Biology subjects

Iannucci, A.

Publications and source records attributed to Iannucci, A..

12 recordsLinked to original sources

bioRxiv2026

Sea stickleback genome reveals repeated chromosomal rearrangements in sticklebacks

Sticklebacks (Gasterosteidae) encompass model organisms which are of particular interest for evolutionary and ecological genomics. Within Gasterosteidae, chromosome number is variable (2n=40-46) and independent fusions of homologous chromosomes have been proposed. The sea stickleback (or fifteen-spined stickleback, Spinachia spinachia ) has the lowest known number of chromosomes (2n=40) and hence is crucial in understanding chromosome evolution among sticklebacks, but is so far missing in genomic datasets. Here, we present a high-quality diploid genome assembly of S. spinachia. PacBio HiFi and Hi-C reads were assembled into a genome of 407.5 Mb in size, consisting of 20 chromosomes, with an N50 of 6.6 Mb and 98.96% complete single-copy BUSCO genes. A phylogenetic tree inferred across five stickleback species and four outgroup genomes from 19,156 genes, alongside synteny analyses and ancestral chromosome reconstructions, confirms S. spinachia as the sister species to the four-spined stickleback (Apeltes quadracus) and not as the sister group to all other sticklebacks as once thought. It has one species-specific chromosome fusion and shares two fusions with the three-spined stickleback (Gasterosteus aculeatus), none of which are present in its sister species. One of these fusions is also present in Pungitius, leading to reinterpretion of this fusion as ancestral to Gasterosteidae, with subsequent fission in Apeltes. This implies a lower ancestral chromosome number in Gasterosteidae (2n=44) than previously thought. The other fusion shared with G. aculeatus presents a case of convergence. Our results suggest that karyotype evolution in Gasterosteidae has been shaped by ancestral chromosome fusion, convergent fusion, and secondary fission.

evolutionary biology↗

bioRxiv2026

Autozygosity and genetic load as sensitive early warnings of butterfly population decline

Insects are commonly expected to be protected from genomic erosion by high fecundity, short generation times, and large census sizes. Yet, insect populations can decline and eventually go extinct, underscoring the need for genomic indicators that provide actionable early warnings of population collapse. Here, we test this expectation by comparing contemporary and historical genomes of the Ponza grayling, Hipparchia sbordonii, an endangered butterfly endemic to the Pontine Islands in the Mediterranean, with the genomes of a widespread European congeneric species, H. semele. Using whole-genome resequencing, outgroup-based variant polarization, demographic reconstruction, runs of homozygosity, selection scans, and annotation-based genetic-load analyses, we show that H. sbordonii has undergone sustained demographic contraction, including a sharp recent decline. Despite limited temporal change in mean genome-wide heterozygosity, we observe extensive autozygosity, elevated inbreeding, and a clear shift from masked to realized genetic load in contemporary H. sbordonii. R'XY analysis revealed similar relative frequencies of high-impact derived variants in H. sbordonii and H. semele, suggesting ineffective purging during population collapse, whereas low- and moderate-impact variants were relatively enriched in H. sbordonii, particularly within candidate regions under selection. This indicates a more complex dynamic, in which functional variation has been shaped by the combined effects of drift, relaxed purifying selection, and possible local adaptation. Our study shows that declining butterfly populations bear distinctive signatures of genomic erosion, mirroring patterns well documented in vertebrates. Yet recent demographic collapse in H. sbordonii is more clearly captured by long runs of homozygosity and realized genetic load than by changes in mean genome-wide heterozygosity, highlighting their potential as early warning indicators for monitoring declining insect populations.

evolutionary biology↗

bioRxiv2026

The relationship between genomic variation and genetic load: insights from small island populations

Small populations face high extinction risks. This can be explained by several non-genetic and genetic factors, the latter including the loss of genetic diversity and evolutionary potential, as well as the accumulation of harmful mutations (genetic load). Using whole-genome data from island populations with different effective sizes, we estimated genetic variation and load and explored the relationship between these quantities. An extremely small population of the Aeolian wall lizard, Podarcis raffonei, likely isolated for tens of thousands of years, shows the lowest genome-wide heterozygosity observed in wild eukaryotes (one polymorphic site every 300 kb on average). Despite this, its realized genetic load is comparable to that observed in another larger and more genetically variable population. Both populations have lower variation and higher load than the much more abundant sister species, the Sicilian wall lizard. These observations are consistent with the hypothesis that populations experiencing severe bottlenecks may persist for extended periods with extremely low genomic variation, provided that their burden of deleterious mutations remains within tolerable bounds.

genomics↗

bioRxiv2025

Hakai links m6A RNA methylation to immune regulation in colorectal cancer

BackgroundThe mA modification is the most abundant RNA epigenetic mark in colorectal cancer (CRC). In this study, we focused on Hakai, a methyltransferase writer-associated protein whose molecular function within the complex and link to CRC immune regulation remain poorly characterized. MethodsWe performed RNA-seq to assess transcriptomic changes after Hakai silencing in CRC models and MeRIP-seq to profile methylation alterations. Validation was carried out by Western blot, flow cytometry, ELISA, and RT-qPCR. Protein interactions within the writer complex were analysed by co-immunoprecipitation, and changes in protein localization by cell fractionation assays. Peripheral blood from healthy donors and lamina propria mononuclear cells from CRC patients were incubated with supernatants from Hakai-silenced CRC cells to evaluate effects on immune responses. ResultsHakai silencing induced phenotypic changes in both monolayer and 3D CRC cultures, while its impact on the global transcriptome was limited. However, significant alterations in the methylation of immune response-related genes and reduced total mA levels were observed. Hakai interacted with the writer-associated protein VIRMA, and its silencing altered the subcellular localization of METTL3. Moreover, conditioned media from Hakai-silenced CRC cells modulated the expression of immune response markers in patient-derived gut immune cells. ConclusionsHakai acts as a component of the mA writer complex in CRC cells, influencing RNA methylation and the expression of immune-related genes. These findings suggest that Hakai silencing may enhance antitumour immune activity and represent a potential strategy to boost cancer immunity in colorectal cancer.

cancer biology↗

bioRxiv2025

One Sea, Different Whales: Genomics Sheds Light on a Small Population of Fin Whales

Whales play a crucial role in marine ecosystems, yet many populations face growing environmental pressures. Among them, the fin whale, Balaenoptera physalus, from the Mediterranean Sea remains poorly characterized at the genomic level despite its classification as Endangered and decreasing in population size due to habitat degradation, climate change, and human-induced disturbances. Previous studies based on bioacoustics and telemetry data suggest the presence of resident and migratory subgroups, but the genetic isolation of this population remains uncertain. Here, we sequenced and analysed for the first time whole genomes of the Mediterranean fin whale to provide a comprehensive genomic characterization of this population, assessing its genomic variability, genetic load, population structure and potential for adaptation to environmental stressors. By comparing genomic data from Mediterranean fin whales with populations from the North Atlantic, North Pacific, and the Sea of Cortez (also sequenced in the present study), we aim to determine the degree of genetic isolation and contextualize the Mediterranean population within a broader evolutionary and conservation framework. Our results showed that while Mediterranean fin whales form a distinct genetic cluster, they are not entirely isolated from North Atlantic populations, with gene flow persisting at low levels. Furthermore, we identified a complex substructure within the Mediterranean, supporting the existence of a resident subpopulation. Although this population preserves moderate levels of genomic diversity and adaptive potential, it remains vulnerable to genomic erosion due to continued demographic decline, limited connectivity, and increasing environmental stressors. These findings underscore the urgency of targeted conservation actions and long-term genetic monitoring, especially as climate change accelerates and introduces increasingly unpredictable selective pressures that may exacerbate the risk of genomic erosion and threaten population viability.

genomics↗

bioRxiv2025

Coexisting with humans: genomic and behavioural consequences in a small and isolated bear population

Climate and land use change have increased human-wildlife interactions, potentially reducing wild species density and prompting behavioural adaptations to urbanised environments. It is still debated if behavioural responses are mainly the result of phenotypic plasticity or if they were driven by anthropic selective pressures, especially in small populations. Our study focused on the Apennine brown bear population (Ursus arctos marsicanus), which has coexisted with humans in Central Italy for millennia. We characterised genomic diversity and identified adaptation signals distinctive to this population by comparing whole genome resequencing data across the Holarctic species range. We show that Apennine brown bears possess a unique genomic diversity pattern including selective signatures at genes associated with reduced aggressiveness, possibly involving alternative splicing mechanism. Our findings suggest that even in small and long-isolated populations, selection may shape behavioural traits. We hypothesise that human-induced selection has influenced these changes, reducing conflicts and contributing to the long-term persistence of the Apennine bear and its coexistence with humans.

genomics↗

bioRxiv2025

17β-estradiol status alters NMDAR function and antipsychotic-like activity in female rats

Low 17{beta}-estradiol (E2) in females of reproductive age, and marked E2 decline with menopause, contributes to heightened symptom severity in schizophrenia (i.e. cognitive dysfunction) and diminished response to antipsychotic medications. However, the underlying mechanisms are unknown. N-methyl-D-aspartate receptor (NMDAR) hypofunction contributes to the pathophysiology of schizophrenia, yet impact of E2 depletion on NMDAR function is not well characterized. Quantitative electroencephalography (qEEG), specifically gamma power, is a well-established functional readout of cortical activity that is elevated in patients with schizophrenia and is sensitive to alterations in NMDAR function. Using qEEG and touchscreen cognitive assessments, present studies investigated the effects of E2 on NMDAR function by administering MK-801 (NMDAR antagonist) to ovariectomized rats with or without E2 implants (Ovx+E and Ovx, respectively). Ovx rats were more sensitive to MK-801-induced elevations in gamma power and attentional impairments compared to Ovx+E rats. Further investigation revealed these effects were mediated by reduced synaptic GluN2A expression. Consistent with clinical reports, olanzapine (second-generation antipsychotic) was less effective in mitigating MK-801-induced elevations in gamma power in Ovx rats. Lastly, we examined antipsychotic-like activity of a Group II metabotropic glutamate receptor (mGlu2/3) positive allosteric modulator (PAM), SBI-0646535, as a novel therapeutic in E2-deprived conditions. SBI-0646535 reversed MK-801-induced elevations in gamma power equally regardless of E2 status. Collectively, these studies established a relationship between E2 deprivation and NMDAR function that is in part GluN2A-dependent, supporting the notion that E2 deprivation increases susceptibility to NMDAR hypofunction. This highlights the need to examine age/hormone-specific factors when considering antipsychotic response and designing novel pharmacotherapies.

animal behavior and cognition↗

bioRxiv2023

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A global genome database of all of Earths species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all [~]1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.

genomics↗

bioRxiv2023

Reference genome of the ant Lasius platythorax

Ants are a highly diversified insect family of the order Hymenoptera, with many fascinating characteristics such as eusociality, chemical communication, farming, or social parasitism. Moreover, ants frequent a wide variety of habitats from dry deserts, grasslands, and savannas to cold temperate forests. The ability of ants to inhabit such diverse habitat ranges demonstrates their adaptability and ecological resilience. However, little is known about the genetic underpinnings of this vast array of traits and their adaptive potential. Here, we generated a high-quality genome assembly for the ant species Lasius platythorax using long-read PacBio HiFi in combination with chromatin conformation capture (Hi-C) sequencing. We successfully assembled the genome into 15 chromosome-level scaffolds ranging from 7.9 to 19.2 Mb and encompassing 204.6 Mb out of 235.3 Mb (total assembly), and a BUSCO score of 86% (Hymenoptera_odb10). Comparative genomics between the two sister species will provide insights into the genomic basis of trait differentiation.

genomics↗

bioRxiv2022

Pangenomics provides insights into the role of synanthropy in barn swallow evolution

Insights into the evolution of non-model organisms are often limited by the lack of reference genomes. As part of the Vertebrate Genomes Project, we present a new reference genome and a pangenome produced with High-Fidelity long reads for the barn swallow Hirundo rustica. We then generated a reference-free multialignment with other bird genomes to identify genes under selection. Conservation analyses pointed at genes enriched for transcriptional regulation and neurodevelopment. The most conserved gene is CAMK2N2, with a potential role in fear memory formation. In addition, using all publicly available data, we generated a comprehensive catalogue of genetic markers. Genome-wide linkage disequilibrium scans identified potential selection signatures at multiple loci. The top candidate region comprises several genes and includes BDNF, a gene involved in stress response, fear memory formation, and tameness. We propose that the strict association with humans in this species is linked with the evolution of pathways typically under selection in domesticated taxa.

genomics↗

bioRxiv2021

Organ-specific microbiota enhances the terrestrial lifestyle of a brachyuran crab

Brachyuran crabs originated in the oceans and evolved specific morphological and physiological adaptations to live in freshwater, intertidal and even terrestrial habitats but the role of a selection mechanism involving symbiotic microorganisms long these colonization processes are not known. In this work we investigated the associated microbiota of three populations of a terrestrial brachyuran crab, Chiromantes haematocheir, to find evidence of a conserved crab-specific microbiome unrelated to the population of origin and dissimilar from environmental microbial assemblages. Bacterial 16S rRNA gene and fungal ITS sequences were obtained from selected crab organs and environmental matrices to profile microbial communities. In spite of the presence of truly marine larval stages and no gregarious behaviour, favouring microbiota exchanges, we found common, organ-specific microbiota, associated to the gut and the gills of the crabs (with more than 15% of the genera detected specifically enriched only in one organ). Our results suggest an early establishment of a new common, stable microbiota in the transition from water to land.

zoology↗

bioRxiv2019

A high-resolution, chromosome-assigned Komodo dragon genome reveals adaptations in the cardiovascular, muscular, and chemosensory systems of monitor lizards

Monitor lizards are unique among ectothermic reptiles in that they have a high aerobic capacity and distinctive cardiovascular physiology which resembles that of endothermic mammals. We have sequenced the genome of the Komodo dragon (Varanus komodoensis), the largest extant monitor lizard, and present a high resolution de novo chromosome-assigned genome assembly for V. komodoensis, generated with a hybrid approach of long-range sequencing and single molecule physical mapping. Comparing the genome of V. komodoensis with those of related species showed evidence of positive selection in pathways related to muscle energy metabolism, cardiovascular homeostasis, and thrombosis. We also found species-specific expansions of a chemoreceptor gene family related to pheromone and kairomone sensing in V. komodoensis and several other lizard lineages. Together, these evolutionary signatures of adaptation reveal genetic underpinnings of the unique Komodo sensory, cardiovascular, and muscular systems, and suggest that selective pressure altered thrombosis genes to help Komodo dragons evade the anticoagulant effects of their own saliva. As the only sequenced monitor lizard genome, the Komodo dragon genome is an important resource for understanding the biology of this lineage and of reptiles worldwide.

genomics↗