The unexplored diversity of rough-seeded lupins provides rich genomic resources and insights into lupin evolution Karolina Susek, Leonardo Vincenzi, Magdalena Tomaszewska, Magdalena Kroc, Edoardo Franco, et al. Nature Communications, 2025 Lupin crops provide nutritious seeds as an excellent source of dietary protein. However, extensive genomic resources are needed for crop improvement, focusing on key traits such as nutritional value and climate resiliency, to ensure global food security based on sustainable and healthy diets for all. Such resources can be derived either from related lupin species or crop wild relatives, which represent a large and untapped source of genetic variation for crop improvement. Here, we report genome assemblies of the cross-compatible species Lupinus cosentinii (Mediterranean) and its pan-Saharan wild relative L. digitatus, which are well adapted to drought-prone environments and partially domesticated. We show that both species are tetraploids, and their repetitive DNA content differs considerably from that of the main lupin crops L. angustifolius and L. albus. We present the complex evolutionary process within the rough-seeded lupins as a species-based model involving polyploidization and rediploidization. Our data also provide the foundation for a systematic analysis of genomic diversity among lupin species to promote their exploitation for crop improvement and sustainable agriculture.
The italian national genomic strategy: current status, challenges, and future perspectives in clinical practice and public health Francesco Andrea Causio, Sara Farina, Alessandra Maio, Flavia Beccia, Luigi Russo, et al. Journal of Community Genetics, 2025 This article presents the outcomes of a national initiative aimed at developing a technical document to support the future Italian National Genomic Strategy, carried out from 2021 to 2024 through the collaboration of 14 research institutions. The project was designed to align with major European genomic initiatives, particularly the “1 + Million Genomes” (1 + MG) Declaration and its supporting programs, including Beyond 1 Million Genomes (B1 + MG), the Genomic Data Infrastructure (GDI), and Genome of Europe (GoE). The initiative was structured around 12 National Mirror Groups (NMGs), each addressing a specific domain such as clinical implementation, ethical and legal issues, data governance, health economics, and public engagement. Through expert consensus and coordinated activities, the project produced a comprehensive technical document outlining seven strategic lines and related intervention areas. These include the integration of genomic testing into clinical practice, development of specialized genomic centers, creation of a national genomic data infrastructure, professional training, and public education. The proposed strategy emphasizes equitable access to genomic medicine, the use of health technology assessment to evaluate new technologies, and the importance of citizen engagement and literacy. By fostering collaboration among institutions, healthcare professionals, and the public, the final goal is to position Italy as a leader in genomic medicine and ensure the responsible, effective, and ethical use of genomics in public health and clinical care.
Exploring Bat–Virus Interactions: Insights from a Study in the Gobi Desert Sabrina Canziani, Davide Lelli, Paolo Agnelli, Claudio Augugliaro, Munkhtsetseg Bazarragchaa, et al. Pathogens, 2025 In May 2022, an expedition was conducted in the Gobi Desert, Mongolia, to investigate the viral diversity of bats, recognized as reservoirs of emerging zoonotic viruses. Bats were captured in six oases using mist nets and were identified morphologically and molecularly. Fecal samples were collected and screened using molecular protocol targeting viral agents of relevance to human and animal health, including coronaviruses, orthoreoviruses, herpesviruses, adenoviruses, flaviviruses, phleboviruses, paramyxoviruses, pestiviruses, and Influenza A viruses. In total, 74 bats were sampled. The most represented bat genus was Plecotus, followed by Hypsugo, Vespertilio, and Myotis. Coronavirus RNA was detected in eleven samples (14.86%), Mammalian orthoreovirus RNA in two samples (2.70%), and herpesvirus DNA in three samples (4.05%). No other targeted viruses were detected. These data expand our understanding of viral circulation in bats from previously unstudied regions. By expanding our understanding of the viral diversity harbored by bats, this study contributes to ongoing efforts to better characterize their role in the ecology and evolution of emerging zoonotic viruses. Continuous surveillance in remote and biodiverse areas is essential to identify potential threats to public and animal health and to improve preparedness for future viral emergence.
The evolutionary history of the common bean (Phaseolus vulgaris) revealed by chloroplast and nuclear genomes analysis Giulia Frascarelli, Teresa R. Galise, Nunzio D’Agostino, Donata Cafasso, Salvatore Cozzolino, et al. Theoretical and Applied Genetics, 2025 Key message The origin of common bean was investigated throughout chloroplast and nuclear WGS data considering recombination events. Our results support the Mesoamerican origin of common bean. Abstract The remarkable evolutionary history of the common bean (Phaseolus vulgaris L.) has led to the emergence of three wild main gene pools corresponding to three different eco-geographical areas: Mesoamerica, the Andes and northern Peru/Ecuador. Recent works proposed novel scenarios, and the northern Peru/Ecuador population has been described as a new species called P. debouckii, rekindling the debate about the origin of P. vulgaris. Here we shed light on the origin of P. vulgaris by analyzing the chloroplast and nuclear genomes of a large varietal collection representing the entire geographical distribution of wild forms including a large collection of Mesoamerican and Andean individuals. We assembled 37 chloroplast genomes de novo and used them to construct a time frame for the divergence of the genotypes under investigation, revealing that the separation of the Mesoamerican and northern Peru/Ecuador gene pools occurred ~ 0.15 Mya. Our results clearly support a Mesoamerican origin of the common bean and reject the recent P. deboukii hypothesis. These results also imply two independent migratory events from Mesoamerica to the North and South Andes, probably facilitated by birds. Our work represents a paradigmatic example of the importance of taking into account the genetic rearrangements produced by recombination when investigating phylogeny and of the analysis of wild forms when studying the evolutionary history of a crop species.
Adaptive gene loss in the common bean pan-genome during range expansion and domestication Gaia Cortinovis, Leonardo Vincenzi, Robyn Anderson, Giovanni Marturano, Jacob Ian Marsh, et al. Nature Communications, 2024 The common bean (Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals ~234 Mb of additional sequences containing 6,905 protein-coding genes missing from the reference, constituting 49% of all presence/absence variants (PAVs). More non-synonymous mutations are found in PAVs than core genes, probably reflecting the lower effective population size of PAVs and fitness advantages due to the purging effect of gene loss. Our results suggest pan-genome shrinkage occurred during wild range expansion. Selection signatures provide evidence that partial or complete gene loss was a key adaptive genetic change in common bean populations with major implications for plant adaptation. The pan-genome is a valuable resource for food legume research and breeding for climate change mitigation and sustainable agriculture.
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The italian national genomic strategy: current status, challenges, and future perspectives in clinical practice and public health FA Causio, S Farina, A Maio, F Beccia, L Russo, V Baccolini, M Chiara, ... Journal of Community Genetics, 1-5 , 2025 2025 Citations: 1
Exploring Bat–Virus Interactions: Insights from a Study in the Gobi Desert S Canziani, D Lelli, P Agnelli, C Augugliaro, M Bazarragchaa, S Bertolino, ... Pathogens 14 (9), 870 , 2025 2025 Citations: 1
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The lncRNA LOC100257036 and vvimiR156 modulate gibberellin signaling through AGAMOUS during cluster formation in Sistan Yaghooti grape S Sahraei, N Mahdinezhad, A Emamjomeh, K Kavousi, M Solouki, ... Scientific Reports 15 (1), 29687 , 2025 2025
di Firenze L Leonardelli, M Delledonne, A Brusco, K Chrzanowska, A Schinzel, ... 2025
Bats as reservoir hosts of emerging viruses in Italy: eco-epidemiological investigations to protect public health and biodiversity D Lelli, A Lavazza, T Trogu, E Sozzi, M Carrera, A Castelli, C Tolini, ... 9th National Congress of the Italian Society for Virology-One Virology One … , 2025 2025
The unexplored diversity of rough-seeded lupins provides rich genomic resources and insights into lupin evolution K Susek, L Vincenzi, M Tomaszewska, M Kroc, E Franco, E Cosentino, ... Nature Communications 16 (1), 4358 , 2025 2025 Citations: 4
The evolutionary history of the common bean ( Phaseolus vulgaris ) revealed by chloroplast and nuclear genomes analysis G Frascarelli, TR Galise, N D’Agostino, D Cafasso, S Cozzolino, ... Theoretical and Applied Genetics 138 (2), 47 , 2025 2025 Citations: 7
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Transcriptomic analysis reveals role of lncRNA LOC100257036 to regulate AGAMOUS during cluster compactness of Vitis vinifera cv. sistan yaghooti S Sahraei, N Mahdinezhad, A Emamjomeh, K Kavousi, M Solouki, ... Scientific Reports 14 (1), 28331 , 2024 2024 Citations: 4
Mosaicism in malformations of cortical development: Implications for the diagnostic workflow F Fineschi, B Straka, C Mandorlini, M Vlckova, V Cetica, ... EPILEPSIA 65, 48-48 , 2024 2024
Adaptive gene loss in the common bean pan-genome during range expansion and domestication G Cortinovis, L Vincenzi, R Anderson, G Marturano, JI Marsh, PE Bayer, ... Nature communications 15 (1), 6698 , 2024 2024 Citations: 47
Landscape genomics highlights the adaptive evolution of chickpea L Rocchetti, M Rodriguez, A Pieri, S Papalini, L De Antoni, E Vitali, ... bioRxiv, 2024.06. 06.597750 , 2024 2024 Citations: 1
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