering potential targets for breeding or genetic engineering to enhance resilience and reduce fungicide dependency.