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Han GD, Ma DD, Du LN, Zhao ZJ. Chromosomal-scale genome assembly of the Mediterranean mussel Mytilus galloprovincialis. Sci Data 2024; 11:644. [PMID: 38886364 PMCID: PMC11183127 DOI: 10.1038/s41597-024-03497-5] [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: 04/19/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
The Mediterranean mussel, Mytilus galloprovincialis, is a significant marine bivalve species that has ecological and economic importance. This species is robustly resilient and highly invasive. Despite the scientific and commercial interest in studying its biology and aquaculture, there remains a need for a high-quality, chromosome-scale reference genome. In this study, we have assembled a high-quality chromosome-scale reference genome for M. galloprovincialis. The total length of our reference genome is 1.41 Gb, with a scaffold N50 sequence length of 96.9 Mb. BUSCO analysis revealed a 97.5% completeness based on complete BUSCOs. Compared to the four other available M. galloprovincialis assemblies, the assembly described here is dramatically improved in both contiguity and completeness. This new reference genome will greatly contribute to a deeper understanding of the resilience and invasiveness of M. galloprovincialis.
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Affiliation(s)
- Guo-Dong Han
- College of Life Science, Yantai University, Yantai, Shandong, 264005, China.
| | - Dan-Dan Ma
- College of Life Science, Yantai University, Yantai, Shandong, 264005, China
| | - Li-Na Du
- College of Life Science, Yantai University, Yantai, Shandong, 264005, China
| | - Zhen-Jun Zhao
- College of Life Science, Yantai University, Yantai, Shandong, 264005, China
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2
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Gleason LU, Fekete FJ, Tanner RL, Dowd WW. Multi-omics reveals largely distinct transcript- and protein-level responses to the environment in an intertidal mussel. J Exp Biol 2023; 226:jeb245962. [PMID: 37902141 PMCID: PMC10690110 DOI: 10.1242/jeb.245962] [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: 04/14/2023] [Accepted: 10/12/2023] [Indexed: 10/31/2023]
Abstract
Organismal responses to stressful environments are influenced by numerous transcript- and protein-level mechanisms, and the relationships between expression changes at these levels are not always straightforward. Here, we used paired transcriptomic and proteomic datasets from two previous studies from gill of the California mussel, Mytilus californianus, to explore how simultaneous transcript and protein abundance patterns may diverge under different environmental scenarios. Field-acclimatized mussels were sampled from two disparate intertidal sites; individuals from one site were subjected to three further treatments (common garden, low-intertidal or high-intertidal outplant) that vary in temperature and feeding time. Assessing 1519 genes shared between the two datasets revealed that both transcript and protein expression patterns differentiated the treatments at a global level, despite numerous underlying discrepancies. There were far more instances of differential expression between treatments in transcript only (1451) or protein only (226) than of the two levels shifting expression concordantly (68 instances). Upregulated expression of cilium-associated transcripts (likely related to feeding) was associated with relatively benign field treatments. In the most stressful treatment, transcripts, but not proteins, for several molecular chaperones (including heat shock proteins and endoplasmic reticulum chaperones) were more abundant, consistent with a threshold model for induction of translation of constitutively available mRNAs. Overall, these results suggest that the relative importance of transcript- and protein-level regulation (translation and/or turnover) differs among cellular functions and across specific microhabitats or environmental contexts. Furthermore, the degree of concordance between transcript and protein expression can vary across benign versus acutely stressful environmental conditions.
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Affiliation(s)
- Lani U. Gleason
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA 95819, USA
| | - Florian J. Fekete
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA 95819, USA
| | - Richelle L. Tanner
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
| | - W. Wesley Dowd
- School of Biological Sciences, Washington State University, Pullman, WA 99163, USA
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3
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Sun Y, Liu X, Xie X, Bai Y, Wang S, Teng W, Li D, Li H, Yu Z, Zhang M, Zhou Z, Liu X, Nie H, Du S, Li X, Li Q, Wang Q. A high-quality chromosome-level genome assembly of the bivalve mollusk Mactra veneriformis. G3 (BETHESDA, MD.) 2022; 12:jkac229. [PMID: 36165708 PMCID: PMC9635629 DOI: 10.1093/g3journal/jkac229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Mactra veneriformis (Bivalvia: Mactridae) is a bivalve mollusk of major economic importance in China. Decreased natural yields of M. veneriformis have led to an urgent need for genomic resources. To address this problem and the currently limited knowledge of molecular evolution in this genus, we here report a high-quality chromosome-level genome assembly of M. veneriformis. Our approach yielded a 939.32 Mb assembled genome with an N50 contig length of 7,977.84 kb. Hi-C scaffolding of the genome resulted in assembly of 19 pseudochromosomes. Repetitive elements made up ∼51.79% of the genome assembly. A total of 29,315 protein-coding genes (PCGs) were predicted in M. veneriformis. Construction of a genome-level phylogenetic tree demonstrated that M. veneriformis and Ruditapes philippinarum diverged around 231 million years ago (MYA). Inter-species comparisons revealed that 493 gene families have undergone expansion and 449 have undergone contraction in the M. veneriformis genome. Chromosome-based macrosynteny analysis revealed a high degree of synteny between the 19 chromosomes of M. veneriformis and those of Patinopecten yessoensis. These results suggested that M. veneriformis has a similar karyotype to that of P. yessoensis, and that a highly conserved 19-chromosome karyotype was formed in the early differentiation stages of bivalves. In summary, the genomic resources generated in this work serve as a valuable reference for investigating the molecular mechanisms underlying biological functions in M. veneriformis and will facilitate future genetic improvement and disease treatment in this economically important species. Furthermore, the assembled genome greatly improves our understanding of early genomic evolution of the Bivalvia.
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Affiliation(s)
| | | | | | | | - Shuo Wang
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Weiming Teng
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Dacheng Li
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Hualin Li
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Zuoan Yu
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Ming Zhang
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Zunchun Zhou
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Xu Liu
- Panjin Guanghe Crab Industry Co., LTD, Panjin 124299, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Shaojun Du
- Department of Biochemistry and Molecular Biology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD 21202, USA
| | - Xiaodong Li
- Key Laboratory of Zoonosis, Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Qi Li
- Corresponding author: Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Qingzhi Wang
- Corresponding author: Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China.
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Weng N, Meng J, Huo S, Wu F, Wang WX. Hemocytes of bivalve mollusks as cellular models in toxicological studies of metals and metal-based nanomaterials. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 312:120082. [PMID: 36057327 DOI: 10.1016/j.envpol.2022.120082] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/05/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Understanding the impacts of environmental pollutants on immune systems is indispensable in ecological and health risk assessments due to the significance of normal immunological functions in all living organisms. Bivalves as sentinel organisms with vital ecological importance are widely distributed in aquatic environments and their innate immune systems are the sensitive targets of environmental pollutants. As the central component of innate immunity, bivalve hemocytes are endowed with specialized endolysosomal systems for particle internalization and metal detoxification. These intrinsic biological features make them a unique cellular model for metal- and nano-immunotoxicology research. In this review, we firstly provided a general overview of bivalve's innate immunity and the classification and immune functions of hemocytes. We then summarized the recent progress on the interactions of metals and nanoparticles with bivalve hemocytes, with emphasis on the involvement of hemocytes in metal regulation and detoxification, the interactions of hemocytes and nanoparticles at eco/bio-nano interface and hemocyte-mediated immune responses to the exposure of metals and nanoparticles. Finally, we proposed the key knowledge gaps and future research priorities in deciphering the fundamental biological processes of the interactions of environmental pollutants with the innate immune system of bivalves as well as in developing bivalve hemocytes into a promising cellular model for nano-immuno-safety assessment.
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Affiliation(s)
- Nanyan Weng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Jie Meng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Shouliang Huo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Wen-Xiong Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China.
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Corrochano-Fraile A, Davie A, Carboni S, Bekaert M. Evidence of multiple genome duplication events in Mytilus evolution. BMC Genomics 2022; 23:340. [PMID: 35501689 PMCID: PMC9063065 DOI: 10.1186/s12864-022-08575-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 04/20/2022] [Indexed: 12/12/2022] Open
Abstract
Background Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new high-quality reference genome for Mytilus edulis and investigating the evolutionary history within the Mytilidae family, in relation to other species in the class Bivalvia. Results Here we present, for the first time, the discovery of multiple whole genome duplication events in the Mytilidae family and, more generally, in the class Bivalvia. In addition, the calculation of evolution rates for three species of the Mytilinae subfamily sheds new light onto the taxa evolution and highlights key orthologs of interest for the study of Mytilus species divergences. Conclusions The reference genome presented here will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies. Mytilidae have the capability to become a model shellfish for climate change adaptation using genome-enabled systems biology and multi-disciplinary studies of interactions between abiotic stressors, pathogen attacks, and aquaculture practises. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08575-9.
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Affiliation(s)
- Ana Corrochano-Fraile
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Andrew Davie
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Stefano Carboni
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK. .,International Marine Centre, Loc. Sa Mardini snc, 09170, Torre Grande, OR, Italy.
| | - Michaël Bekaert
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
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Araújo MJ, Sousa ML, Felpeto AB, Turkina MV, Fonseca E, Martins JC, Vasconcelos V, Campos A. Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species. Proteomes 2021; 9:proteomes9040046. [PMID: 34842808 PMCID: PMC8628934 DOI: 10.3390/proteomes9040046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 02/07/2023] Open
Abstract
Proteomics has been recently introduced in aquaculture research, and more methodological studies are needed to improve the quality of proteomics studies. Therefore, this work aims to compare three sample preparation methods for shotgun LC–MS/MS proteomics using tissues of two aquaculture species: liver of turbot Scophthalmus maximus and hepatopancreas of Mediterranean mussel Mytilus galloprovincialis. We compared the three most common sample preparation workflows for shotgun analysis: filter-aided sample preparation (FASP), suspension-trapping (S-Trap), and solid-phase-enhanced sample preparations (SP3). FASP showed the highest number of protein identifications for turbot samples, and S-Trap outperformed other methods for mussel samples. Subsequent functional analysis revealed a large number of Gene Ontology (GO) terms in turbot liver proteins (nearly 300 GO terms), while fewer GOs were found in mussel proteins (nearly 150 GO terms for FASP and S-Trap and 107 for SP3). This result may reflect the poor annotation of the genomic information in this specific group of animals. FASP was confirmed as the most consistent method for shotgun proteomic studies; however, the use of the other two methods might be important in specific experimental conditions (e.g., when samples have a very low amount of protein).
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Affiliation(s)
- Mário Jorge Araújo
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Maria Lígia Sousa
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Aldo Barreiro Felpeto
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Maria V. Turkina
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Clinical Sciences, Linköping University, 581 83 Linköping, Sweden;
| | - Elza Fonseca
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - José Carlos Martins
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
| | - Vítor Vasconcelos
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Alexandre Campos
- CIIMAR-UP-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal; (M.J.A.); (M.L.S.); (A.B.F.); (E.F.); (J.C.M.); (V.V.)
- Correspondence:
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Transcriptomic Profile of the Cockle Cerastoderma edule Exposed to Seasonal Diarrhetic Shellfish Toxin Contamination. Toxins (Basel) 2021; 13:toxins13110784. [PMID: 34822568 PMCID: PMC8625317 DOI: 10.3390/toxins13110784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 02/04/2023] Open
Abstract
Bivalves constitute an important source of proteins for human consumption, but some accumulate biotoxins such as diarrhetic shellfish toxins (DSTs), constituting a risk to human health. The cockle Cerastoderma edule is one of the most important species harvested in the Portuguese coast but also one of the most affected species due to recurrent DSTs exposure. However, little is known regarding the effects of the toxins produced by blooming dinoflagellates on C. edule. Herein, we explore the Differentially Expressed Genes (DEGs) of two tissues (gills and digestive gland) from wild cockles sampled in Portugal, through their whole transcriptomic response in two different seasons (exposed and not exposed to DSTs). The de novo transcriptome assembly returned 684,723 contigs, N50 of 1049, and 98.53% completeness. Altogether, 1098 DEGs were identified, of which 353 DEGs were exclusive for the digestive gland, 536 unique for the gills and 209 DEGs were common. Among DEGs were identified known DSTs-biomarkers including glutathione peroxidase, glutathione S-transferase, superoxide dismutase, cytochrome P450, ABC transporters, actin and tubulin-related proteins, Heat shock proteins and complement C1Q-like proteins. This study provides the first transcriptomic profile of C. edule, giving new insights about its molecular responses under different environmental conditions of DSTs exposure.
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Craig RJ, Yushenova IA, Rodriguez F, Arkhipova IR. An ancient clade of Penelope-like retroelements with permuted domains is present in the green lineage and protists, and dominates many invertebrate genomes. Mol Biol Evol 2021; 38:5005-5020. [PMID: 34320655 PMCID: PMC8557442 DOI: 10.1093/molbev/msab225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Penelope-like elements (PLEs) are an enigmatic clade of retrotransposons whose reverse transcriptases (RTs) share a most recent common ancestor with telomerase RTs. The single ORF of canonical endonuclease (EN)+ PLEs encodes RT and a C-terminal GIY–YIG EN that enables intrachromosomal integration, whereas EN− PLEs lack EN and are generally restricted to chromosome termini. EN+ PLEs have only been found in animals, except for one case of horizontal transfer to conifers, whereas EN− PLEs occur in several kingdoms. Here, we report a new, deep-branching PLE clade with a permuted domain order, whereby an N-terminal GIY–YIG EN is linked to a C-terminal RT by a short domain with a characteristic CxC motif. These N-terminal EN+ PLEs share a structural organization, including pseudo-LTRs and complex tandem/inverted insertions, with canonical EN+ PLEs from Penelope/Poseidon, Neptune, and Nematis clades, and show insertion bias for microsatellites, but lack canonical hammerhead ribozyme motifs. However, their phylogenetic distribution is much broader. The Naiads, found in numerous invertebrate phyla, can reach tens of thousands of copies per genome. In spiders and clams, Naiads independently evolved to encode selenoproteins containing multiple selenocysteines. Chlamys, which lack the CCHH motif universal to PLE ENs, occur in green algae, spike mosses (targeting ribosomal DNA), and slime molds. Unlike canonical PLEs, RTs of N-terminal EN+ PLEs contain the insertion-in-fingers domain (IFD), strengthening the link between PLEs and telomerases. Additionally, we describe Hydra, a novel metazoan C-terminal EN+ clade. Overall, we conclude that PLE diversity, taxonomic distribution, and abundance are comparable with non-LTR and LTR-retrotransposons.
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Affiliation(s)
- Rory J Craig
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
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Untargeted Metabolomics Approach for the Discovery of Environment-Related Pyran-2-ones Chemodiversity in a Marine-Sourced Penicillium restrictum. Mar Drugs 2021; 19:md19070378. [PMID: 34210084 PMCID: PMC8305465 DOI: 10.3390/md19070378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 11/17/2022] Open
Abstract
Very little is known about chemical interactions between fungi and their mollusc host within marine environments. Here, we investigated the metabolome of a Penicillium restrictum MMS417 strain isolated from the blue mussel Mytilus edulis collected on the Loire estuary, France. Following the OSMAC approach with the use of 14 culture media, the effect of salinity and of a mussel-derived medium on the metabolic expression were analysed using HPLC-UV/DAD-HRMS/MS. An untargeted metabolomics study was performed using principal component analysis (PCA), orthogonal projection to latent structure discriminant analysis (O-PLSDA) and molecular networking (MN). It highlighted some compounds belonging to sterols, macrolides and pyran-2-ones, which were specifically induced in marine conditions. In particular, a high chemical diversity of pyran-2-ones was found to be related to the presence of mussel extract in the culture medium. Mass spectrometry (MS)- and UV-guided purification resulted in the isolation of five new natural fungal pyran-2-one derivatives—5,6-dihydro-6S-hydroxymethyl-4-methoxy-2H-pyran-2-one (1), (6S, 1’R, 2’S)-LL-P880β (3), 5,6-dihydro-4-methoxy-6S-(1’S, 2’S-dihydroxy pent-3’(E)-enyl)-2H-pyran-2-one (4), 4-methoxy-6-(1’R, 2’S-dihydroxy pent-3’(E)-enyl)-2H-pyran-2-one (6) and 4-methoxy-2H-pyran-2-one (7)—together with the known (6S, 1’S, 2’S)-LL-P880β (2), (1’R, 2’S)-LL-P880γ (5), 5,6-dihydro-4-methoxy-2H-pyran-2-one (8), (6S, 1’S, 2’R)-LL-P880β (9), (6S, 1’S)-pestalotin (10), 1’R-dehydropestalotin (11) and 6-pentyl-4-methoxy-2H-pyran-2-one (12) from the mussel-derived culture medium extract. The structures of 1-12 were determined by 1D- and 2D-MMR experiments as well as high-resolution tandem MS, ECD and DP4 calculations. Some of these compounds were evaluated for their cytotoxic, antibacterial, antileishmanial and in-silico PTP1B inhibitory activities. These results illustrate the utility in using host-derived media for the discovery of new natural products.
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10
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Tunjić-Cvitanić M, Pasantes JJ, García-Souto D, Cvitanić T, Plohl M, Šatović-Vukšić E. Satellitome Analysis of the Pacific Oyster Crassostrea gigas Reveals New Pattern of Satellite DNA Organization, Highly Scattered across the Genome. Int J Mol Sci 2021; 22:ijms22136798. [PMID: 34202698 PMCID: PMC8268682 DOI: 10.3390/ijms22136798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/22/2022] Open
Abstract
Several features already qualified the invasive bivalve species Crassostrea gigas as a valuable non-standard model organism in genome research. C. gigas is characterized by the low contribution of satellite DNAs (satDNAs) vs. mobile elements and has an extremely low amount of heterochromatin, predominantly built of DNA transposons. In this work, we have identified 52 satDNAs composing the satellitome of C. gigas and constituting about 6.33% of the genome. Satellitome analysis reveals unusual, highly scattered organization of relatively short satDNA arrays across the whole genome. However, peculiar chromosomal distribution and densities are specific for each satDNA. The inspection of the organizational forms of the 11 most abundant satDNAs shows association with constitutive parts of Helitron mobile elements. Nine of the inspected satDNAs are dominantly found in mobile element-associated form, two mostly appear standalone, and only one is present exclusively as Helitron-associated sequence. The Helitron-related satDNAs appear in more chromosomes than other satDNAs, indicating that these mobile elements could be leading satDNA propagation in C. gigas. No significant accumulation of satDNAs on certain chromosomal positions was detected in C. gigas, thus establishing a novel pattern of satDNA organization on the genome level.
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Affiliation(s)
- Monika Tunjić-Cvitanić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.T.-C.); (M.P.)
| | - Juan J. Pasantes
- Centro de Investigación Mariña, Universidade de Vigo, Dpto de Bioquímica, Xenética e Inmunoloxía, 36310 Vigo, Spain;
| | - Daniel García-Souto
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain;
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Tonči Cvitanić
- Rimac Automobili d.o.o., Ljubljanska ulica 7, 10431 Sveta Nedelja, Croatia;
| | - Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.T.-C.); (M.P.)
| | - Eva Šatović-Vukšić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.T.-C.); (M.P.)
- Correspondence:
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11
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Potts RWA, Gutierrez AP, Penaloza CS, Regan T, Bean TP, Houston RD. Potential of genomic technologies to improve disease resistance in molluscan aquaculture. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200168. [PMID: 33813884 PMCID: PMC8059958 DOI: 10.1098/rstb.2020.0168] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 01/04/2023] Open
Abstract
Molluscan aquaculture is a major contributor to global seafood production, but is hampered by infectious disease outbreaks that can cause serious economic losses. Selective breeding has been widely used to improve disease resistance in major agricultural and aquaculture species, and has clear potential in molluscs, albeit its commercial application remains at a formative stage. Advances in genomic technologies, especially the development of cost-efficient genomic selection, have the potential to accelerate genetic improvement. However, tailored approaches are required owing to the distinctive reproductive and life cycle characteristics of molluscan species. Transgenesis and genome editing, in particular CRISPR/Cas systems, have been successfully trialled in molluscs and may further understanding and improvement of genetic resistance to disease through targeted changes to the host genome. Whole-organism genome editing is achievable on a much greater scale compared to other farmed species, making genome-wide CRISPR screening approaches plausible. This review discusses the current state and future potential of selective breeding, genomic tools and genome editing approaches to understand and improve host resistance to infectious disease in molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Robert W. A. Potts
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Dorset DT4 8UB, UK
| | - Alejandro P. Gutierrez
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Carolina S. Penaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Tim Regan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
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12
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Yévenes M, Núñez-Acuña G, Gallardo-Escárate C, Gajardo G. Adaptive Differences in Gene Expression in Farm-Impacted Seedbeds of the Native Blue Mussel Mytilus chilensis. Front Genet 2021; 12:666539. [PMID: 34093658 PMCID: PMC8174845 DOI: 10.3389/fgene.2021.666539] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 01/02/2023] Open
Abstract
The study of adaptive population differences is relevant for evolutionary biology, as it evidences the power of selective local forces relative to gene flow in maintaining adaptive phenotypes and their underlying genetic determinants. However, human-mediated hybridization through habitat translocations, a common and recurrent aquaculture practice where hybrids could eventually replace local genotypes, risk populations' ability to cope with perturbations. The endemic marine mussel Mytilus chilensis supports a booming farming industry in the inner sea of Chiloé Island, southern Chile, which entirely relies on artificially collected seeds from natural beds that are translocated to ecologically different fattening centers. A matter of concern is how farm-impacted seedbeds will potentially cope with environmental shifts and anthropogenic perturbations. This study provides the first de novo transcriptome of M. chilensis; assembled from tissue samples of mantles and gills of individuals collected in ecologically different farm-impacted seedbeds, Cochamó (41°S) and Yaldad (43°S). Both locations and tissue samples differentially expressed transcripts (DETs) in candidate adaptive genes controlling multiple fitness traits, involved with metabolism, genetic and environmental information processing, and cellular processes. From 189,743 consensus contigs assembled: 1,716 (Bonferroni p value ≤ 0.05) were DETs detected in different tissues of samples from different locations, 210 of them (fold change ≥ | 100|) in the same tissue of samples from a different location, and 665 (fold change ≥ | 4|) regardless of the tissue in samples from a different location. Site-specific DETs in Cochamó (169) and Yaldad (150) in candidate genes controlling tolerance to temperature and salinity shifts, and biomineralization exhibit a high number of nucleotide genetic variants with regular occurrence (frequency > 99%). This novel M. chilensis transcriptome should help assessing and monitoring the impact of translocations in wild and farm-impacted mussel beds in Chiloé Island. At the same time, it would help designing effective managing practices for conservation, and translocation traceability.
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Affiliation(s)
- Marco Yévenes
- Programa de Doctorado en Ciencias, Mención Conservación y Manejo de Recursos Naturales, Universidad de Los Lagos, Osorno, Chile
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Gustavo Núñez-Acuña
- Laboratorio de Biotecnología y Genómica Acuícola, Centro Interdisciplinario para la Investigación en Acuicultura, Universidad de Concepción, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Laboratorio de Biotecnología y Genómica Acuícola, Centro Interdisciplinario para la Investigación en Acuicultura, Universidad de Concepción, Concepción, Chile
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
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13
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Yang JL, Feng DD, Liu J, Xu JK, Chen K, Li YF, Zhu YT, Liang X, Lu Y. Chromosome-level genome assembly of the hard-shelled mussel Mytilus coruscus, a widely distributed species from the temperate areas of East Asia. Gigascience 2021; 10:6247647. [PMID: 33891010 PMCID: PMC8063583 DOI: 10.1093/gigascience/giab024] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/24/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The hard-shelled mussel (Mytilus coruscus) is widely distributed in the temperate seas of East Asia and is an important commercial bivalve in China. Chromosome-level genome information of this species will contribute not only to the development of hard-shelled mussel genetic breeding but also to studies on larval ecology, climate change biology, marine biology, aquaculture, biofouling, and antifouling. FINDINGS We applied a combination of Illumina sequencing, Oxford Nanopore Technologies sequencing, and high-throughput chromosome conformation capture technologies to construct a chromosome-level genome of the hard-shelled mussel, with a total length of 1.57 Gb and a median contig length of 1.49 Mb. Approximately 90.9% of the assemblies were anchored to 14 linkage groups. We assayed the genome completeness using BUSCO. In the metazoan dataset, the present assemblies have 89.4% complete, 1.9% incomplete, and 8.7% missing BUSCOs. Gene modeling enabled the annotation of 37,478 protein-coding genes and 26,917 non-coding RNA loci. Phylogenetic analysis showed that M. coruscus is the sister taxon to the clade including Modiolus philippinarum and Bathymodiolus platifrons. Conserved chromosome synteny was observed between hard-shelled mussel and king scallop, suggesting that this is shared ancestrally. Transcriptomic profiling indicated that the pathways of catecholamine biosynthesis and adrenergic signaling in cardiomyocytes might be involved in metamorphosis. CONCLUSIONS The chromosome-level assembly of the hard-shelled mussel genome will provide novel insights into mussel genome evolution and serve as a fundamental platform for studies regarding the planktonic-sessile transition, genetic diversity, and genomic breeding of this bivalve.
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Affiliation(s)
- Jin-Long Yang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.,Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
| | - Dan-Dan Feng
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
| | - Jie Liu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
| | - Jia-Kang Xu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
| | - Ke Chen
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
| | - Yi-Feng Li
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
| | - You-Ting Zhu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
| | - Xiao Liang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
| | - Ying Lu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
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14
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Sigwart JD, Lindberg DR, Chen C, Sun J. Molluscan phylogenomics requires strategically selected genomes. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200161. [PMID: 33813889 DOI: 10.1098/rstb.2020.0161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The extraordinary diversity in molluscan body plans, and the genomic mechanisms that enable it, remains one of the great questions of evolution. The eight distinct living taxonomic classes of molluscs are each unambiguously monophyletic; however, significant controversy remains about the phylogenetic relationships among those eight branches. Molluscs are the second-largest animal phylum, with over 100 000 living species with broad biological, economic and medical interest. To date, only around 53 genome assemblies have been accessioned to NCBI GenBank covering only four of the eight living molluscan classes. Furthermore, the molluscan taxa where partial or whole-genome assemblies are available are often aberrantly fast evolving or recently derived lineages. Characteristic adaptations provide interesting targets for whole-genome projects, in animals like the scaly-foot snail or octopus, but without basal-branching lineages for comparison, the context of recently derived features cannot be assessed. The currently available genomes also create a non-optimal set of taxa for resolving deeper phylogenetic branches: they are a small sample representing a large group, and those that are available come primarily from a rarefied pool. Thoughtful selection of taxa for future projects should focus on the blank areas of the molluscan tree, which are ripe with opportunities to delve into peculiarities of genome evolution, and reveal the biology and evolutionary history of molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Julia D Sigwart
- Senckenberg Research Institute, 60325 Frankfurt am Main, Germany.,Queen's University Belfast Marine Laboratory, Portaferry, Newtownards BT22 1PF, UK.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong
| | - David R Lindberg
- Department of Integrative Biology, University of California, Berkeley, USA
| | - Chong Chen
- X-STAR, Japan Agency for Marine Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Jin Sun
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, People's Republic of China
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15
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Inoue K, Yoshioka Y, Tanaka H, Kinjo A, Sassa M, Ueda I, Shinzato C, Toyoda A, Itoh T. Genomics and Transcriptomics of the green mussel explain the durability of its byssus. Sci Rep 2021; 11:5992. [PMID: 33727571 PMCID: PMC7971044 DOI: 10.1038/s41598-021-84948-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/18/2021] [Indexed: 11/09/2022] Open
Abstract
Mussels, which occupy important positions in marine ecosystems, attach tightly to underwater substrates using a proteinaceous holdfast known as the byssus, which is tough, durable, and resistant to enzymatic degradation. Although various byssal proteins have been identified, the mechanisms by which it achieves such durability are unknown. Here we report comprehensive identification of genes involved in byssus formation through whole-genome and foot-specific transcriptomic analyses of the green mussel, Perna viridis. Interestingly, proteins encoded by highly expressed genes include proteinase inhibitors and defense proteins, including lysozyme and lectins, in addition to structural proteins and protein modification enzymes that probably catalyze polymerization and insolubilization. This assemblage of structural and protective molecules constitutes a multi-pronged strategy to render the byssus highly resistant to environmental insults.
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Affiliation(s)
- Koji Inoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan.
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8563, Japan
| | - Hiroyuki Tanaka
- Department of Biological Information, Tokyo Institute of Technology, Meguro, Tokyo, 152-8550, Japan
| | - Azusa Kinjo
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
| | - Mieko Sassa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8563, Japan
| | - Ikuo Ueda
- School of Marine Biosciences, Kitasato University, Kanagawa, 252-0373, Japan.,Faculty of Science, Kanagawa University, Hiratsuka, 259-1293, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology, Meguro, Tokyo, 152-8550, Japan
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16
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Varney RM, Speiser DI, McDougall C, Degnan BM, Kocot KM. The Iron-Responsive Genome of the Chiton Acanthopleura granulata. Genome Biol Evol 2021; 13:evaa263. [PMID: 33320175 PMCID: PMC7850002 DOI: 10.1093/gbe/evaa263] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2020] [Indexed: 12/27/2022] Open
Abstract
Molluscs biomineralize structures that vary in composition, form, and function, prompting questions about the genetic mechanisms responsible for their production and the evolution of these mechanisms. Chitons (Mollusca, Polyplacophora) are a promising system for studies of biomineralization because they build a range of calcified structures including shell plates and spine- or scale-like sclerites. Chitons also harden the calcified teeth of their rasp-like radula with a coat of iron (as magnetite). Here we present the genome of the West Indian fuzzy chiton Acanthopleura granulata, the first from any aculiferan mollusc. The A. granulata genome contains homologs of many genes associated with biomineralization in conchiferan molluscs. We expected chitons to lack genes previously identified from pathways conchiferans use to make biominerals like calcite and nacre because chitons do not use these materials in their shells. Surprisingly, the A. granulata genome has homologs of many of these genes, suggesting that the ancestral mollusc may have had a more diverse biomineralization toolkit than expected. The A. granulata genome has features that may be specialized for iron biomineralization, including a higher proportion of genes regulated directly by iron than other molluscs. A. granulata also produces two isoforms of soma-like ferritin: one is regulated by iron and similar in sequence to the soma-like ferritins of other molluscs, and the other is constitutively translated and is not found in other molluscs. The A. granulata genome is a resource for future studies of molluscan evolution and biomineralization.
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Affiliation(s)
- Rebecca M Varney
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama
| | - Daniel I Speiser
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina
| | - Carmel McDougall
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Kevin M Kocot
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama
- Alabama Museum of Natural History, Tuscaloosa, Alabama
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17
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Can Proteomics Be Considered as a Valuable Tool to Assess the Toxicity of Nanoparticles in Marine Bivalves? JOURNAL OF MARINE SCIENCE AND ENGINEERING 2020. [DOI: 10.3390/jmse8121033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Exposure to nanoparticles (NPs) has been identified as a major concern for marine ecosystems. Because of their peculiar physico-chemical features, NPs are accumulated in marine organisms, which suffer a variety of adverse effects. In particular, bivalve mollusks represent a unique target for NPs, mainly because they are suspension-feeders with highly developed processes for cellular internalization of nano- and micrometric particles. Several studies have demonstrated that the uptake and the accumulation of NPs can induce sub-lethal effects towards marine bivalves. However, to understand the real risk of NP exposures the application of the so-called “omics” techniques (e.g., proteomics, genomics, metabolomics, lipidomics) has been suggested. In particular, proteomics has been used to study the effects of NPs and their mechanism(s) of action in marine bivalves, but to date its application is still limited. The present review aims at summarizing the state of the art concerning the application of proteomics as a tool to investigate the effects of nanoparticles on the proteome of marine bivalves, and to critically discuss the advantages and limitations of proteomics in this field of research. Relying on results obtained by studies that applied proteomics on bivalve tissues, proteomics application needs to be considered cautiously as a promising and valuable tool to shed light on toxicity and mechanism(s) of action of NPs. Although on one hand, the analysis of the current literature demonstrated undeniable strengths, potentiality and reliability of proteomics, on the other hand a number of limitations suggest that some gaps of knowledge need to be bridged, and methodological and technical improvements are necessary before proteomics can be readily and routinely applied to nanotoxicology studies.
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18
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Popovic I, Bierne N, Gaiti F, Tanurdžić M, Riginos C. Pre-introduction introgression contributes to parallel differentiation and contrasting hybridization outcomes between invasive and native marine mussels. J Evol Biol 2020; 34:175-192. [PMID: 33251632 DOI: 10.1111/jeb.13746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 11/01/2020] [Accepted: 11/11/2020] [Indexed: 12/28/2022]
Abstract
Non-native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis, in the absence (South Africa and California) and presence of hybridization with a native congener (Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post-introduction differentiation from native-range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic-derived introductions displaying high differentiation (maxFST > 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein-coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages (M. planulatus and Atlantic M. galloprovincialis). Additionally, contigs putatively introgressed with divergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome-wide trends and also diverged in parallel in both Atlantic-derived introductions. These results suggest that divergent demographic histories experienced by introduced lineages, including pre-introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.
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Affiliation(s)
- Iva Popovic
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution UMR 5554, Université de Montpellier, CNRS-IRD-EPHE-UM, Montpellier, France
| | - Federico Gaiti
- Weill Cornell Medicine, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Miloš Tanurdžić
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
| | - Cynthia Riginos
- School of Biological Sciences, University of Queensland, St Lucia, Qld, Australia
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19
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Gerdol M, Moreira R, Cruz F, Gómez-Garrido J, Vlasova A, Rosani U, Venier P, Naranjo-Ortiz MA, Murgarella M, Greco S, Balseiro P, Corvelo A, Frias L, Gut M, Gabaldón T, Pallavicini A, Canchaya C, Novoa B, Alioto TS, Posada D, Figueras A. Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel. Genome Biol 2020; 21:275. [PMID: 33168033 PMCID: PMC7653742 DOI: 10.1186/s13059-020-02180-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/15/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive mortalities in other bivalves. Although these traits have been recently linked with the maintenance of a high genetic variation within natural populations, the factors underlying the evolutionary success of this species remain unclear. RESULTS Here, after the assembly of a 1.28-Gb reference genome and the resequencing of 14 individuals from two independent populations, we reveal a complex pan-genomic architecture in M. galloprovincialis, with a core set of 45,000 genes plus a strikingly high number of dispensable genes (20,000) subject to presence-absence variation, which may be entirely missing in several individuals. We show that dispensable genes are associated with hemizygous genomic regions affected by structural variants, which overall account for nearly 580 Mb of DNA sequence not included in the reference genome assembly. As such, this is the first study to report the widespread occurrence of gene presence-absence variation at a whole-genome scale in the animal kingdom. CONCLUSIONS Dispensable genes usually belong to young and recently expanded gene families enriched in survival functions, which might be the key to explain the resilience and invasiveness of this species. This unique pan-genome architecture is characterized by dispensable genes in accessory genomic regions that exceed by orders of magnitude those observed in other metazoans, including humans, and closely mirror the open pan-genomes found in prokaryotes and in a few non-metazoan eukaryotes.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, Università degli Studi di Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Rebeca Moreira
- Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Jessica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Anna Vlasova
- CRG - Centre for Genomic Regulation, Doctor Aiguader, 88, 08003 Barcelona, Spain
| | - Umberto Rosani
- Department of Biology, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Paola Venier
- Department of Biology, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Miguel A. Naranjo-Ortiz
- CRG - Centre for Genomic Regulation, Doctor Aiguader, 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Maria Murgarella
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Samuele Greco
- Department of Life Sciences, Università degli Studi di Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Pablo Balseiro
- Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
- Norce Norwegian Research Centre AS, Bergen, Norway
| | - André Corvelo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- New York Genome Center, New York, NY 10013 USA
| | - Leonor Frias
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Toni Gabaldón
- CRG - Centre for Genomic Regulation, Doctor Aiguader, 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Current address: Barelona Supercomputing Centre (BSC-CNS) and Institute for Research in Biomedicine (IRB), 08034 Barcelona, Spain
| | - Alberto Pallavicini
- Department of Life Sciences, Università degli Studi di Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
- Anton Dohrn Zoological Station, 80121 Villa Comunale, Naples, Italy
| | - Carlos Canchaya
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute, 36310 Vigo, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
| | - Tyler S. Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute, 36310 Vigo, Spain
| | - Antonio Figueras
- Instituto de Investigaciones Marinas (IIM - CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
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20
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Simon A, Fraïsse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch JJ, Bierne N. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. J Evol Biol 2020; 34:208-223. [PMID: 33045123 DOI: 10.1111/jeb.13709] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 08/20/2020] [Accepted: 09/16/2020] [Indexed: 12/19/2022]
Abstract
The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study 'replicated' instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.
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Affiliation(s)
- Alexis Simon
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Christelle Fraïsse
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.,Institute of Science and Technology Austria, Klosterneuburg, Austria, Austria
| | - Tahani El Ayari
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Petr Strelkov
- St. Petersburg State University, St. Petersburg, Russia.,Laboratory of Monitoring and Conservation of Natural Arctic Ecosystems, Murmansk Arctic State University, Murmansk, Russia
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Nicolas Bierne
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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21
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Cervera A, de la Peña M. Small circRNAs with self-cleaving ribozymes are highly expressed in diverse metazoan transcriptomes. Nucleic Acids Res 2020; 48:5054-5064. [PMID: 32198887 PMCID: PMC7229834 DOI: 10.1093/nar/gkaa187] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/13/2022] Open
Abstract
Ribozymes are catalytic RNAs present in modern genomes but regarded as remnants of a prebiotic RNA world. The paradigmatic hammerhead ribozyme (HHR) is a small self-cleaving motif widespread from bacterial to human genomes. Here, we report that most of the classical type I HHRs frequently found in the genomes of animals are contained within a novel family of non-autonomous non-LTR retrotransposons of the retrozyme class. These retroelements are expressed as abundant linear and circular RNAs of ∼170-400 nt in different animal tissues. Bioinformatic and in vitro analyses indicate an efficient self-cleavage of the HHRs harboured in most invertebrate retrozymes, whereas HHRs in retrozymes of vertebrates, such as the axolotl and other amphibians, require to act as dimeric motifs to reach higher self-cleavage rates. Ligation assays of retrozyme RNAs with a protein ligase versus HHR self-ligation indicate that, most likely, tRNA ligases and not the ribozymes are involved in the step of RNA circularization. Altogether, these results confirm the existence of a new and conserved pathway in animals and, likely, eukaryotes in general, for the efficient biosynthesis of RNA circles through small ribozymes, which opens the door for the development of new tools in the emerging field of study of circRNAs.
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Affiliation(s)
- Amelia Cervera
- IBMCP (CSIC-UPV). C/ Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Marcos de la Peña
- IBMCP (CSIC-UPV). C/ Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
- To whom correspondence should be addressed. Tel: +34 963 877 915; Fax: +34 963 877 859;
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22
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Khan B, Ho KT, Burgess RM. Application of Biomarker Tools Using Bivalve Models Toward the Development of Adverse Outcome Pathways for Contaminants of Emerging Concern. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2020; 39:1472-1484. [PMID: 32452040 PMCID: PMC7657996 DOI: 10.1002/etc.4757] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/10/2020] [Accepted: 05/18/2020] [Indexed: 05/24/2023]
Abstract
As contaminant exposures in aquatic ecosystems continue to increase, the need for streamlining research efforts in environmental toxicology using predictive frameworks also grows. One such framework is the adverse outcome pathway (AOP). An AOP framework organizes and utilizes toxicological information to connect measurable molecular endpoints to an adverse outcome of regulatory relevance via a series of events at different levels of biological organization. Molecular endpoints or biomarkers are essential to develop AOPs and are valuable early warning signs of the toxicity of pollutants, including contaminants of emerging concern. Ecological risk-assessment approaches using tools such as biomarkers and AOPs benefit from identification of molecular targets conserved across species. Bivalve models are useful in such approaches and integral to our understanding of ecological and human health risks associated with contaminant exposures. We discuss the value of using biomarker approaches in bivalve models to meet the demands of twenty-first-century toxicology. Environ Toxicol Chem 2020;39:1472-1484. © 2020 SETAC.
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Affiliation(s)
- Bushra Khan
- ORISE Research Participant at the US Environmental
Protection Agency, ORD-CEMM, Atlantic Coastal Environmental Sciences Division, 27
Tarzwell Drive, Narragansett, RI 02882, USA
| | - Kay T. Ho
- US Environmental Protection Agency, ORD-CEMM, Atlantic
Coastal Environmental Sciences Division, 27 Tarzwell Drive, Narragansett, RI 02882,
USA
| | - Robert M. Burgess
- US Environmental Protection Agency, ORD-CEMM, Atlantic
Coastal Environmental Sciences Division, 27 Tarzwell Drive, Narragansett, RI 02882,
USA
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23
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Campos A, Freitas M, de Almeida AM, Martins JC, Domínguez-Pérez D, Osório H, Vasconcelos V, Reis Costa P. OMICs Approaches in Diarrhetic Shellfish Toxins Research. Toxins (Basel) 2020; 12:E493. [PMID: 32752012 PMCID: PMC7472309 DOI: 10.3390/toxins12080493] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/22/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022] Open
Abstract
Diarrhetic shellfish toxins (DSTs) are among the most prevalent marine toxins in Europe's and in other temperate coastal regions. These toxins are produced by several dinoflagellate species; however, the contamination of the marine trophic chain is often attributed to species of the genus Dinophysis. This group of toxins, constituted by okadaic acid (OA) and analogous molecules (dinophysistoxins, DTXs), are highly harmful to humans, causing severe poisoning symptoms caused by the ingestion of contaminated seafood. Knowledge on the mode of action and toxicology of OA and the chemical characterization and accumulation of DSTs in seafood species (bivalves, gastropods and crustaceans) has significantly contributed to understand the impacts of these toxins in humans. Considerable information is however missing, particularly at the molecular and metabolic levels involving toxin uptake, distribution, compartmentalization and biotransformation and the interaction of DSTs with aquatic organisms. Recent contributions to the knowledge of DSTs arise from transcriptomics and proteomics research. Indeed, OMICs constitute a research field dedicated to the systematic analysis on the organisms' metabolisms. The methodologies used in OMICs are also highly effective to identify critical metabolic pathways affecting the physiology of the organisms. In this review, we analyze the main contributions provided so far by OMICs to DSTs research and discuss the prospects of OMICs with regard to the DSTs toxicology and the significance of these toxins to public health, food safety and aquaculture.
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Affiliation(s)
- Alexandre Campos
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
| | - Marisa Freitas
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
- ESS-P.Porto, School of Health, Polytechnic Institute of Porto. Rua Dr. António Bernardino de Almeida, 400, 4200-072 Porto, Portugal
| | - André M. de Almeida
- LEAF-Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal;
| | - José Carlos Martins
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
| | - Dany Domínguez-Pérez
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
| | - Hugo Osório
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal;
- Ipatimup—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
- Faculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal
| | - Vitor Vasconcelos
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal; (M.F.); (J.C.M.); (D.D.-P.); (V.V.)
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro Reis Costa
- IPMA—Instituto Português do Mar da Atmosfera, Rua Alfredo Magalhães Ramalho, 6, 1495-006 Lisbon, Portugal;
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24
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Tunjić Cvitanić M, Vojvoda Zeljko T, Pasantes JJ, García-Souto D, Gržan T, Despot-Slade E, Plohl M, Šatović E. Sequence Composition Underlying Centromeric and Heterochromatic Genome Compartments of the Pacific Oyster Crassostrea gigas. Genes (Basel) 2020; 11:genes11060695. [PMID: 32599860 PMCID: PMC7348941 DOI: 10.3390/genes11060695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/10/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023] Open
Abstract
Segments of the genome enriched in repetitive sequences still present a challenge and are omitted in genome assemblies. For that reason, the exact composition of DNA sequences underlying the heterochromatic regions and the active centromeres are still unexplored for many organisms. The centromere is a crucial region of eukaryotic chromosomes responsible for the accurate segregation of genetic material. The typical landmark of centromere chromatin is the rapidly-evolving variant of the histone H3, CenH3, while DNA sequences packed in constitutive heterochromatin are associated with H3K9me3-modified histones. In the Pacific oyster Crassostrea gigas we identified its centromere histone variant, Cg-CenH3, that shows stage-specific distribution in gonadal cells. In order to investigate the DNA composition of genomic regions associated with the two specific chromatin types, we employed chromatin immunoprecipitation followed by high-throughput next-generation sequencing of the Cg-CenH3- and H3K9me3-associated sequences. CenH3-associated sequences were assigned to six groups of repetitive elements, while H3K9me3-associated-ones were assigned only to three. Those associated with CenH3 indicate the lack of uniformity in the chromosomal distribution of sequences building the centromeres, being also in the same time dispersed throughout the genome. The heterochromatin of C. gigas exhibited general paucity and limited chromosomal localization as predicted, with H3K9me3-associated sequences being predominantly constituted of DNA transposons.
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Affiliation(s)
- Monika Tunjić Cvitanić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
| | - Tanja Vojvoda Zeljko
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
| | - Juan J. Pasantes
- Departamento de Bioquímica, Xenética e Inmunoloxía, Centro de Investigación Mariña (CIM), Universidade de Vigo, 36310 Vigo, Spain; (J.J.P.); (D.G.-S.)
| | - Daniel García-Souto
- Departamento de Bioquímica, Xenética e Inmunoloxía, Centro de Investigación Mariña (CIM), Universidade de Vigo, 36310 Vigo, Spain; (J.J.P.); (D.G.-S.)
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Praza do Obradoiro, 0, 15705 Santiago de Compostela, Spain
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Tena Gržan
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
| | - Evelin Despot-Slade
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
| | - Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
- Correspondence: (M.P.); (E.Š.)
| | - Eva Šatović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (M.T.C.); (T.V.Z.); (T.G.); (E.D.-S.)
- Correspondence: (M.P.); (E.Š.)
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25
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Knöbel L, Breusing C, Bayer T, Sharma V, Hiller M, Melzner F, Stuckas H. Comparative de novo assembly and annotation of mantle tissue transcriptomes from the Mytilus edulis species complex (M. edulis, M. galloprovincialis, M. trossulus). Mar Genomics 2020. [DOI: 10.1016/j.margen.2019.100700] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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Etherington GJ, Heavens D, Baker D, Lister A, McNelly R, Garcia G, Clavijo B, Macaulay I, Haerty W, Di Palma F. Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal. Gigascience 2020; 9:5836134. [PMID: 32396200 PMCID: PMC7216774 DOI: 10.1093/gigascience/giaa045] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 02/28/2020] [Accepted: 04/15/2020] [Indexed: 01/05/2023] Open
Abstract
Background Whilst much sequencing effort has focused on key mammalian model organisms such as mouse and human, little is known about the relationship between genome sequencing techniques for non-model mammals and genome assembly quality. This is especially relevant to non-model mammals, where the samples to be sequenced are often degraded and of low quality. A key aspect when planning a genome project is the choice of sequencing data to generate. This decision is driven by several factors, including the biological questions being asked, the quality of DNA available, and the availability of funds. Cutting-edge sequencing technologies now make it possible to achieve highly contiguous, chromosome-level genome assemblies, but rely on high-quality high molecular weight DNA. However, funding is often insufficient for many independent research groups to use these techniques. Here we use a range of different genomic technologies generated from a roadkill European polecat (Mustela putorius) to assess various assembly techniques on this low-quality sample. We evaluated different approaches for de novo assemblies and discuss their value in relation to biological analyses. Results Generally, assemblies containing more data types achieved better scores in our ranking system. However, when accounting for misassemblies, this was not always the case for Bionano and low-coverage 10x Genomics (for scaffolding only). We also find that the extra cost associated with combining multiple data types is not necessarily associated with better genome assemblies. Conclusions The high degree of variability between each de novo assembly method (assessed from the 7 key metrics) highlights the importance of carefully devising the sequencing strategy to be able to carry out the desired analysis. Adding more data to genome assemblies does not always result in better assemblies, so it is important to understand the nuances of genomic data integration explained here, in order to obtain cost-effective value for money when sequencing genomes.
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Affiliation(s)
| | - Darren Heavens
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - David Baker
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Ashleigh Lister
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Rose McNelly
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Gonzalo Garcia
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Bernardo Clavijo
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Iain Macaulay
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Wilfried Haerty
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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27
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Li R, Zhang W, Lu J, Zhang Z, Mu C, Song W, Migaud H, Wang C, Bekaert M. The Whole-Genome Sequencing and Hybrid Assembly of Mytilus coruscus. Front Genet 2020; 11:440. [PMID: 32457802 PMCID: PMC7227121 DOI: 10.3389/fgene.2020.00440] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/09/2020] [Indexed: 01/13/2023] Open
Abstract
The hard-shelled mussel (Mytilus coruscus) is an economically important shellfish that has been cultivated for the last decade. Due to over-exploitation, most mussel stocks have dramatically declined. Efforts to study this species' natural distribution, genetics, breeding, and cultivation have been hindered by the lack of a high-quality reference genome. To address this, we produced a hybrid high-quality reference genome of M. coruscus using a long-read platform to assemble the genome and short-read, high-quality technology to accurately correct for sequence errors. The genome was assembled into 10,484 scaffolds, a total length of 1.90 Gb, and a scaffold N50 of 898 kb. Ab initio annotation of the M. coruscus genome assembly identified a total of 42,684 genes. This accurate reference genome of M. coruscus provides an essential resource with the advantage of enabling the genome-scale selective breeding of M. coruscus. More importantly, it will also help in deciphering the speciation and local adaptation of the Mytilus species.
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Affiliation(s)
- Ronghua Li
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China.,Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Weijia Zhang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Junkai Lu
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Zhouyi Zhang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Changkao Mu
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Weiwei Song
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Herve Migaud
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China.,Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | - Chunlin Wang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.,Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo, China
| | - Michaël Bekaert
- Faculty of Natural Sciences, Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
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28
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Cardoso JCR, Félix RC, Ferreira V, Peng M, Zhang X, Power DM. The calcitonin-like system is an ancient regulatory system of biomineralization. Sci Rep 2020; 10:7581. [PMID: 32371888 PMCID: PMC7200681 DOI: 10.1038/s41598-020-64118-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/06/2020] [Indexed: 12/27/2022] Open
Abstract
Biomineralization is the process by which living organisms acquired the capacity to accumulate minerals in tissues. Shells are the biomineralized exoskeleton of marine molluscs produced by the mantle but factors that regulate mantle shell building are still enigmatic. This study sought to identify candidate regulatory factors of molluscan shell mineralization and targeted family B G-protein coupled receptors (GPCRs) and ligands that include calcium regulatory factors in vertebrates, such as calcitonin (CALC). In molluscs, CALC receptor (CALCR) number was variable and arose through lineage and species-specific duplications. The Mediterranean mussel (Mytilus galloprovincialis) mantle transcriptome expresses six CALCR-like and two CALC-precursors encoding four putative mature peptides. Mussel CALCR-like are activated in vitro by vertebrate CALC but only receptor CALCRIIc is activated by the mussel CALCIIa peptide (EC50 = 2.6 ×10-5 M). Ex-vivo incubations of mantle edge tissue and mantle cells with CALCIIa revealed they accumulated significantly more calcium than untreated tissue and cells. Mussel CALCIIa also significantly decreased mantle acid phosphatase activity, which is associated with shell remodelling. Our data indicate the CALC-like system as candidate regulatory factors of shell mineralization. The identification of the CALC system from molluscs to vertebrates suggests it is an ancient and conserved calcium regulatory system of mineralization.
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Affiliation(s)
- João C R Cardoso
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Rute C Félix
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Vinícius Ferreira
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - MaoXiao Peng
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Xushuai Zhang
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Deborah M Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.
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29
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Kenny NJ, McCarthy SA, Dudchenko O, James K, Betteridge E, Corton C, Dolucan J, Mead D, Oliver K, Omer AD, Pelan S, Ryan Y, Sims Y, Skelton J, Smith M, Torrance J, Weisz D, Wipat A, Aiden EL, Howe K, Williams ST. The gene-rich genome of the scallop Pecten maximus. Gigascience 2020; 9:giaa037. [PMID: 32352532 PMCID: PMC7191990 DOI: 10.1093/gigascience/giaa037] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/26/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms the basis of a valuable commercial fishery and plays a key role in coastal ecosystems and food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which it has evolved some immunity. The molecular origins of this immunity are of interest to evolutionary biologists, pharmaceutical companies, and fisheries management. FINDINGS Here we report the genome assembly of this species, conducted as part of the Wellcome Sanger 25 Genomes Project. This genome was assembled from PacBio reads and scaffolded with 10X Chromium and Hi-C data. Its 3,983 scaffolds have an N50 of 44.8 Mb (longest scaffold 60.1 Mb), with 92% of the assembly sequence contained in 19 scaffolds, corresponding to the 19 chromosomes found in this species. The total assembly spans 918.3 Mb and is the best-scaffolded marine bivalve genome published to date, exhibiting 95.5% recovery of the metazoan BUSCO set. Gene annotation resulted in 67,741 gene models. Analysis of gene content revealed large numbers of gene duplicates, as previously seen in bivalves, with little gene loss, in comparison with the sequenced genomes of other marine bivalve species. CONCLUSIONS The genome assembly of P. maximus and its annotated gene set provide a high-quality platform for studies on such disparate topics as shell biomineralization, pigmentation, vision, and resistance to algal toxins. As a result of our findings we highlight the sodium channel gene Nav1, known to confer resistance to saxitoxin and tetrodotoxin, as a candidate for further studies investigating immunity to domoic acid.
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Affiliation(s)
- Nathan J Kenny
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
| | - Shane A McCarthy
- University of Cambridge, Department of Genetics,Cambridge CB2 3EH, UK
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005-1827, USA
| | - Katherine James
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
| | | | - Craig Corton
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Jale Dolucan
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Dan Mead
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Karen Oliver
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Pelan
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Yan Ryan
- School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- Institute of Infection and Global Health, Liverpool University, iC2, 146 Brownlow Hill, Liverpool L3 5RF, UK
| | - Ying Sims
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | | | | | | | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anil Wipat
- School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Erez L Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- The Center for Theoretical Biological Physics, Rice University, 6100 Main St, Houston, TX 77005-1827, USA
- Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech University, Shanghai, China
- School of Agriculture and Environment, University of Western Australia, Perth, Australia
| | - Kerstin Howe
- Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Suzanne T Williams
- Natural History Museum, Department of Life Sciences,Cromwell Road, London SW7 5BD, UK
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30
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Auguste M, Balbi T, Ciacci C, Canonico B, Papa S, Borello A, Vezzulli L, Canesi L. Shift in Immune Parameters After Repeated Exposure to Nanoplastics in the Marine Bivalve Mytilus. Front Immunol 2020; 11:426. [PMID: 32351496 PMCID: PMC7174705 DOI: 10.3389/fimmu.2020.00426] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/25/2020] [Indexed: 12/14/2022] Open
Abstract
Bivalves are widespread in coastal environments subjected to a wide range of environmental fluctuations: however, the rapidly occurring changes due to several anthropogenic factors can represent a significant threat to bivalve immunity. The mussel Mytilus spp. has extremely powerful immune defenses toward different potential pathogens and contaminant stressors. In particular, the mussel immune system represents a significant target for different types of nanoparticles (NPs), including amino-modified nanopolystyrene (PS-NH2) as a model of nanoplastics. In this work, the effects of repeated exposure to PS-NH2 on immune responses of Mytilus galloprovincialis were investigated after a first exposure (10 μg/L; 24 h), followed by a resting period (72-h depuration) and a second exposure (10 μg/L; 24 h). Functional parameters were measured in hemocytes, serum, and whole hemolymph samples. In hemocytes, transcription of selected genes involved in proliferation/apoptosis and immune response was evaluated by qPCR. First exposure to PS-NH2 significantly affected hemocyte mitochondrial and lysosomal parameters, serum lysozyme activity, and transcription of proliferation/apoptosis markers; significant upregulation of extrapallial protein precursor (EPp) and downregulation of lysozyme and mytilin B were observed. The results of functional hemocyte parameters indicate the occurrence of stress conditions that did not however result in changes in the overall bactericidal activity. After the second exposure, a shift in hemocyte subpopulations, together with reestablishment of basal functional parameters and of proliferation/apoptotic markers, was observed. Moreover, hemolymph bactericidal activity, as well as transcription of five out of six immune-related genes, all codifying for secreted proteins, was significantly increased. The results indicate an overall shift in immune parameters that may act as compensatory mechanisms to maintain immune homeostasis after a second encounter with PS-NH2.
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Affiliation(s)
- Manon Auguste
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Teresa Balbi
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Caterina Ciacci
- Department of Biomolecular Sciences (DIBS), University of Urbino, Urbino, Italy
| | - Barbara Canonico
- Department of Biomolecular Sciences (DIBS), University of Urbino, Urbino, Italy
| | - Stefano Papa
- Department of Biomolecular Sciences (DIBS), University of Urbino, Urbino, Italy
| | - Alessio Borello
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Luigi Vezzulli
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Laura Canesi
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
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31
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Yang Z, Zhang L, Hu J, Wang J, Bao Z, Wang S. The evo-devo of molluscs: Insights from a genomic perspective. Evol Dev 2020; 22:409-424. [PMID: 32291964 DOI: 10.1111/ede.12336] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Molluscs represent one of ancient and evolutionarily most successful groups of marine invertebrates, with a tremendous diversity of morphology, behavior, and lifestyle. Molluscs are excellent subjects for evo-devo studies; however, understanding of the evo-devo of molluscs has been largely hampered by incomplete fossil records and limited molecular data. Recent advancement of genomics and other technologies has greatly fueled the molluscan "evo-devo" field, and decoding of several molluscan genomes provides unprecedented insights into molluscan biology and evolution. Here, we review the recent progress of molluscan genome sequencing as well as novel insights gained from their genomes, by emphasizing how molluscan genomics enhances our understanding of the evo-devo of molluscs.
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Affiliation(s)
- Zhihui Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Jing Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,The Sars-Fang Centre, Ocean University of China, Qingdao, China
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32
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Oh R, Lee MJ, Kim YO, Nam BH, Kong HJ, Kim JW, Park JY, Seo JK, Kim DG. Myticusin-beta, antimicrobial peptide from the marine bivalve, Mytilus coruscus. FISH & SHELLFISH IMMUNOLOGY 2020; 99:342-352. [PMID: 32061872 DOI: 10.1016/j.fsi.2020.02.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/07/2020] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
We isolated and purified an antimicrobial peptide (AMP) from the mantle of the hard-shelled mussel, Mytilus coruscus. The peptide was purified through C18 reversed-phase high-performance liquid chromatography, and displayed antibacterial activity. Total molecular mass of 11,182 Da was determined using matrix-assisted laser desorption ionization time-of-flight mass spectrophotometry. The N-terminal 23-amino acid sequence of its purified peak was obtained through Edman degradation, revealing 82% identity with myticusin-1 of M. coruscus. Complete sequence of the target peptide was determined through cDNA cloning and rapid amplification of cDNA ends. The complete sequence comprised 574 bp with a 387-bp open reading frame (ORF) encoding 24 amino acids of a signal peptide and 104 amino acids of a mature peptide, which was named myticusin-beta. Furthermore, we discovered two novel isoforms of myticusin-beta. We constructed and expressed recombinant myticusin-beta, which displayed antimicrobial activity against gram-positive (Bacillus cereus, Bacillus subtilis, Clostridium perfringens, Staphylococcus aureus, Streptococcus iniae, Streptococcus mutans) and gram-negative bacteria (Escherichia coli, Pseudomonas aeruginosa, Vibrio alginolyticus, Klebsiella pneumoniae). Purified recombinant myticusin-beta also showed anti-parasitic activity at various concentrations. A short AMP analog was designed and synthesized based on the sequence of myticusin-beta, with markedly improved antimicrobial activity. Expression of myticusin-beta was detected in the mantle at the highest level, followed by hemocytes. The results obtained in this work suggest that myticusin-beta is an immune-related AMP of M. coruscus and an effective alternative to antibiotics.
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Affiliation(s)
- Ryunkyoung Oh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Min Jeong Lee
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Ju-Won Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Jung-Yeon Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea
| | - Jung-Kil Seo
- Department of Food Science and Biotechnology, Kunsan National University, Kunsan, 54150, South Korea
| | - Dong-Gyun Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, 46083, Republic of Korea.
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33
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Chao YC, Merritt M, Schaefferkoetter D, Evans TG. High-throughput quantification of protein structural change reveals potential mechanisms of temperature adaptation in Mytilus mussels. BMC Evol Biol 2020; 20:28. [PMID: 32054457 PMCID: PMC7020559 DOI: 10.1186/s12862-020-1593-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/05/2020] [Indexed: 11/10/2022] Open
Abstract
Background Temperature exerts a strong influence on protein evolution: species living in thermally distinct environments often exhibit adaptive differences in protein structure and function. However, previous research on protein temperature adaptation has focused on small numbers of proteins and on proteins adapted to extreme temperatures. Consequently, less is known about the types and quantity of evolutionary change that occurs to proteins when organisms adapt to small shifts in environmental temperature. In this study, these uncertainties were addressed by developing software that enabled comparison of structural changes associated with temperature adaptation (hydrogen bonding, salt bridge formation, and amino acid use) among large numbers of proteins from warm- and cold-adapted species of marine mussels, Mytilus galloprovincialis and Mytilus trossulus, respectively. Results Small differences in habitat temperature that characterize the evolutionary history of Mytilus mussels were sufficient to cause protein structural changes consistent with temperature adaptation. Hydrogen bonds and salt bridges that increase stability and protect against heat-induced denaturation were more abundant in proteins from warm-adapted M. galloprovincialis compared with proteins from cold-adapted M. trossulus. These structural changes were related to deviations in the use of polar and charged amino acids that facilitate formation of hydrogen bonds and salt bridges within proteins, respectively. Enzymes, in particular those within antioxidant and cell death pathways, were over-represented among proteins with the most hydrogen bonds and salt bridges in warm-adapted M. galloprovincialis. Unlike extremophile proteins, temperature adaptation in Mytilus proteins did not involve substantial changes in the number of hydrophobic or large volume amino acids, nor in the content of glycine or proline. Conclusions Small shifts in organism temperature tolerance, such as that needed to cope with climate warming, may result from structural and functional changes to a small percentage of the proteome. Proteins in which function is dependent on large conformational change, notably enzymes, may be particularly sensitive to temperature perturbation and represent foci for natural selection. Protein temperature adaptation can occur through different types and frequencies of structural change, and adaptive mechanisms used to cope with small shifts in habitat temperature appear different from mechanisms used to retain protein function at temperature extremes.
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Affiliation(s)
- Ying-Chen Chao
- Department of Biological Sciences, California State University East Bay, Hayward, CA, 94542, USA
| | - Melanie Merritt
- Department of Biological Sciences, California State University East Bay, Hayward, CA, 94542, USA
| | - Devin Schaefferkoetter
- Department of Biological Sciences, California State University East Bay, Hayward, CA, 94542, USA
| | - Tyler G Evans
- Department of Biological Sciences, California State University East Bay, Hayward, CA, 94542, USA.
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34
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Popovic I, Riginos C. Comparative genomics reveals divergent thermal selection in warm‐ and cold‐tolerant marine mussels. Mol Ecol 2020; 29:519-535. [DOI: 10.1111/mec.15339] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Iva Popovic
- School of Biological Sciences University of Queensland St Lucia Qld Australia
| | - Cynthia Riginos
- School of Biological Sciences University of Queensland St Lucia Qld Australia
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35
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Fujii Y, Gerdol M, Kawsar SMA, Hasan I, Spazzali F, Yoshida T, Ogawa Y, Rajia S, Kamata K, Koide Y, Sugawara S, Hosono M, Tame JRH, Fujita H, Pallavicini A, Ozeki Y. A GM1b/asialo-GM1 oligosaccharide-binding R-type lectin from purplish bifurcate mussels Mytilisepta virgata and its effect on MAP kinases. FEBS J 2019; 287:2612-2630. [PMID: 31769916 PMCID: PMC7317968 DOI: 10.1111/febs.15154] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 09/16/2019] [Accepted: 11/22/2019] [Indexed: 12/23/2022]
Abstract
A 15‐kDa lectin, termed SeviL, was isolated from Mytilisepta virgata (purplish bifurcate mussel). SeviL forms a noncovalent dimer that binds strongly to ganglio‐series GM1b oligosaccharide (Neu5Acɑ2‐3Galβ1‐3GalNAcβ1‐4Galβ1‐4Glc) and its precursor, asialo‐GM1 (Galβ1‐3GalNAcβ1‐4Galβ1‐4Glc). SeviL also interacts weakly with the glycan moiety of SSEA‐4 hexaose (Neu5Acα2‐3Galβ1‐3GalNAcβ1‐3Galα1‐4Galβ1‐4Glc). A partial protein sequence of the lectin was determined by mass spectrometry, and the complete sequence was identified from transcriptomic analysis. SeviL, consisting of 129 amino acids, was classified as an R(icin B)‐type lectin, based on the presence of the QxW motif characteristic of this fold. SeviL mRNA is highly expressed in gills and, in particular, mantle rim tissues. Orthologue sequences were identified in other species of the family Mytilidae, including Mytilus galloprovincialis, from which lectin MytiLec‐1 was isolated and characterized in our previous studies. Thus, mytilid species contain lectins belonging to at least two distinct families (R‐type lectins and mytilectins) that have a common β‐trefoil fold structure but differing glycan‐binding specificities. SeviL displayed notable cytotoxic (apoptotic) effects against various cultured cell lines (human breast, ovarian, and colonic cancer; dog kidney) that possess asialo‐GM1 oligosaccharide at the cell surface. This cytotoxic effect was inhibited by the presence of anti‐asialo‐GM1 oligosaccharide antibodies. With HeLa ovarian cancer cells, SeviL showed dose‐ and time‐dependent activation of kinase MKK3/6, p38 MAPK, and caspase‐3/9. The transduction pathways activated by SeviL via the glycosphingolipid oligosaccharide were triggered apoptosis. Database Nucleotide sequence data have been deposited in the GenBank database under accession numbers MK434191, MK434192, MK434193, MK434194, MK434195, MK434196, MK434197, MK434198, MK434199, MK434200, and MK434201.
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Affiliation(s)
- Yuki Fujii
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, Sasebo, Japan
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Italy
| | - Sarkar M A Kawsar
- Department of Chemistry, Faculty of Science, University of Chittagong, Bangladesh.,School of Sciences, Yokohama City University, Japan
| | - Imtiaj Hasan
- School of Sciences, Yokohama City University, Japan.,Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Bangladesh
| | | | - Tatsusada Yoshida
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, Sasebo, Japan
| | - Yukiko Ogawa
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, Sasebo, Japan
| | - Sultana Rajia
- School of Sciences, Yokohama City University, Japan.,Department of Pharmacy, Varendra University, Rajshahi, Bangladesh
| | - Kenichi Kamata
- Graduate School of Medical Life Science, Yokohama City University, Japan
| | | | - Shigeki Sugawara
- Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Masahiro Hosono
- Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, Japan
| | - Hideaki Fujita
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, Sasebo, Japan
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Italy.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Italy
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36
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Larraín MA, González P, Pérez C, Araneda C. Comparison between single and multi-locus approaches for specimen identification in Mytilus mussels. Sci Rep 2019; 9:19714. [PMID: 31873129 PMCID: PMC6928075 DOI: 10.1038/s41598-019-55855-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/30/2019] [Indexed: 01/19/2023] Open
Abstract
Mytilus mussels have been the object of much research given their sentinel role in coastal ecosystems and significant value as an aquaculture resource appreciated for both, its flavour and nutritional content. Some of the most-studied Mytilus species are M. edulis, M. galloprovincialis, M. chilensis and M. trossulus. As species identification based on morphological characteristics of Mytilus specimens is difficult, molecular markers are often used. Single-locus markers can give conflicting results when used independently; not all markers differentiate among all species, and the markers target genomic regions with different evolutionary histories. We evaluated the concordance between the PCR-RFLP markers most commonly-used for species identification in mussels within the Mytilus genus (Me15-16, ITS, mac-1, 16S rRNA and COI) when used alone (mono-locus approach) or together (multi-locus approach). In this study, multi-locus strategy outperformed the mono-locus methods, clearly identifying all four species and also showed similar specimen identification performance than a 49 SNPs panel. We hope that these findings will contribute to a better understanding of DNA marker-based analysis of Mytilus taxa. These results support the use of a multi-locus approach when studying this important marine resource, including research on food quality and safety, sustainable production and conservation.
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Affiliation(s)
- María Angélica Larraín
- Food Quality Research Center, Universidad de Chile, Santiago, Chile.
- Departamento de Ciencia de los Alimentos y Tecnología Química, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.
| | - Pía González
- Food Quality Research Center, Universidad de Chile, Santiago, Chile
- Programa de Magister en Alimentos. Mención Gestión, Calidad e Inocuidad de los Alimentos. Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Claudio Pérez
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Cristián Araneda
- Food Quality Research Center, Universidad de Chile, Santiago, Chile
- Laboratorio de Genética y Biotecnología en Acuicultura, Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
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37
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Miglioli A, Dumollard R, Balbi T, Besnardeau L, Canesi L. Characterization of the main steps in first shell formation in Mytilus galloprovincialis: possible role of tyrosinase. Proc Biol Sci 2019; 286:20192043. [PMID: 31771478 DOI: 10.1098/rspb.2019.2043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bivalve biomineralization is a highly complex and organized process, involving several molecular components identified in adults and larval stages. However, information is still scarce on the ontogeny of the organic matrix before calcification occurs. In this work, first shell formation was investigated in the mussel Mytilus galloprovincialis. The time course of organic matrix and CaCO3 deposition were followed at close times post fertilization (24, 26, 29, 32, 48 h) by calcofluor and calcein staining, respectively. Both components showed an exponential trend in growth, with a delay between organic matrix and CaCO3 deposition. mRNA levels of genes involved in matrix deposition (chitin synthase; tyrosinase- TYR) and calcification (carbonic anhydrase; extrapallial protein) were quantified by qPCR at 24 and 48 hours post fertilization (hpf) with respect to eggs. All transcripts were upregulated across early development, with TYR showing highest mRNA levels from 24 hpf. TYR transcripts were closely associated with matrix deposition as shown by in situ hybridization. The involvement of tyrosinase activity was supported by data obtained with the enzyme inhibitor N-phenylthiourea. Our results underline the pivotal role of shell matrix in driving first CaCO3 deposition and the importance of tyrosinase in the formation of the first shell in M. galloprovincialis.
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Affiliation(s)
- A Miglioli
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, DISTAV, Università di Genova, Corso Europa 26, 16132 Genova, Italy.,Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Institut de la mer, Sorbonne Université, CNRS, 181 Chemin du Lazaret, 06230 Villefranche-sur-mer, France
| | - R Dumollard
- Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Institut de la mer, Sorbonne Université, CNRS, 181 Chemin du Lazaret, 06230 Villefranche-sur-mer, France
| | - T Balbi
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, DISTAV, Università di Genova, Corso Europa 26, 16132 Genova, Italy
| | - L Besnardeau
- Laboratoire de Biologie du Developpement de Villefranche-sur-mer, Institut de la mer, Sorbonne Université, CNRS, 181 Chemin du Lazaret, 06230 Villefranche-sur-mer, France
| | - L Canesi
- Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, DISTAV, Università di Genova, Corso Europa 26, 16132 Genova, Italy
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38
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Thai BT, Lee YP, Gan HM, Austin CM, Croft LJ, Trieu TA, Tan MH. Whole Genome Assembly of the Snout Otter Clam, Lutraria rhynchaena, Using Nanopore and Illumina Data, Benchmarked Against Bivalve Genome Assemblies. Front Genet 2019; 10:1158. [PMID: 31824566 PMCID: PMC6880199 DOI: 10.3389/fgene.2019.01158] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022] Open
Affiliation(s)
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Christopher M Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Laurence J Croft
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Tuan Anh Trieu
- Faculty of Biology, Ha Noi National University of Education, Ha Noi, Vietnam.,Science and Technique Department, Hung Vuong University, Viet Tri, Vietnam
| | - Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
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39
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Guo Y, Zhang Y, Liu Q, Huang Y, Mao G, Yue Z, Abe EM, Li J, Wu Z, Li S, Zhou X, Hu W, Xiao N. A chromosomal-level genome assembly for the giant African snail Achatina fulica. Gigascience 2019; 8:giz124. [PMID: 31634388 PMCID: PMC6802634 DOI: 10.1093/gigascience/giz124] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/09/2019] [Accepted: 09/27/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Achatina fulica, the giant African snail, is the largest terrestrial mollusk species. Owing to its voracious appetite, wide environmental adaptability, high growth rate, and reproductive capacity, it has become an invasive species across the world, mainly in Southeast Asia, Japan, the western Pacific islands, and China. This pest can damage agricultural crops and is an intermediate host of many parasites that can threaten human health. However, genomic information of A. fulica remains limited, hindering genetic and genomic studies for invasion control and management of the species. FINDINGS Using a k-mer-based method, we estimated the A. fulica genome size to be 2.12 Gb, with a high repeat content up to 71%. Roughly 101.6 Gb genomic long-read data of A. fulica were generated from the Pacific Biosciences sequencing platform and assembled to produce a first A. fulica genome of 1.85 Gb with a contig N50 length of 726 kb. Using contact information from the Hi-C sequencing data, we successfully anchored 99.32% contig sequences into 31 chromosomes, leading to the final contig and scaffold N50 length of 721 kb and 59.6 Mb, respectively. The continuity, completeness, and accuracy were evaluated by genome comparison with other mollusk genomes, BUSCO assessment, and genomic read mapping. A total of 23,726 protein-coding genes were predicted from the assembled genome, among which 96.34% of the genes were functionally annotated. The phylogenetic analysis using whole-genome protein-coding genes revealed that A. fulica separated from a common ancestor with Biomphalaria glabrata ∼182 million years ago. CONCLUSION To our knowledge, the A. fulica genome is the first terrestrial mollusk genome published to date. The chromosome sequence of A. fulica will provide the research community with a valuable resource for population genetics and environmental adaptation studies for the species, as well as investigations of the chromosome-level of evolution within mollusks.
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Affiliation(s)
- Yunhai Guo
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Yi Zhang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Qin Liu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Yun Huang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Guangyao Mao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Zhiyuan Yue
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Eniola M Abe
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Jian Li
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Science, Fudan University, Shanghai 200438, China
| | - Zhongdao Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Shizhu Li
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Xiaonong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China
| | - Wei Hu
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Science, Fudan University, Shanghai 200438, China
| | - Ning Xiao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China
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Rey-Campos M, Moreira R, Gerdol M, Pallavicini A, Novoa B, Figueras A. Immune Tolerance in Mytilus galloprovincialis Hemocytes After Repeated Contact With Vibrio splendidus. Front Immunol 2019; 10:1894. [PMID: 31447861 PMCID: PMC6697025 DOI: 10.3389/fimmu.2019.01894] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/26/2019] [Indexed: 12/13/2022] Open
Abstract
Mediterranean mussels (Mytilus galloprovincialis) are sessile filter feeders that live in close contact with numerous marine microorganisms. As is the case in all invertebrates, mussels lack an adaptive immune system, but they respond to pathogens, injuries or environmental stress in a very efficient manner. However, it is not known if they are able to modify their immune response when they reencounter the same pathogen. In this work, we studied the transcriptomic response of mussel hemocytes before and after two consecutive sublethal challenges with Vibrio splendidus. The first exposure significantly regulated genes related to inflammation, migration and response to bacteria. However, after the second exposure, the differentially expressed genes were related to the control and inhibition of ROS production and the resolution of the inflammatory response. Our results also show that the second injection with V. splendidus led to changes at the transcriptional (control of the expression of pro-inflammatory transcripts), cellular (shift in the hemocyte population distribution), and functional levels (inhibition of ROS production). These results suggest that a modified immune response after the second challenge allowed the mussels to tolerate rather than fight the infection, which minimized tissue damage.
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Affiliation(s)
| | | | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Trieste, Italy.,Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Beatriz Novoa
- Institute of Marine Research (IIM), CSIC, Vigo, Spain
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Rosani U, Bai CM, Maso L, Shapiro M, Abbadi M, Domeneghetti S, Wang CM, Cendron L, MacCarthy T, Venier P. A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks. BMC Evol Biol 2019; 19:149. [PMID: 31337330 PMCID: PMC6651903 DOI: 10.1186/s12862-019-1472-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 07/04/2019] [Indexed: 02/06/2023] Open
Abstract
Background Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila. Results We traced 4 ADAR homologs in 14 lophotrochozoan genomes and we classified them into ADAD, ADAR1 or ADAR2, based on phylogenetic and structural analyses of the enzymatic domain. Using RNA-seq and quantitative real time PCR we demonstrated the upregulation of one ADAR1 homolog in the bivalve Crassostrea gigas and in the gastropod Haliotis diversicolor supertexta during Ostreid herpesvirus-1 or Haliotid herpesvirus-1 infection. Accordingly, we demonstrated an extensive ADAR-mediated editing of viral RNAs. Single nucleotide variation (SNV) profiles obtained by pairing RNA- and DNA-seq data from the viral infected individuals resulted to be mostly compatible with ADAR-mediated A-to-I editing (up to 97%). SNVs occurred at low frequency in genomic hotspots, denoted by the overlapping of viral genes encoded on opposite DNA strands. The SNV sites and their upstream neighbor nucleotide indicated the targeting of selected adenosines. The analysis of viral sequences suggested that, under the pressure of the ADAR editing, the two Malacoherpesviridae genomes have evolved to reduce the number of deamination targets. Conclusions We report, for the first time, evidence of an extensive editing of Malacoherpesviridae RNAs attributable to host ADAR1 enzymes. The analysis of base neighbor preferences, structural features and expression profiles of molluscan ADAR1 supports the conservation of the enzyme function among metazoans and further suggested that ADAR1 exerts an antiviral role in mollusks. Electronic supplementary material The online version of this article (10.1186/s12862-019-1472-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Umberto Rosani
- Department of Biology, University of Padova, 32121, Padova, Italy. .,Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute (AWI), Wadden Sea Station, 25992, List auf Sylt, Germany.
| | - Chang-Ming Bai
- Chinese Academy of Fishery Sciences, Yellow Sea Fisheries Research Institute, Qingdao, China
| | - Lorenzo Maso
- Department of Biology, University of Padova, 32121, Padova, Italy
| | - Maxwell Shapiro
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Miriam Abbadi
- Istituto Zooprofilattico Sperimentale delle Venezie, 35020, Legnaro, Italy
| | | | - Chong-Ming Wang
- Chinese Academy of Fishery Sciences, Yellow Sea Fisheries Research Institute, Qingdao, China
| | - Laura Cendron
- Department of Biology, University of Padova, 32121, Padova, Italy
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Paola Venier
- Department of Biology, University of Padova, 32121, Padova, Italy.
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Cardoso JCR, Ferreira V, Zhang X, Anjos L, Félix RC, Batista FM, Power DM. Evolution and diversity of alpha-carbonic anhydrases in the mantle of the Mediterranean mussel (Mytilus galloprovincialis). Sci Rep 2019; 9:10400. [PMID: 31320702 PMCID: PMC6639325 DOI: 10.1038/s41598-019-46913-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/05/2019] [Indexed: 01/17/2023] Open
Abstract
The α-carbonic anhydrases (α-CAs) are a large and ancient group of metazoan-specific enzymes. They generate bicarbonate from metabolic carbon dioxide and through calcium carbonate crystal formation play a key role in the regulation of mineralized structures. To better understand how α-CAs contribute to shell mineralization in the marine Mediterranean mussel (Mytilus galloprovincialis) we characterized them in the mantle. Phylogenetic analysis revealed that mollusc α-CA evolution was affected by lineage and species-specific events. Ten α-CAs were found in the Mediterranean mussel mantle and the most abundant form was named, MgNACR, as it grouped with oyster nacreins (NACR). Exposure of the Mediterranean mussel to reduced water salinity (18 vs 37 ppt), caused a significant reduction (p < 0.05) in mantle esterase activity and MgNACR transcript abundance (p < 0.05). Protonograms revealed multiple proteins in the mantle with α-CA hydratase activity and mapped to a protein with a similar size to that deduced for monomeric MgNACR. Our data indicate that MgNACR is a major α-CA enzyme in mantle and that by homology with oyster nacreins likely regulates mussel shell production. We propose that species-dependent α-CA evolution may contribute to explain the diversity of bivalve shell structures and their vulnerability to environmental changes.
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Affiliation(s)
- João C R Cardoso
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Vinicius Ferreira
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Xushuai Zhang
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Liliana Anjos
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Rute C Félix
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Frederico M Batista
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,Centre for Environment Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, UK
| | - Deborah M Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, 8005-139, Faro, Portugal. .,International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China. .,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.
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Barranger A, Langan LM, Sharma V, Rance GA, Aminot Y, Weston NJ, Akcha F, Moore MN, Arlt VM, Khlobystov AN, Readman JW, Jha AN. Antagonistic Interactions between Benzo[a]pyrene and Fullerene (C 60) in Toxicological Response of Marine Mussels. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E987. [PMID: 31288459 PMCID: PMC6669530 DOI: 10.3390/nano9070987] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 12/12/2022]
Abstract
This study aimed to assess the ecotoxicological effects of the interaction of fullerene (C60) and benzo[a]pyrene (B[a]P) on the marine mussel, Mytilus galloprovincialis. The uptake of nC60, B[a]P and mixtures of nC60 and B[a]P into tissues was confirmed by Gas Chromatography-Mass Spectrometry (GC-MS), Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) and Inductively Coupled Plasma Mass Spectrometer (ICP-MS). Biomarkers of DNA damage as well as proteomics analysis were applied to unravel the interactive effect of B[a]P and C60. Antagonistic responses were observed at the genotoxic and proteomic level. Differentially expressed proteins (DEPs) were only identified in the B[a]P single exposure and the B[a]P mixture exposure groups containing 1 mg/L of C60, the majority of which were downregulated (~52%). No DEPs were identified at any of the concentrations of nC60 (p < 0.05, 1% FDR). Using DEPs identified at a threshold of (p < 0.05; B[a]P and B[a]P mixture with nC60), gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that these proteins were enriched with a broad spectrum of biological processes and pathways, including those broadly associated with protein processing, cellular processes and environmental information processing. Among those significantly enriched pathways, the ribosome was consistently the top enriched term irrespective of treatment or concentration and plays an important role as the site of biological protein synthesis and translation. Our results demonstrate the complex multi-modal response to environmental stressors in M. galloprovincialis.
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Affiliation(s)
- Audrey Barranger
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Laura M Langan
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Vikram Sharma
- School of Biomedical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Graham A Rance
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
- Nanoscale and Microscale Research Centre, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Yann Aminot
- Centre for Chemical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Nicola J Weston
- Nanoscale and Microscale Research Centre, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Farida Akcha
- Ifremer, Laboratory of Ecotoxicology, F-44311, CEDEX 03 Nantes, France
| | - Michael N Moore
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK
- Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth PL1 3HD, UK
- European Centre for Environment & Human Health (ECEHH), University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, Cornwall TR1 3LJ, UK
| | - Volker M Arlt
- Department of Analytical, Environmental and Forensic Sciences, King's College London, MRC-PHE Centre for Environmental & Health, London SE1 9NH, UK
- NIHR Health Protection Research Unit in Health Impact of Environmental Hazards at King's College London in partnership with Public Health England and Imperial College London, London SE1 9NH, UK
| | - Andrei N Khlobystov
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
- Nanoscale and Microscale Research Centre, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - James W Readman
- Centre for Chemical Sciences, University of Plymouth, Plymouth PL4 8AA, UK
| | - Awadhesh N Jha
- School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, UK.
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The survey and reference assisted assembly of the Octopus vulgaris genome. Sci Data 2019; 6:13. [PMID: 30931949 PMCID: PMC6472339 DOI: 10.1038/s41597-019-0017-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 02/04/2019] [Indexed: 12/15/2022] Open
Abstract
The common octopus, Octopus vulgaris, is an active marine predator known for the richness and plasticity of its behavioral repertoire, and remarkable learning and memory capabilities. Octopus and other coleoid cephalopods, cuttlefish and squid, possess the largest nervous system among invertebrates, both for cell counts and body to brain size. O. vulgaris has been at the center of a long-tradition of research into diverse aspects of its biology. To leverage research in this iconic species, we generated 270 Gb of genomic sequencing data, complementing those available for the only other sequenced congeneric octopus, Octopus bimaculoides. We show that both genomes are similar in size, but display different levels of heterozygosity and repeats. Our data give a first quantitative glimpse into the rate of coding and non-coding regions and support the view that hundreds of novel genes may have arisen independently despite the close phylogenetic distance. We furthermore describe a reference-guided assembly and an open genomic resource (CephRes-gdatabase), opening new avenues in the study of genomic novelties in cephalopods and their biology. Design Type(s) | species comparison design • sequence analysis objective • sequence assembly objective | Measurement Type(s) | whole genome sequencing assay | Technology Type(s) | DNA sequencing | Factor Type(s) | Sample Characteristic(s) | Octopus vulgaris • testis • ocean biome |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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Rey-Campos M, Moreira R, Valenzuela-Muñoz V, Gallardo-Escárate C, Novoa B, Figueras A. High individual variability in the transcriptomic response of Mediterranean mussels to Vibrio reveals the involvement of myticins in tissue injury. Sci Rep 2019; 9:3569. [PMID: 30837561 PMCID: PMC6401078 DOI: 10.1038/s41598-019-39870-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 01/30/2019] [Indexed: 12/26/2022] Open
Abstract
Mediterranean mussels (Mytilus galloprovincialis) are sessile filter feeders that live in close contact with numerous marine microorganisms. As all invertebrates, they lack an adaptive immune response and how these animals are able to respond to a bacterial infection and discriminate it from their normal microbiome is difficult to understand. In this work, we conducted Illumina sequencing of the transcriptome of individual mussels before and after being infected with Vibrio splendidus. The control mussels were injected with filtered seawater. We demonstrate that a great variability exists among individual transcriptomes and that each animal showed an exclusive repertoire of genes not shared with other individuals. The regulated genes in both the control and infected mussels were also analyzed and, unexpectedly, the sampling before the injection was considered a stress stimulus strong enough to trigger and modulate the response in hemocytes, promoting cell migration and proliferation. We found a clear response against the injection of filtered seawater, suggesting a reaction against a tissue injury in which the myticins, the most expressed antimicrobial peptides in mussel, appeared significantly up regulated. Functional experiments with flow cytometry confirmed the transcriptomic results since a significant alteration of hemocyte structures and a decrease in the number of hemocytes positive for myticin C were found only after a Vibrio infection and not observed when mussels were bled before, generating a tissue injury. Therefore, we report the involvement of myticins in the response to a danger signal such as a simple injection in the adductor muscle.
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Affiliation(s)
- Magalí Rey-Campos
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain
| | - Rebeca Moreira
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain
| | - Valentina Valenzuela-Muñoz
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160-C, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, P.O. Box 160-C, Concepción, Chile
| | - Beatriz Novoa
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain
| | - Antonio Figueras
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello, 6, 36208, Vigo, Spain.
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Fernández Robledo JA, Yadavalli R, Allam B, Pales Espinosa E, Gerdol M, Greco S, Stevick RJ, Gómez-Chiarri M, Zhang Y, Heil CA, Tracy AN, Bishop-Bailey D, Metzger MJ. From the raw bar to the bench: Bivalves as models for human health. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:260-282. [PMID: 30503358 PMCID: PMC6511260 DOI: 10.1016/j.dci.2018.11.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/09/2018] [Accepted: 11/24/2018] [Indexed: 05/05/2023]
Abstract
Bivalves, from raw oysters to steamed clams, are popular choices among seafood lovers and once limited to the coastal areas. The rapid growth of the aquaculture industry and improvement in the preservation and transport of seafood have enabled them to be readily available anywhere in the world. Over the years, oysters, mussels, scallops, and clams have been the focus of research for improving the production, managing resources, and investigating basic biological and ecological questions. During this decade, an impressive amount of information using high-throughput genomic, transcriptomic and proteomic technologies has been produced in various classes of the Mollusca group, and it is anticipated that basic and applied research will significantly benefit from this resource. One aspect that is also taking momentum is the use of bivalves as a model system for human health. In this review, we highlight some of the aspects of the biology of bivalves that have direct implications in human health including the shell formation, stem cells and cell differentiation, the ability to fight opportunistic and specific pathogens in the absence of adaptive immunity, as source of alternative drugs, mucosal immunity and, microbiome turnover, toxicology, and cancer research. There is still a long way to go; however, the next time you order a dozen oysters at your favorite raw bar, think about a tasty model organism that will not only please your palate but also help unlock multiple aspects of molluscan biology and improve human health.
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Affiliation(s)
| | | | - Bassem Allam
- Stony Brook University, School of Marine and Atmospheric Sciences, Stony Brook, NY, 11794, USA
| | | | - Marco Gerdol
- University of Trieste, Department of Life Sciences, 34127, Trieste, Italy
| | - Samuele Greco
- University of Trieste, Department of Life Sciences, 34127, Trieste, Italy
| | - Rebecca J Stevick
- University of Rhode Island, Graduate School of Oceanography, Narragansett, RI, 02882, USA
| | - Marta Gómez-Chiarri
- University of Rhode Island, Department of Fisheries, Animal and Veterinary Science, Kingston, RI, 02881, USA
| | - Ying Zhang
- University of Rhode Island, Department of Cell and Molecular Biology, Kingston, RI, 02881, USA
| | - Cynthia A Heil
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Adrienne N Tracy
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA; Colby College, Waterville, 4,000 Mayflower Hill Dr, ME, 04901, USA
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Green DS, Colgan TJ, Thompson RC, Carolan JC. Exposure to microplastics reduces attachment strength and alters the haemolymph proteome of blue mussels (Mytilus edulis). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 246:423-434. [PMID: 30579211 DOI: 10.1016/j.envpol.2018.12.017] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/10/2018] [Accepted: 12/07/2018] [Indexed: 05/20/2023]
Abstract
The contamination of marine ecosystems with microplastics, such as the polymer polyethylene, a commonly used component of single-use packaging, is of global concern. Although it has been suggested that biodegradable polymers, such as polylactic acid, may be used to replace some polyethylene packaging, little is known about their effects on marine organisms. Blue mussels, Mytilus edulis, have become a "model organism" for investigating the effects of microplastics in marine ecosystems. We show here that repeated exposure, over a period of 52 days in an outdoor mesocosm setting, of M. edulis to polyethylene microplastics reduced the number of byssal threads produced and the attachment strength (tenacity) by ∼50%. Exposure to either type of microplastic altered the haemolymph proteome and, although a conserved response to microplastic exposure was observed, overall polyethylene resulted in more changes to protein abundances than polylactic acid. Many of the proteins affected are involved in vital biological processes, such as immune regulation, detoxification, metabolism and structural development. Our study highlights the utility of mass spectrometry-based proteomics to assess the health of key marine organisms and identifies the potential mechanisms by which microplastics, both conventional and biodegradable, could affect their ability to form and maintain reefs.
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Affiliation(s)
- Dannielle S Green
- School of Life Sciences, Anglia Ruskin University, Cambridge, Cambridgeshire, CB11PT, United Kingdom.
| | - Thomas J Colgan
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland; School of Biological and Chemical Sciences, Queen Mary University of London, London, E14NS, United Kingdom
| | - Richard C Thompson
- School of Marine Science and Engineering, Plymouth University, Plymouth, Devon, PL48AA, United Kingdom
| | - James C Carolan
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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Masonbrink RE, Purcell CM, Boles SE, Whitehead A, Hyde JR, Seetharam AS, Severin AJ. An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black, and White Abalone Species. Genome Biol Evol 2019; 11:431-438. [PMID: 30657886 PMCID: PMC6373831 DOI: 10.1093/gbe/evz006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2019] [Indexed: 11/13/2022] Open
Abstract
Abalone are one of the few marine taxa where aquaculture production dominates the global market as a result of increasing demand and declining natural stocks from overexploitation and disease. To better understand abalone biology, aid in conservation efforts for endangered abalone species, and gain insight into sustainable aquaculture, we created a draft genome of the red abalone (Haliotis rufescens). The approach to this genome draft included initial assembly using raw Illumina and PacBio sequencing data with MaSuRCA, before scaffolding using sequencing data generated from Chicago library preparations with HiRise2. This assembly approach resulted in 8,371 scaffolds and total length of 1.498 Gb; the N50 was 1.895 Mb, and the longest scaffold was 13.2 Mb. Gene models were predicted, using MAKER2, from RNA-Seq data and all related expressed sequence tags and proteins from NCBI; this resulted in 57,785 genes with an average length of 8,255 bp. In addition, single nucleotide polymorphisms were called on Illumina short-sequencing reads from five other eastern Pacific abalone species: the green (H. fulgens), pink (H. corrugata), pinto (H. kamtschatkana), black (H. cracherodii), and white (H. sorenseni) abalone. Phylogenetic relationships largely follow patterns detected by previous studies based on 1,784,991 high-quality single nucleotide polymorphisms. Among the six abalone species examined, the endangered white abalone appears to harbor the lowest levels of heterozygosity. This draft genome assembly and the sequencing data provide a foundation for genome-enabled aquaculture improvement for red abalone, and for genome-guided conservation efforts for the other five species and, in particular, for the endangered white and black abalone.
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Affiliation(s)
| | - Catherine M Purcell
- Ocean Associates, Inc. Under Contract to NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, California
| | - Sara E Boles
- Department of Environmental Toxicology, University of California, Davis
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California, Davis
| | - John R Hyde
- NOAA Fisheries, Southwest Fisheries Science Center, La Jolla, California
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Fujii Y, Gerdol M, Hasan I, Koide Y, Matsuzaki R, Ikeda M, Rajia S, Ogawa Y, Kawsar SMA, Ozeki Y. Phylogeny and Properties of a Novel Lectin Family with β-Trefoil Folding in Mussels. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1717.1e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Yuki Fujii
- Department of Pharmaceutical Sciences, Nagasaki International University
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste
| | - Imtiaj Hasan
- Department of Life and Environmental System Science, Yokohama City University
- Department of Biochemistry and Molecular Biology, University of Rajshahi
| | - Yasuhiro Koide
- Department of Life and Environmental System Science, Yokohama City University
| | - Risa Matsuzaki
- Department of Life and Environmental System Science, Yokohama City University
| | - Mayu Ikeda
- Department of Life and Environmental System Science, Yokohama City University
| | - Sultana Rajia
- Department of Life and Environmental System Science, Yokohama City University
- Department of Pharmacy, Faculty of Pharmacy, Varendra University
| | - Yukiko Ogawa
- Department of Pharmaceutical Sciences, Nagasaki International University
| | - S. M. Abe Kawsar
- Department of Life and Environmental System Science, Yokohama City University
- Department of Chemistry, Faculty of Science, University of Chittagong
| | - Yasuhiro Ozeki
- Department of Life and Environmental System Science, Yokohama City University
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