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Mayeur H, Leyhr J, Mulley J, Leurs N, Michel L, Sharma K, Lagadec R, Aury JM, Osborne OG, Mulhair P, Poulain J, Mangenot S, Mead D, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Dolucan J, Dudchenko O, Omer AD, Weisz D, Aiden EL, McCarthy SA, Sims Y, Torrance J, Tracey A, Howe K, Baril T, Hayward A, Martinand-Mari C, Sanchez S, Haitina T, Martin K, Korsching SI, Mazan S, Debiais-Thibaud M. The Sensory Shark: High-quality Morphological, Genomic and Transcriptomic Data for the Small-spotted Catshark Scyliorhinus Canicula Reveal the Molecular Bases of Sensory Organ Evolution in Jawed Vertebrates. Mol Biol Evol 2024; 41:msae246. [PMID: 39657112 PMCID: PMC11979771 DOI: 10.1093/molbev/msae246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 11/21/2024] [Accepted: 11/21/2024] [Indexed: 12/16/2024] Open
Abstract
Cartilaginous fishes (chondrichthyans: chimeras and elasmobranchs -sharks, skates, and rays) hold a key phylogenetic position to explore the origin and diversifications of jawed vertebrates. Here, we report and integrate reference genomic, transcriptomic, and morphological data in the small-spotted catshark Scyliorhinus canicula to shed light on the evolution of sensory organs. We first characterize general aspects of the catshark genome, confirming the high conservation of genome organization across cartilaginous fishes, and investigate population genomic signatures. Taking advantage of a dense sampling of transcriptomic data, we also identify gene signatures for all major organs, including chondrichthyan specializations, and evaluate expression diversifications between paralogs within major gene families involved in sensory functions. Finally, we combine these data with 3D synchrotron imaging and in situ gene expression analyses to explore chondrichthyan-specific traits and more general evolutionary trends of sensory systems. This approach brings to light, among others, novel markers of the ampullae of Lorenzini electrosensory cells, a duplication hotspot for crystallin genes conserved in jawed vertebrates, and a new metazoan clade of the transient-receptor potential (TRP) family. These resources and results, obtained in an experimentally tractable chondrichthyan model, open new avenues to integrate multiomics analyses for the study of elasmobranchs and jawed vertebrates.
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Affiliation(s)
- Hélène Mayeur
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-mer, France
| | - Jake Leyhr
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - John Mulley
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Nicolas Leurs
- Institut des Sciences de l'Evolution de Montpellier, ISEM, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Léo Michel
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-mer, France
| | - Kanika Sharma
- Institute of Genetics, Faculty of Mathematics and Natural Sciences of the University at Cologne, Cologne 50674, Germany
| | - Ronan Lagadec
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-mer, France
| | - Jean-Marc Aury
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry 91057, France
| | - Owen G Osborne
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Peter Mulhair
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Julie Poulain
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry 91057, France
| | - Sophie Mangenot
- Génomique Métabolique, Génoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry 91057, France
| | - Daniel Mead
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Michelle Smith
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Craig Corton
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Karen Oliver
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Jason Skelton
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Emma Betteridge
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Jale Dolucan
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Olga Dudchenko
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Arina D Omer
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
| | - Erez L Aiden
- The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shane A McCarthy
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Ying Sims
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - James Torrance
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Alan Tracey
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Kerstin Howe
- Sequencing Department, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Cornwall TR10 9FE, UK
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Cornwall TR10 9FE, UK
| | - Camille Martinand-Mari
- Institut des Sciences de l'Evolution de Montpellier, ISEM, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sophie Sanchez
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- European Synchrotron Radiation Facility, Grenoble, France
| | - Tatjana Haitina
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Kyle Martin
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Sigrun I Korsching
- Institute of Genetics, Faculty of Mathematics and Natural Sciences of the University at Cologne, Cologne 50674, Germany
| | - Sylvie Mazan
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, Banyuls-sur-mer, France
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l'Evolution de Montpellier, ISEM, University of Montpellier, CNRS, IRD, EPHE, Montpellier, France
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Rahi Roy D, Roy K, Panserat S, Stejskal V, Mraz J, Turchini GM. Long chain polyunsaturated fatty acid (LC-PUFA) composition of fish sperm: nexus of dietary, evolutionary, and biomechanical drivers. Prog Lipid Res 2024; 96:101305. [PMID: 39566856 DOI: 10.1016/j.plipres.2024.101305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 11/06/2024] [Accepted: 11/13/2024] [Indexed: 11/22/2024]
Abstract
Long-chain polyunsaturated fatty acids (LC-PUFA) like arachidonic acid (ARA, 20:4n-6), eicosapentaenoic acid (EPA, 20:5n-3), and docosahexaenoic acid (DHA, 22:6n-3) constitute one-third to half of fish sperm lipids. Fish sperm is rich in phospholipid (PL)-primarily phosphatidylcholine, phosphatidylethanolamine, and sphingomyelin. DHA is generally the most abundant LC-PUFA in each PL class, followed by competition between ARA and EPA. While the total n-6: n-3 PUFA ratio does not correlate significantly with sperm biomechanics, LC-PUFA do. DHA positively influences sperm biomechanics, while ARA and EPA may be negatively associated. Fish sperm maintains lower (≤1) total n-6 PUFA per unit of n-3 PUFA but keep a higher (>1) ARA per unit EPA. A weak dietary influence on sperm EPA and DHA exists but not on ARA. The DHA: EPA ratio in fish sperm is often >1, though values <1 occur. Certain species cannot fortify DHA sufficiently during spermatogenesis, diverging through whole genome duplications. Fish sperm can show ARA: EPA ratios greater or less than 1, due to shifts in prostaglandin pathways in different evolutionary eras. DHA-rich PL bilayers provide unique packing and fusogenic properties, with ARA/EPA-derived eicosanoids guiding sperm rheotaxis/chemotaxis, modulated by DHA-derived resolvins. Docosapentaenoic acid (DPA, 22:5n-3) sometimes substitutes for DHA in fish sperm.
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Affiliation(s)
- Deepali Rahi Roy
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Aquaculture and Protection of Waters, České Budějovice 370 05, Czech Republic
| | - Koushik Roy
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Aquaculture and Protection of Waters, České Budějovice 370 05, Czech Republic.
| | - Stephane Panserat
- Université de Pau Et Des Pays de L'Adour, E2S UPPA, INRAE, NUMEA, 64310 Saint Pée sur Nivelle, France
| | - Vlastimil Stejskal
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Aquaculture and Protection of Waters, České Budějovice 370 05, Czech Republic
| | - Jan Mraz
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Institute of Aquaculture and Protection of Waters, České Budějovice 370 05, Czech Republic
| | - Giovanni M Turchini
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, VIC 3010, Australia
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Zhou Q, Wang J, Li J, Chen Z, Wang N, Li M, Wang L, Si Y, Lu S, Cui Z, Liu X, Chen S. Decoding the fish genome opens a new era in important trait research and molecular breeding in China. SCIENCE CHINA. LIFE SCIENCES 2024; 67:2064-2083. [PMID: 39145867 DOI: 10.1007/s11427-023-2670-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/01/2024] [Indexed: 08/16/2024]
Abstract
Aquaculture represents the fastest-growing global food production sector, as it has become an essential component of the global food supply. China has the world's largest aquaculture industry in terms of production volume. However, the sustainable development of fish culture is hindered by several concerns, including germplasm degradation and disease outbreaks. The practice of genomic breeding, which relies heavily on genome information and genotypephenotype relationships, has significant potential for increasing the efficiency of aquaculture production. In 2014, the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in China. Since then, domestic researchers have made dramatic progress in functional genomic studies. To date, the genomes of more than 60 species of fish in China have been assembled and annotated. Based on these reference genomes, evolutionary, comparative, and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes, including growth and development, sex determination, disease resistance, metamorphosis, and pigmentation. Furthermore, genomic tools and breeding techniques such as SNP arrays, genomic selection, and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding activities. This review aims to summarize the current status, advances, and perspectives of the genome resources, genomic study of important traits, and genomic breeding techniques of fish in China. The review will provide aquaculture researchers, fish breeders, and farmers with updated information concerning fish genomic research and breeding technology. The summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.
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Affiliation(s)
- Qian Zhou
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Jialin Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Jiongtang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100041, China
| | - Zhangfan Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Na Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Ming Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Lei Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Yufeng Si
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Sheng Lu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Zhongkai Cui
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Xuhui Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China
| | - Songlin Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong, 266237, China.
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Mayeur H, Leyhr J, Mulley J, Leurs N, Michel L, Sharma K, Lagadec R, Aury JM, Osborne OG, Mulhair P, Poulain J, Mangenot S, Mead D, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Dolucan J, Dudchenko O, Omer AD, Weisz D, Aiden EL, McCarthy S, Sims Y, Torrance J, Tracey A, Howe K, Baril T, Hayward A, Martinand-Mari C, Sanchez S, Haitina T, Martin K, Korsching SI, Mazan S, Debiais-Thibaud M. The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catshark Scyliorhinus canicula reveal the molecular bases of sensory organ evolution in jawed vertebrates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595469. [PMID: 39005470 PMCID: PMC11244906 DOI: 10.1101/2024.05.23.595469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Cartilaginous fishes (chimaeras and elasmobranchs -sharks, skates and rays) hold a key phylogenetic position to explore the origin and diversifications of jawed vertebrates. Here, we report and integrate reference genomic, transcriptomic and morphological data in the small-spotted catshark Scyliorhinus canicula to shed light on the evolution of sensory organs. We first characterise general aspects of the catshark genome, confirming the high conservation of genome organisation across cartilaginous fishes, and investigate population genomic signatures. Taking advantage of a dense sampling of transcriptomic data, we also identify gene signatures for all major organs, including chondrichthyan specializations, and evaluate expression diversifications between paralogs within major gene families involved in sensory functions. Finally, we combine these data with 3D synchrotron imaging and in situ gene expression analyses to explore chondrichthyan-specific traits and more general evolutionary trends of sensory systems. This approach brings to light, among others, novel markers of the ampullae of Lorenzini electro-sensory cells, a duplication hotspot for crystallin genes conserved in jawed vertebrates, and a new metazoan clade of the Transient-receptor potential (TRP) family. These resources and results, obtained in an experimentally tractable chondrichthyan model, open new avenues to integrate multiomics analyses for the study of elasmobranchs and jawed vertebrates.
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Nachtigall PG, Durham AM, Rokyta DR, Junqueira-de-Azevedo ILM. ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages. Gigascience 2024; 13:giad116. [PMID: 38241143 PMCID: PMC10797961 DOI: 10.1093/gigascience/giad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/19/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND The rapid development of sequencing technologies resulted in a wide expansion of genomics studies using venomous lineages. This facilitated research focusing on understanding the evolution of adaptive traits and the search for novel compounds that can be applied in agriculture and medicine. However, the toxin annotation of genomes is a laborious and time-consuming task, and no consensus pipeline is currently available. No computational tool currently exists to address the challenges specific to toxin annotation and to ensure the reproducibility of the process. RESULTS Here, we present ToxCodAn-Genome, the first software designed to perform automated toxin annotation in genomes of venomous lineages. This pipeline was designed to retrieve the full-length coding sequences of toxins and to allow the detection of novel truncated paralogs and pseudogenes. We tested ToxCodAn-Genome using 12 genomes of venomous lineages and achieved high performance on recovering their current toxin annotations. This tool can be easily customized to allow improvements in the final toxin annotation set and can be expanded to virtually any venomous lineage. ToxCodAn-Genome is fast, allowing it to run on any personal computer, but it can also be executed in multicore mode, taking advantage of large high-performance servers. In addition, we provide a guide to direct future research in the venomics field to ensure a confident toxin annotation in the genome being studied. As a case study, we sequenced and annotated the toxin repertoire of Bothrops alternatus, which may facilitate future evolutionary and biomedical studies using vipers as models. CONCLUSIONS ToxCodAn-Genome is suitable to perform toxin annotation in the genome of venomous species and may help to improve the reproducibility of further studies. ToxCodAn-Genome and the guide are freely available at https://github.com/pedronachtigall/ToxCodAn-Genome.
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Affiliation(s)
- Pedro G Nachtigall
- Laboratório de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, 05503-900 SP, Brazil
- Department of Biological Science, Florida State University, Tallahassee, 32306-4295 FL, USA
| | - Alan M Durham
- Departamento de Ciência da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo (USP), São Paulo, 05508-090 SP, Brazil
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, 32306-4295 FL, USA
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