[en] [en] BACKGROUND: Red mullet (Mullus barbatus) is a key species in Mediterranean fisheries, yet its stock structure and population dynamics remain poorly understood due to a lack of comprehensive genomic resources. This study provides the first high-quality reference genome for M. barbatus and a comprehensive set of SNP markers to investigate its population structure and adaptive potential across the Mediterranean.
RESULTS: Using the newly generated chromosome-level reference genome, we re-analyzed a Mediterranean-wide reduced-representation genomic dataset. Our analysis reveals a panmictic population structure with strong genetic connectivity across the species' range, likely driven by extensive larval dispersal and multigenerational gene flow. Despite minimal genome-wide differentiation, outlier analysis identified candidate loci under directional selection, linked to key biological processes such as ontogeny and environmental adaptation.
CONCLUSIONS: This study presents the first genomic resource for M. barbatus, providing valuable insights into its genetic structure and adaptive mechanisms. While the identification of loci under selection offers promising leads, these findings are preliminary due to the limited genomic coverage of the dataset. Nonetheless, they pave the way for future genomic studies to explore how M. barbatus adapts to environmental and anthropogenic pressures. These results hold significant implications for the sustainable management of Mediterranean fisheries, especially in the context of climate change and conservation.
Disciplines :
Genetics & genetic processes Zoology
Author, co-author :
Massa, Piergiorgio ; Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM), Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Sant'Alberto 163, Ravenna, 48123, Italy. piergiorgio.massa2@unibo.it
Leitão, Henrique G ; Evolutionary Ecology, Department of Biology, University of Antwerp, Antwerp, Belgium
Manousaki, Tereza ; Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, 715 00, Crete, Greece
Cariani, Alessia ; Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM), Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Sant'Alberto 163, Ravenna, 48123, Italy ; National Inter-University Consortium for Marine Sciences (CoNISMa), Piazzale Flaminio 9, Roma, 00196, Italy
Svardal, Hannes ; Evolutionary Ecology, Department of Biology, University of Antwerp, Antwerp, Belgium. hannes.svardal@uantwerpen.be ; Naturalis Biodiversity Center, Leiden, The Netherlands. hannes.svardal@uantwerpen.be
Tsaparis, Dimitris ; Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, 715 00, Crete, Greece
Cannas, Rita ; National Inter-University Consortium for Marine Sciences (CoNISMa), Piazzale Flaminio 9, Roma, 00196, Italy ; Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
Zane, Lorenzo ; National Inter-University Consortium for Marine Sciences (CoNISMa), Piazzale Flaminio 9, Roma, 00196, Italy ; Department of Biology (DiBio), University of Padova, Via Ugo Bassi 58/b, Padova, 35131, Italy
De Pooter, Tim ; Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium ; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
Spedicato, Maria Teresa ; Fondazione COISPA ETS, Bari, Italy
Strazisar, Mojca ; Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium ; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
Ciofi, Claudio ; Department of Biology, University of Florence, Sesto Fiorentino (FI), Florence, Italy
Ferrari, Alice ; Laboratory of Genetics & Genomics of Marine Resources and Environment (GenoDREAM), Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Sant'Alberto 163, Ravenna, 48123, Italy ; National Inter-University Consortium for Marine Sciences (CoNISMa), Piazzale Flaminio 9, Roma, 00196, Italy
Diedericks, Genevieve ; Evolutionary Ecology, Department of Biology, University of Antwerp, Antwerp, Belgium
Diroma, Maria Angela ; Department of Biology, University of Florence, Sesto Fiorentino (FI), Florence, Italy
Formenti, Giulio ; The Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Ave, New York, 10021, USA
Ivanova, Petya ; Institute of Oceanology - Bulgarian Аcademy of Sciences, Parvi may Street 40, PO 152 9000, Varna, Bulgaria
Mc Cartney, Ann M ; Genomics Institute, University of California, Santa Cruz, California, USA
Mouton, Alice ; Université de Liège - ULiège > Département des sciences et gestion de l'environnement (Arlon Campus Environnement) > Socio-économie, Environnement et Développement (SEED)
Natali, Chiara ; Department of Biology, University of Florence, Sesto Fiorentino (FI), Florence, Italy
Marino, Ilaria Am ; Department of Biology (DiBio), University of Padova, Via Ugo Bassi 58/b, Padova, 35131, Italy ; National Biodiversity Future Center (NBFC), Piazza Marina 61, Palermo, 90133, Italy
Tsigenopoulos, Costas S ; Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (H.C.M.R.), Heraklion, 715 00, Crete, Greece. tsigeno@hcmr.gr
FWO - Fonds Wetenschappelijk Onderzoek Vlaanderen EC EASME - European Commission. Executive Agency for Small and Medium-sized Enterprises
Funding text :
MED_UNITs project - Study on Advancing fisheries assessment and management advice in the Mediterranean and Black Sea by aligning biological and management units of priority species - was carried out within the European Research Contract (EASME/EMFF/2017/1.3.2.3/01/SI2.793201, implementing the Framework Contract EASME/EMFF/2016/032) funded by the Executive Agency for Small-and Medium-sized Enterprises (EASME) of the European Commission (DG MARE). H.S. acknowledges support from the Flemish University Research Fund (BOF) and from the University of Antwerp through a startup grant. H.G.L. was supported by the Research Foundation\u2014Flanders (FWO PhD fellowship 1156622 N). Sequencing of Omni-C and RNA libraries was supported by the University of Florence through internal funding to CC. NovaSeq 6000 Reagent Kits for Omni-C and RNA libraries sequencing were provided by Illumina EMEA support to the European Reference Genome Atlas pilot project. We also would like to thank Dovetail Genomics, Part of Cantata Bio LLC; Integrated DNA Technologies (IDT); MagBio Genomics Europe GmbH; Zymo Research; Agilent Technologies that have kindly donated kits, reagents to the ERGA pilot Library preparation Hubs. A.C., P.M. and A.F. acknowledge support from the University of Bologna (Canziani legacy and RFO grants).MED_UNITs project - Study on Advancing fisheries assessment and management advice in the Mediterranean and Black Sea by aligning biological and management units of priority species - was carried out within the European Research Contract (EASME/EMFF/2017/1.3.2.3/01/SI2.793201, implementing the Framework Contract EASME/EMFF/2016/032) funded by the Executive Agency for Small-and Medium-sized Enterprises (EASME) of the European Commission (DG MARE). H.S. acknowledges support from the Flemish University Research Fund (BOF) and from the University of Antwerp through a startup grant. H.G.L. was supported by the Research Foundation\u2014Flanders (FWO PhD fellowship 1156622\u00A0N). Sequencing of Omni-C and RNA libraries was supported by the University of Florence through internal funding to CC. NovaSeq 6000 Reagent Kits for Omni-C and RNA libraries sequencing were provided by Illumina EMEA support to the European Reference Genome Atlas pilot project. We also would like to thank Dovetail Genomics, Part of Cantata Bio LLC; Integrated DNA Technologies (IDT); MagBio Genomics Europe GmbH; Zymo Research; Agilent Technologies that have kindly donated kits, reagents to the ERGA pilot Library preparation Hubs. A.C., P.M. and A.F. acknowledge support from the University of Bologna (Canziani legacy and RFO grants).
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