Biology subjects

Avanzi, C.

Publications and source records attributed to Avanzi, C..

10 recordsLinked to original sources

bioRxiv2026

Rapid evolutionary responses to climate change in maritime pine (Pinus pinaster Ait.) despite widespread adaptive lag

Climate change is profoundly affecting species worldwide and poses a major threat to their long-term persistence. Although trees may have the potential for rapid adaptation to changing climates, empirical evidence remains limited, and whether these long-lived organisms can adapt quickly enough to keep pace with ongoing climate change is still an open question. To investigate real-time responses to contemporary climate change, we combined genomic data from 82 range-wide populations of the widespread tree Pinus pinaster Ait. with intensive sampling of two successive cohorts from two natural populations. Using an original genotype-environment association (GEA) approach to quantify climate (mal)adaptation, we found that most individuals from both target populations showed evidence of an adaptive lag to current climatic conditions, and are predicted to face substantial risk of maladaptation under future climates. Importantly, changes in genomic composition at climate-associated loci between cohorts were consistent with rapid evolutionary responses to ongoing climate change and could not be explained by neutral demographic processes alone, as supported by forward-time genetic simulations. We also observed a lower realised genetic load in the younger cohort, suggesting that the dynamics of deleterious mutations may change with climatic pressure. Our work provides evidence suggesting genetic responses to contemporary climate change within a single generation, including signals of rapid evolutionary changes in genomic composition at climate-associated loci and signatures of purifying selection, despite widespread adaptive lag to current climates. These findings challenge the view that trees only respond slowly to environmental change and highlight the need to integrate evolutionary dynamics into predictive models of species persistence under future climates.

genomics↗

bioRxiv2026

Haplotype-resolved chromosome-level genome assembly of four European white oak species

European white oaks (Quercus section Quercus) are ecologically and economically important forest trees characterized by extensive shared genetic variation and a history of interspecific gene flow. Genomic resources remain uneven across species, limiting comparative analyses and pangenome development. Here, we present haplotype-resolved chromosome-scale genome assemblies and genome annotations for four European white oak species: Quercus robur, Q. petraea, Q. pubescens, and Q. frainetto. The assemblies were generated from PacBio HiFi sequencing data and include both phased haplotypes for each species. Genome sizes range from 779 to 817 Mb and all assemblies are organized into 12 chromosome-scale pseudomolecules with high completeness and contiguity. We additionally provide species-specific repeat annotations, structurally and functionally annotated protein-coding gene sets, and complete organellar genomes. The dataset includes the first reference genomes for Q. pubescens and Q. frainetto, together with newly generated assemblies for Q. robur and Q. petraea produced using a consistent sequencing and analysis workflow. These resources provide a standardized framework for comparative genomics, pangenome construction, genome evolution studies, and investigations of adaptation and introgression across European white oaks.

genomics↗

bioRxiv2026

Minimal effective dose of telacebec administered orally in a murine model of leprosy

Leprosy treatment requires prolonged therapy with challenging patient follow-up. New regimens are needed to simplify current treatments. A recent clinical trial evaluating bedaquiline has shown promising results; however, to prevent the emergence of drug resistance, additional therapeutic options are required. Telacebec (TCB), an imidazopyridine amide targeting the Mycobacterium leprae electron transport chain, represents a promising candidate. In this study, we determined the minimal effective dose (MED) of TCB against M. leprae in vivo by using the proportional bactericidal method in the mouse footpad model. Results were analyzed by using microscopy, RLEP qPCR and molecular viability. The MED obtained was 20 mg/kg. TCB doses [≥]20 mg/kg achieved complete bacterial clearance, similar to bedaquiline 25mg/kg. Molecular enumeration confirmed these findings whereas molecular viability assessment had limited applicability due to insufficient bacterial burden. These findings provide a strong foundation for clinical trial design and the development of combination therapies.

microbiology↗

bioRxiv2025

The FORGENIUS genomic resources: new genotyping tools and genomic data for 23 forest tree species and their Genetic Conservation Units

Genetic diversity is a critical but often overlooked component of biological diversity. The European H2020 FORGENIUS project is precisely aimed at increasing the quality and quantity of genetic data to start monitoring the European network of forest Genetic Conservation Units (GCUs). A first step in this direction was developing standardized genomic resources for 23 forest tree species, spanning from rare and scattered (e.g., Abies nebrodensis and Torminalis glaberrima) to widespread, economically relevant ones (e.g., Fagus sylvatica, Picea abies and Pinus sylvestris). Here, we describe the development and application of targeted genotyping tools, primarily based on Single Primer Enrichment Technology (SPET), along with existing SNP arrays for the selected species. The SPET panels developed in FORGENIUS were designed to capture {square}10,000 loci per species, balancing species-specific and randomly distributed regions to ensure broad genome coverage and minimize ascertainment bias. Across 7,192 genotyped trees, we identified over 1.8 million single nucleotide polymorphisms (SNPs) covering approximately 50 Mb of DNA sequence. SPET panels demonstrated high genotyping efficiency and cross-species transferability, especially within genera such as Quercus and Abies. They represent a cost-effective, flexible, and scalable solution for population-level genetic assessments across diverse taxa, enabling standardized, genome-wide characterization of the GCU network. These resources not only promote the establishment of genetic monitoring, support genetically informed conservation strategies and improve our understanding of adaptive responses in European forests, but also enhance species delimitation and hybrid detection, and enable the characterization of phylogenetically related but previously underexplored species.

genomics↗

bioRxiv2025

Near-infrared spectroscopy-based models correctly classify Abies alba seed origin and predict germination properties

Forestry industry requires high-quantity and quality seeds for afforestation and assisted migration programs. Finding reliable non-destructive methods to characterize seeds would significantly enhance efforts to identify climate-adapted populations. This study presents near-infrared (NIR) spectroscopy models to classify seed origin and predict germination characteristics at different temperatures non-destructively. We focus on Abies alba Mill., a key European forest tree with genetic variation along climatic gradients and seeds with shallow physiological dormancy. Seeds from six populations were analyzed using NIR spectroscopy, and germination was tested at 15{degrees}C, 20{degrees}C, and 25{degrees}C after stratification treatments at 4{degrees}C (0 or 3 weeks). Population classification accuracy using Partial Least Squares Discriminant Analysis was 69%, with significant NIR peaks at 1712, 1929, and 2111 nm, linked to moisture content and storage compounds. NIR spectra explained 51% and 65% of the variation in germination probability and timing using Partial Least Squares Regression, with significant peaks at 1712, 1929, 2111, 1632, and 2073 nm. General Linear Mixed-Effects Models showed that a NIR predictor contributed to 39% of the germination probability variance explained by fixed-effects, and the stratification treatment was the most important driver explaining germination time. Our results proved the utility of NIR-based tools to effectively classify bulked seeds and predict germination, opening new perspectives to nursery and forestry sectors and populations adaptation and adjustments to warming climate. This study will facilitate further investigations on the physiological processes that occur during dormancy, a critical process for forest regeneration given the expected impact of shorter and warmer winters on seed behavior.

ecology↗

bioRxiv2023

Spatial conservation prioritisation for intraspecific genetic diversity of three forest tree species with a fragmented distribution in Italy

The Kunming-Montreal Global Biodiversity Framework recognised the urgency of taking action to conserve intraspecific genetic diversity (IGD) as an insurance against habitat degradation and environmental change. Recent work suggests that 90-99% of IGD should be conserved to safeguard viability of future generations. Here, we addressed such a conservation issue in three forest tree species in Italy: silver fir (Abies alba Mill.), Heldreichs pine (Pinus heldreichii H. Christ), and pedunculate oak (Quercus robur L.). We used microsatellite markers to measure IGD of 36 (A. alba), 15 (P. heldreichii) and 25 (Q. robur) natural sites, including several putative glacial refugia. We developed a spatial conservation planning (SCP) analysis to quantify the genetic irreplaceability of each site and identify the minimum set coverage ensuring IGD protection. Finally, we compared SCP results with the contributions to allelic diversity within and between sites, total allelic diversity and private allelic richness. We found that between 44% and 73% of sites were required to conserve 90-99% of the alleles, and that this conservation effort held even when targeting lower percentages of alleles to protect (50-75%). Glacial refugia were often included in the minimum set coverage, confirming theoretical and biogeographical expectations. Finally, sites with high genetic irreplaceability were found to have higher private allelic richness on average. These results are discussed in the light of the biogeographic history of the species studied and the current policies for the conservation of forest genetic resources.

evolutionary biology↗

bioRxiv2023

The latitudinal trend in genetic diversity and distinctiveness of Quercus robur rear edge forest remnants calls for new conservation priorities

Knowledge of the spatial distribution of intraspecific genetic variation is essential for planning conservation actions, designing networks of protected areas, and informing possible assisted migration strategies. Although the Italian peninsula harbours unique genetic variation as a legacy of Quaternary migrations, only sporadic genetic information is available for forest tree species. Here, we present the first geographically comprehensive genetic characterisation of Quercus robur, an iconic broadleaved species of European floodplain forests, in an area which acted as a primary glacial refugium for the species. 745 individuals from 25 populations were sampled and genotyped with 16 microsatellite markers. Their genetic structure was assessed through various metrics of diversity and distinctiveness, as well as by Bayesian clustering and multivariate methods. The demographic history of inferred gene pools was evaluated through Approximate Bayesian Computation analysis. Genetic distinctiveness showed a decline with increasing latitude, while allelic richness reached its peak in central Italy. A south-to-north trend in the complexity of the genetic structure was observed, with peninsular Italy being characterised by intermingled gene pools in contrast to the relative homogeneity exhibited by northern populations. Demographic inference indicated that the southern gene pool has been genetically isolated since the penultimate interglacial, whereas populations from central Italy persisted locally in a mosaic of small refugia during the last glaciation. Our results brought out the complexity of the genetic structure of forest trees populations in southern Europe. At least three Q. robur refugia contributed to the genetic layout of extant populations after the last glacial period, but refugial areas were probably even more numerous in central Italy. Such a detailed characterization sheds new light on the priorities to be established for the conservation of highly fragmented Q. robur populations in an area rich in diversified genetic lineages.

genetics↗

bioRxiv2021

A new paradigm for leprosy diagnosis based on host gene expression

Transcriptional profiling is a powerful tool to investigate and detect human diseases. In this study, we used bulk RNA-sequencing (RNA-Seq) to compare the transcriptomes in skin lesions of leprosy patients or controls affected by other dermal conditions such as granuloma annulare, a confounder for paucibacillary leprosy. We identified five genes capable of accurately distinguishing multibacillary and paucibacillary leprosy from other skin conditions. Indoleamine 2,3-dioxygenase 1 (IDO1) expression alone was highly discriminatory, followed by TLR10, BLK, CD38, and SLAMF7, whereas the HS3ST2 and CD40LG mRNA separated multi- and paucibacillary leprosy. Finally, from the main differentially expressed genes (DEG) and enriched pathways, we conclude that paucibacillary disease is characterized by epithelioid transformation and granuloma formation, with an exacerbated cellular immune response, while multibacillary leprosy features epithelial-mesenchymal transition with phagocytic and lipid biogenesis patterns in the skin. These findings will help catalyze the development of better diagnostic tools and potential host-based therapeutic interventions. Finally, our data may help elucidate host-pathogen interplay driving disease clinical manifestations. Author SummaryDespite effective treatment, leprosy is still a significant public health issue in more than 120 countries, with more than 200 000 new cases yearly. The disease is caused mainly by Mycobacterium leprae, a slow-growing bacillus still uncultivable in axenic media. This limitation has hampered basic research into host-pathogen interaction and the development of new diagnostic assays. Currently, leprosy is diagnosed clinically, with no standalone diagnostic assay accurate enough for all clinical forms. Here, we use RNA-seq transcriptome profiling in leprosy lesions and granuloma annulare to identify mRNA biomarkers with potential diagnostic applications. Also, we explored new pathways that can be useful in further understanding the host-pathogen interaction and how the bacteria bypass host immune defenses. We found that IDO1, a gene involved with tryptophan catabolism, is an excellent candidate for distinguishing leprosy lesions from other dermatoses. Additionally, we observed that a previous signature of keratinocyte development and cornification negatively correlates with epithelial-mesenchymal transition genes in the skin, suggesting new ways in which the pathogen may subvert its host to survive and spread throughout the body. Our study identifies new mRNA biomarkers that can improve leprosy diagnostics and describe new insights about host-pathogen interactions in human skin.

molecular biology↗

bioRxiv2021

Fine-scale spatial genetic structure across the species range reflects recent colonization of high elevation habitats in silver fir (Abies alba Mill.)

Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations resilience and adaptive potential. The spatial distribution of genetic diversity, referred to as fine-scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies alba Mill.) population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east-west isolation-by-distance pattern consistent with the post-glacial colonization history of the species. Genetic differentiation among sites (FCT=0.148) was an order of magnitude greater than between elevations within sites (FSC=0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modeling revealed that elevation and, to a lesser extent, post-glacial colonization history, but not climatic and habitat variables, were the best predictors of FGSG across populations. These results may suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide complementary information about demographic history and could be used for defining conservation priorities.

evolutionary biology↗

bioRxiv2020

Leprosy in wild chimpanzees

Humans are considered the main host for Mycobacterium leprae, the aetiologic agent of leprosy, but spill-over to other mammals such as nine-banded armadillos and red squirrels occurs. Although naturally acquired leprosy has also been described in captive nonhuman primates, the exact origins of infection remain unclear. Here, we report on leprosy-like lesions in two wild populations of western chimpanzees (Pan troglodytes verus) in the Cantanhez National Park, Guinea-Bissau, and the Tai National Park, Cote dIvoire, West Africa. Longitudinal monitoring of both populations revealed the progression of disease symptoms compatible with advanced leprosy. Screening of faecal and necropsy samples confirmed the presence of M. leprae as the causative agent at each site and phylogenomic comparisons with other strains from humans and other animals show that the chimpanzee strains belong to different and rare genotypes (4N/O and 2F). The independent evolutionary origin of M. leprae in two geographically distant populations of wild chimpanzees, with no prolonged direct contact with humans, suggests multiple introductions of M. leprae from an unknown animal or environmental source.

evolutionary biology↗