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Capasso C, Supuran CT. Overview on tyrosinases: Genetics, molecular biology, phylogenetic relationship. Enzymes 2024; 56:1-30. [PMID: 39304284 DOI: 10.1016/bs.enz.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Tyrosinases (TYRs) are enzymes found in various organisms that are crucial for melanin biosynthesis, coloration, and UV protection. They play vital roles in insect cuticle sclerotization, mollusk shell formation, fungal and bacterial pigmentation, biofilm formation, and virulence. Structurally, TYRs feature copper-binding sites that are essential for catalytic activity, facilitating substrate oxidation via interactions with conserved histidine residues. TYRs exhibit diversity across animals, plants, fungi, mollusks, and bacteria, reflecting their roles and function. Eukaryotic TYRs undergo post-translational modifications, such as glycosylation, which affect protein folding and activity. Bacterial TYRs are categorized into five types based on their structural variation, domain organization and enzymatic properties, showing versatility across bacterial species. Moreover, bacterial TYRs, akin to fungal TYRs, have been implicated in the synthesis of secondary metabolites with antimicrobial properties. TYRs share significant sequence homology with hemocyanins, oxygen-carrier proteins in mollusks and arthropods, highlighting their evolutionary relationships. The evolution of TYRs underscores the dynamic nature of these enzymes and reflects adaptive strategies across diverse taxa.
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Affiliation(s)
- Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, CNR, Napoli, Italy.
| | - Claudiu T Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Florence, Italy
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2
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Fang J, Yang C, Liao Y, Wang Q, Deng Y. Transcriptomic and metabolomic analyses reveal sex-related differences in the gonads of Pinctada fucata martensii. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101304. [PMID: 39116717 DOI: 10.1016/j.cbd.2024.101304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/28/2024] [Accepted: 07/29/2024] [Indexed: 08/10/2024]
Abstract
Pinctada fucata martensii is an economically important bivalve mollusk, as this species makes a major contribution to seawater pearl production. Pearl production efficiency varies between the sexes of P. f. martensii, but many aspects of the molecular mechanisms underlying sex determination and sex differentiation in P. f. martensii remain unclear. Here, transcriptomic and metabonomic analyses were conducted to identify the major genes and metabolic changes associated with sex determination and gametogenesis. We identified a total of 3426 differentially expressed genes (DEGs) between females and males. These included Fem-1c and Foxl2, which are involved in sex determination and sex differentiation, and SOHLH2, Nanos1 and TSSK4, which are involved in gametogenesis. We also identified a total of 5231 significant differential metabolites (SDMs) between females and males. These DEGs were enriched in 47 metabolic pathways, including "ABC transporters," "purine metabolism," and "glycerophospholipid metabolism." Our findings provide new insights into the molecular mechanisms underlying sex determination, sex differentiation, and gametogenesis and will aid future studies of P. f. martensii.
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Affiliation(s)
- Jiaying Fang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Chuangye Yang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China
| | - Yongshan Liao
- Pearl Research Institute, Guangdong Ocean University, Zhanjiang, China
| | - Qingheng Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yuewen Deng
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China; Pearl Research Institute, Guangdong Ocean University, Zhanjiang, China.
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3
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Anjos C, Duarte D, Fatsini E, Matias D, Cabrita E. Comparative transcriptome analysis reveals molecular damage associated with cryopreservation in Crassostrea angulata D-larvae rather than to cryoprotectant exposure. BMC Genomics 2024; 25:591. [PMID: 38867206 PMCID: PMC11167747 DOI: 10.1186/s12864-024-10473-1] [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: 10/25/2023] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND The Portuguese oyster Crassostrea angulata, a bivalve of significant economic and ecological importance, has faced a decline in both production and natural populations due to pathologies, climate change, and anthropogenic factors. To safeguard its genetic diversity and improve reproductive management, cryopreservation emerges as a valuable strategy. However, the cryopreservation methodologies lead to some damage in structures and functions of the cells and tissues that can affect post-thaw quality. Transcriptomics may help to understand the molecular consequences related to cryopreservation steps and therefore to identify different freezability biomarkers. This study investigates the molecular damage induced by cryopreservation in C. angulata D-larvae, focusing on two critical steps: exposure to cryoprotectant solution and the freezing/thawing process. RESULTS Expression analysis revealed 3 differentially expressed genes between larvae exposed to cryoprotectant solution and fresh larvae and 611 differentially expressed genes in cryopreserved larvae against fresh larvae. The most significantly enriched gene ontology terms were "carbohydrate metabolic process", "integral component of membrane" and "chitin binding" for biological processes, cellular components and molecular functions, respectively. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified the "neuroactive ligand receptor interaction", "endocytosis" and "spliceosome" as the most enriched pathways. RNA sequencing results were validate by quantitative RT-PCR, once both techniques presented the same gene expression tendency and a group of 11 genes were considered important molecular biomarkers to be used in further studies for the evaluation of cryodamage. CONCLUSIONS The current work provided valuable insights into the molecular repercussions of cryopreservation on D-larvae of Crassostrea angulata, revealing that the freezing process had a more pronounced impact on larval quality compared to any potential cryoprotectant-induced toxicity. Additionally, was identify 11 genes serving as biomarkers of freezability for D-larvae quality assessment. This research contributes to the development of more effective cryopreservation protocols and detection methods for cryodamage in this species.
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Affiliation(s)
- Catarina Anjos
- Centre of Marine Sciences-CCMAR/CIMAR.LA, University of Algarve, Faro, 8005-139, Portugal
- Portuguese Institute for Sea and Atmosphere-IPMA, Av. 5 de Outubro, Olhão, 8700-305, Portugal
| | - Daniel Duarte
- Centre of Marine Sciences-CCMAR/CIMAR.LA, University of Algarve, Faro, 8005-139, Portugal
| | - Elvira Fatsini
- Centre of Marine Sciences-CCMAR/CIMAR.LA, University of Algarve, Faro, 8005-139, Portugal
| | - Domitília Matias
- Portuguese Institute for Sea and Atmosphere-IPMA, Av. 5 de Outubro, Olhão, 8700-305, Portugal
| | - Elsa Cabrita
- Centre of Marine Sciences-CCMAR/CIMAR.LA, University of Algarve, Faro, 8005-139, Portugal.
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4
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Guo Z, Li C, Liang H, Zhu J. Identification and functional characterization of a superoxide dismutase (CuZnSOD) from Pinctada fucata martensii. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109599. [PMID: 38701990 DOI: 10.1016/j.fsi.2024.109599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Copper/zinc superoxide dismutase (Cu/Zn-SOD) can effectively eliminate reactive oxygen species (ROS),avoid damage from O2 to the body, and maintain O2 balance. In this study, multi-step high-performance liquid chromatography (HPLC), combined with Mass Spectrometry (MS), was used to isolate and identify Cu/Zn-SOD from the serum of Pinctada fucata martensii (P. f. martensii) and was designated as PmECSOD. With a length of 1864 bp and an open reading frame (ORF) of 1422 bp, the cDNA encodes a 473 amino acid protein. The PmECSOD transcript was detected in multiple tissues by quantitative real-time PCR (qRT-PCR), with its highest expression level being in the gills. Additionally, the temporal expression of PmECSOD mRNA in the hemolymph was highest at 48 h after in vivo stimulation with Escherichia coli and Micrococcus luteus. The results from this study provide a valuable base for further exploration of molluscan innate immunity and immune response.
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Affiliation(s)
- Zhijie Guo
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Chaojie Li
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Haiying Liang
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, Guangdong, 524088, China.
| | - Jiaping Zhu
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
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Wang P, Meng Z, Deng K, Gao Z, Cai J. Vpr driving DNA methylation variation of CD4 + T cells in HIV-1 infection. Virol J 2024; 21:97. [PMID: 38671522 PMCID: PMC11046818 DOI: 10.1186/s12985-024-02363-5] [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: 02/04/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Despite the existence of available therapeutic interventions for HIV-1, this virus remains a significant global threat, leading to substantial morbidity and mortality. Within HIV-1-infected cells, the accessory viral protein r (Vpr) exerts control over diverse biological processes, including cell cycle progression, DNA repair, and apoptosis. The regulation of gene expression through DNA methylation plays a crucial role in physiological processes, exerting its influence without altering the underlying DNA sequence. However, a thorough examination of the impact of Vpr on DNA methylation in human CD4 + T cells has not been conducted. METHODS In this study, we employed base-resolution whole-genome bisulfite sequencing (WGBS), real-time quantitative RCR and western blot to explore the effect of Vpr on DNA methylation of host cells under HIV-1 infection. RESULTS We observed that HIV-1 infection leads to elevated levels of global DNA methylation in primary CD4 + T cells. Specifically, Vpr induces significant modifications in DNA methylation patterns, particularly affecting regions within promoters and gene bodies. These alterations notably influence genes related to immune-related pathways and olfactory receptor activity. Moreover, Vpr demonstrates a distinct ability to diminish the levels of methylation in histone genes. CONCLUSIONS These findings emphasize the significant involvement of Vpr in regulating transcription through the modulation of DNA methylation patterns. Together, the results of this investigation will considerably enhance our understanding of the influence of HIV-1 Vpr on the DNA methylation of host cells, offer potential avenues for the development of more effective treatments.
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Affiliation(s)
- Peipei Wang
- Department of Infectious Diseases, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhuoyue Meng
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Kai Deng
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhiliang Gao
- Department of Infectious Diseases, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Jinfeng Cai
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BMC Biol 2024; 22:9. [PMID: 38233809 PMCID: PMC10795318 DOI: 10.1186/s12915-024-01814-3] [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: 08/07/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. RESULTS The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. CONCLUSIONS Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Robin A Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Paul S Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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Puritz JB, Guo X, Hare M, He Y, Hillier LW, Jin S, Liu M, Lotterhos KE, Minx P, Modak T, Proestou D, Rice ES, Tomlinson C, Warren WC, Witkop E, Zhao H, Gomez-Chiarri M. A second unveiling: Haplotig masking of the eastern oyster genome improves population-level inference. Mol Ecol Resour 2024; 24:e13801. [PMID: 37186213 DOI: 10.1111/1755-0998.13801] [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: 09/29/2022] [Revised: 12/16/2022] [Accepted: 03/20/2023] [Indexed: 05/17/2023]
Abstract
Genome assembly can be challenging for species that are characterized by high amounts of polymorphism, heterozygosity, and large effective population sizes. High levels of heterozygosity can result in genome mis-assemblies and a larger than expected genome size due to the haplotig versions of a single locus being assembled as separate loci. Here, we describe the first chromosome-level genome for the eastern oyster, Crassostrea virginica. Publicly released and annotated in 2017, the assembly has a scaffold N50 of 54 mb and is over 97.3% complete based on BUSCO analysis. The genome assembly for the eastern oyster is a critical resource for foundational research into molluscan adaptation to a changing environment and for selective breeding for the aquaculture industry. Subsequent resequencing data suggested the presence of haplotigs in the original assembly, and we developed a post hoc method to break up chimeric contigs and mask haplotigs in published heterozygous genomes and evaluated improvements to the accuracy of downstream analysis. Masking haplotigs had a large impact on SNP discovery and estimates of nucleotide diversity and had more subtle and nuanced effects on estimates of heterozygosity, population structure analysis, and outlier detection. We show that haplotig masking can be a powerful tool for improving genomic inference, and we present an open, reproducible resource for the masking of haplotigs in any published genome.
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Affiliation(s)
- Jonathan B Puritz
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - Matthew Hare
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA
| | - Yan He
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - LaDeana W Hillier
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Shubo Jin
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - Ming Liu
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
| | - Pat Minx
- Donald Danforth Plant Science Center, Olivette, Missouri, USA
| | - Tejashree Modak
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, Rhode Island, USA
| | - Dina Proestou
- USDA Agricultural Research Service, National Cold Water Marine Aquaculture Center, Kingston, Rhode Island, USA
| | - Edward S Rice
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, USA
| | - Wesley C Warren
- Departments of Animal Sciences and Surgery, Institute of Informatics and Data Sciences, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Erin Witkop
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Honggang Zhao
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Kingston, Rhode Island, USA
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Johansen M, Saenko S, Schilthuizen M, Blaxter M, Davison A. Fine mapping of the Cepaea nemoralis shell colour and mid-banded loci using a high-density linkage map. Heredity (Edinb) 2023; 131:327-337. [PMID: 37758900 PMCID: PMC10673960 DOI: 10.1038/s41437-023-00648-z] [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: 03/31/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Molluscs are a highly speciose phylum that exhibits an astonishing array of colours and patterns, yet relatively little progress has been made in identifying the underlying genes that determine phenotypic variation. One prominent example is the land snail Cepaea nemoralis for which classical genetic studies have shown that around nine loci, several physically linked and inherited together as a 'supergene', control the shell colour and banding polymorphism. As a first step towards identifying the genes involved, we used whole-genome resequencing of individuals from a laboratory cross to construct a high-density linkage map, and then trait mapping to identify 95% confidence intervals for the chromosomal region that contains the supergene, specifically the colour locus (C), and the unlinked mid-banded locus (U). The linkage map is made up of 215,593 markers, ordered into 22 linkage groups, with one large group making up ~27% of the genome. The C locus was mapped to a ~1.3 cM region on linkage group 11, and the U locus was mapped to a ~0.7 cM region on linkage group 15. The linkage map will serve as an important resource for further evolutionary and population genomic studies of C. nemoralis and related species, as well as the identification of candidate genes within the supergene and for the mid-banding phenotype.
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Affiliation(s)
- Margrethe Johansen
- School of Life Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK.
| | - Suzanne Saenko
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, 2333CR, The Netherlands
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden, 2333BE, The Netherlands
| | - Menno Schilthuizen
- Evolutionary Ecology, Naturalis Biodiversity Center, Leiden, 2333CR, The Netherlands
- Animal Sciences, Institute of Biology Leiden, Leiden University, Leiden, 2333BE, The Netherlands
| | - Mark Blaxter
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Angus Davison
- School of Life Sciences, University Park, University of Nottingham, Nottingham, NG7 2RD, UK
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Gu Z, Yang J, Lu J, Yang M, Deng Y, Jiao Y. Whole-genome bisulfite sequencing reveals the function of DNA methylation in the allotransplantation immunity of pearl oysters. Front Immunol 2023; 14:1247544. [PMID: 37854612 PMCID: PMC10579932 DOI: 10.3389/fimmu.2023.1247544] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/18/2023] [Indexed: 10/20/2023] Open
Abstract
Introduction In the pearl culture industry, a major challenge is the overactive immunological response in pearl oysters resulting from allotransplantation, leading to shell-bead rejection and death. To better understand the molecular mechanisms of postoperative recovery and the regulatory role of DNA methylation in gene expression, we analyzed the changes in DNA methylation levels after allotransplantation in pearl oyster Pinctada fucata martensii, and elucidated the regulatory function of DNA methylation in promoter activity of nicotinic acetylcholine receptor (nAChR) gene. Methods We constructed nine DNA methylomes at different time points after allotransplantation and used bisulfite genomic sequencing PCR technology (BSP) to verify the methylation status in the promoter of nAChR. We performed Dual luciferase assays to determine the effect of the dense methylation region in the promoter on transcriptional activity and used DNA pull-down and mass spectrometry analysis to assess the capability of transcription factor binding with the dense methylation region. Result The DNA methylomes reveal that CG-type methylation is predominant, with a trend opposite to non-CG-type methylation. Promoters, particularly CpG island-rich regions, were less frequently methylated than gene function elements. We identified 5,679 to 7,945 differentially methylated genes (DMGs) in the gene body, and 2,146 to 3,385 DMGs in the promoter at each time point compared to the pre-grafting group. Gene ontology and pathway enrichment analyses showed that these DMGs were mainly associated with "cellular process", "Membrane", "Epstein-Barr virus infection", "Notch signaling pathway", "Fanconi anemia pathway", and "Nucleotide excision repair". Our study also found that the DNA methylation patterns of the promoter region of nAChR gene were consistent with the DNA methylomics data. We further demonstrated that the dense methylation region in the promoter of nAChR affects transcriptional activity, and that the methylation status in the promoter modulates the binding of different transcription factors, particularly transcriptional repressors. Conclusion These findings enhance our understanding of the immune response and regulation mechanism induced by DNA methylation in pearl oysters after allotransplantation.
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Affiliation(s)
- Zefeng Gu
- Fishery College, Guangdong Ocean University, Zhanjiang, China
| | - Jingmiao Yang
- Fishery College, Guangdong Ocean University, Zhanjiang, China
| | - Jinzhao Lu
- Fishery College, Guangdong Ocean University, Zhanjiang, China
| | - Min Yang
- Fishery College, Guangdong Ocean University, Zhanjiang, China
| | - Yuewen Deng
- Fishery College, Guangdong Ocean University, Zhanjiang, China
- Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, China
- Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang, China
- Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, China
- Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, China
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10
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Yang C, Wu H, Chen J, Liao Y, Mkuye R, Deng Y, Du X. Integrated transcriptomic and metabolomic analysis reveals the response of pearl oyster (Pinctada fucata martensii) to long-term hypoxia. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106133. [PMID: 37586225 DOI: 10.1016/j.marenvres.2023.106133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/27/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
The frequency at which organisms are exposed to hypoxic conditions in aquatic environments is increasing due to coastal eutrophication and global warming. To reveal the effects of long-term hypoxic stress on metabolic changes of pearl oyster, commonly known as Pinctada (Pinctada fucata martensii), the present study performed the integrated analysis of transcriptomics and metabolomics to investigate the global changes of genes and metabolites following 25 days hypoxia challenge. Transcriptome analysis detected 1108 differentially expressed genes (DEGs) between the control group and the hypoxia group. The gene ontology (GO) analysis of DEGs revealed that they are significantly enriched in functions such as "microtubule-based process", "histone (H3-K4, H3-K27, and H4-K20) trimethylation", "histone H4 acetylation", "kinesin complex", and "ATPase activity", and KEGG pathway functions, such as "DNA replication", "Apoptosis", and "MAPK signaling pathways". Metabolome analysis identified 68 significantly different metabolites from all identified metabolites, and associated with 25 metabolic pathways between the control and hypoxia groups. These pathways included aminoacyl-tRNA biosynthesis, arginine and proline metabolism, and phenylalanine metabolism. Our integrated analysis suggested that pearl oysters were subject to oxidative stress, apoptosis, immune inhibition, and neuronal excitability reduction under long-term hypoxic conditions. We also found a remarkable depression in a variety of biological functions under long-term hypoxia, including metabolic rates, biomineralization activities, and the repression of reorganization of the cytoskeleton and cell metabolism. These findings provide a basis for elucidating the mechanisms used by marine bivalves to cope with long-term hypoxic stress.
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Affiliation(s)
- Chuangye Yang
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Hailing Wu
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jiayi Chen
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yongshan Liao
- Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China
| | - Robert Mkuye
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yuewen Deng
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China; Guangdong Marine Ecology Early Warning and Monitoring Laboratory, Zhanjiang, 524088, China.
| | - Xiaodong Du
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
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11
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Bai Y, Liu S, Hu Y, Yu H, Kong L, Xu C, Li Q. Multi-omic insights into the formation and evolution of a novel shell microstructure in oysters. BMC Biol 2023; 21:204. [PMID: 37775818 PMCID: PMC10543319 DOI: 10.1186/s12915-023-01706-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Molluscan shell, composed of a diverse range of architectures and microstructures, is a classic model system to study the relationships between molecular evolution and biomineralized structure formation. The shells of oysters differ from those of other molluscs by possessing a novel microstructure, chalky calcite, which facilitates adaptation to the sessile lifestyle. However, the genetic basis and evolutionary origin of this adaptive innovation remain largely unexplored. RESULTS We report the first whole-genome assembly and shell proteomes of the Iwagaki oyster Crassostrea nippona. Multi-omic integrative analyses revealed that independently expanded and co-opted tyrosinase, peroxidase, TIMP genes may contribute to the chalky layer formation in oysters. Comparisons with other molluscan shell proteomes imply that von Willebrand factor type A and chitin-binding domains are basic members of molluscan biomineralization toolkit. Genome-wide identification and analyses of these two domains in 19 metazoans enabled us to propose that the well-known Pif may share a common origin in the last common ancestor of Bilateria. Furthermore, Pif and LamG3 genes acquire new genetic function for shell mineralization in bivalves and the chalky calcite formation in oysters likely through a combination of gene duplication and domain reorganization. CONCLUSIONS The spatial expression of SMP genes in the mantle and molecular evolution of Pif are potentially involved in regulation of the chalky calcite deposition, thereby shaping the high plasticity of the oyster shell to adapt to a sessile lifestyle. This study further highlights neo-functionalization as a crucial mechanism for the diversification of shell mineralization and microstructures in molluscs, which may be applied more widely for studies on the evolution of metazoan biomineralization.
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Affiliation(s)
- Yitian Bai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yiming Hu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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12
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Qin K, Jiang S, Xu H, Yuan Z, Sun L. Pyroptotic gasdermin exists in Mollusca and is vital to eliminating bacterial infection. Cell Rep 2023; 42:112414. [PMID: 37074912 DOI: 10.1016/j.celrep.2023.112414] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 02/28/2023] [Accepted: 04/04/2023] [Indexed: 04/20/2023] Open
Abstract
Gasdermin (GSDM) is a family of proteins that execute pyroptosis in vertebrate. In invertebrate, pyroptotic GSDM was documented only in coral. Recent studies identified abundant GSDM structural homologs in Mollusca, but their functions are unclear. Herein, we report a functional GSDM from Pacific abalone Haliotis discus (HdGSDME). HdGSDME is specifically activated by abalone caspase 3 (HdCASP3) cleavage at two distinct sites, generating two active isoforms with pyroptotic and cytotoxic activities. HdGSDME possesses evolutionarily conserved residues that proved to be essential to the N-terminal pore-formation and C-terminal auto-inhibition capacities. Bacterial challenge activates the HdCASP3-HdGSDME pathway and induces pyroptosis and extracellular traps in abalone. Blockage of the HdCASP3-HdGSDME axis promotes bacterial invasion and host mortality. Collectively, this study reveals the existence of functionally conserved and yet distinct-featured GSDM in Mollusca and provides insights into the function and evolution of invertebrate GSDM.
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Affiliation(s)
- Kunpeng Qin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China; College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuai Jiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China; College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Hang Xu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China; College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zihao Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Li Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China; College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China.
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13
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Liang X, Zhang Y, Jiao Y, Mai J, Deng Y, Du X. Identification and comparative analysis of miRNA transcriptomes after allograft and xenograft transplantation in Pinctada fucata martensii. FISH & SHELLFISH IMMUNOLOGY 2023; 137:108752. [PMID: 37080325 DOI: 10.1016/j.fsi.2023.108752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Effective immune regulation after transplantation during pearl production is crucial for the cultivation of high-quality pearls. MicroRNAs (miRNAs) play an important role in a variety of physiological processes. To understand the regulatory rules of miRNAs after transplantation in Pinctada funcata martensii, we constructed 13 miRNA transcriptomes, including the control group (Con), allograft (Al), and xenograft (Xe) transplantation at six time points (6, 12, and 24 h and 3, 6, and 12 days), in which the xenografted mantle tissue was from Pinctada maxima. We identified 159 differentially expressed miRNAs (DEMs) and found that these DEMs showed high expression at 12 h, 24 h, and 3 days after transplantation. A total of 130 DEMs, such as Let-7, were present in the Al and Xe groups; miR-34 and 16 other DEMs were specifically present in the Al group; miR-216b and 13 other DEMs were specifically present in the Xe group. Compared with the Con group, the target genes of DEMs in the Al group were significantly enriched in protein complex, cytoskeleton, and macromolecular complex, and the Xe group was significantly enriched in ribonucleoside metabolic process, nucleoside binding, and cell division. Compared with the Al group, the target genes in the Xe group were significantly enriched in response to DNA damage stimulation. Overall, multiple pathways associated with cellular activity were enriched in higher numbers of genes in the Xe group than in the Al group. These findings enriched the information on immune regulatory mechanisms at the expression level of miRNAs in P. f. martensii after transplantation.
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Affiliation(s)
- Xueru Liang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yuting Zhang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
| | - Jieni Mai
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yuewen Deng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China
| | - Xiaodong Du
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China
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14
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Gallardo-Escárate C, Valenzuela-Muñoz V, Nuñez-Acuña G, Valenzuela-Miranda D, Tapia FJ, Yévenes M, Gajardo G, Toro JE, Oyarzún PA, Arriagada G, Novoa B, Figueras A, Roberts S, Gerdol M. Chromosome-Level Genome Assembly of the Blue Mussel Mytilus chilensis Reveals Molecular Signatures Facing the Marine Environment. Genes (Basel) 2023; 14:876. [PMID: 37107634 PMCID: PMC10137854 DOI: 10.3390/genes14040876] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
The blue mussel Mytilus chilensis is an endemic and key socioeconomic species inhabiting the southern coast of Chile. This bivalve species supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to diverse physical-chemical ocean farming conditions. Furthermore, mussel production is threatened by a broad range of microorganisms, pollution, and environmental stressors that eventually impact its survival and growth. Herein, understanding the genomic basis of the local adaption is pivotal to developing sustainable shellfish aquaculture. We present a high-quality reference genome of M. chilensis, which is the first chromosome-level genome for a Mytilidae member in South America. The assembled genome size was 1.93 Gb, with a contig N50 of 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, and assembled into 14 chromosomes in congruence with the karyological evidence. The M. chilensis genome comprises 34,530 genes and 4795 non-coding RNAs. A total of 57% of the genome contains repetitive sequences with predominancy of LTR-retrotransposons and unknown elements. Comparative genome analysis of M. chilensis and M. coruscus was conducted, revealing genic rearrangements distributed into the whole genome. Notably, transposable Steamer-like elements associated with horizontal transmissible cancer were explored in reference genomes, suggesting putative relationships at the chromosome level in Bivalvia. Genome expression analysis was also conducted, showing putative genomic differences between two ecologically different mussel populations. The evidence suggests that local genome adaptation and physiological plasticity can be analyzed to develop sustainable mussel production. The genome of M. chilensis provides pivotal molecular knowledge for the Mytilus complex.
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Affiliation(s)
| | | | - Gustavo Nuñez-Acuña
- Center for Aquaculture Research, University of Concepción, Concepción 4070386, Chile
| | | | - Fabian J. Tapia
- Center for Aquaculture Research, University of Concepción, Concepción 4070386, Chile
| | - Marco Yévenes
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno 5310230, Chile
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno 5310230, Chile
| | - Jorge E. Toro
- Facultad de Ciencias, Instituto de Ciencias Marinas y Limnológicas (ICML), Universidad Austral de Chile, Valdivia 5110566, Chile
| | - Pablo A. Oyarzún
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andres Bello, Quintay 2340000, Chile
| | - Gloria Arriagada
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad Andrés Bello, Santiago 8370186, Chile
- FONDAP Center for Genome Regulation, Santiago 8370415, Chile
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), 36208 Vigo, Spain
| | - Antonio Figueras
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), 36208 Vigo, Spain
| | - Steven Roberts
- School of Aquatic and Fishery Sciences (SAFS), University of Washington, Seattle, WA 98195, USA
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
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15
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Zheng Z, Hao R, Yang C, Jiao Y, Wang Q, Huang R, Liao Y, Jian J, Ming Y, Yin L, He W, Wang Z, Li C, He Q, Chen K, Deng Y, Du X. Genome-wide association study analysis to resolve the key regulatory mechanism of biomineralization in Pinctada fucata martensii. Mol Ecol Resour 2023; 23:680-693. [PMID: 36458936 DOI: 10.1111/1755-0998.13743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/17/2022] [Accepted: 11/30/2022] [Indexed: 12/04/2022]
Abstract
Biomineralization-controlled exo-/endoskeleton growth contributes to body growth and body size diversity. Molluscan shells undergo ectopic biomineralization to form the exoskeleton and biocalcified "pearl" involved in invading defence. Notably, exo-/endoskeletons have a common ancestral origin, but their regulation and body growth are largely unknown. This study employed the pearl oyster, Pinctada fucata marntensii, a widely used experimental model for biomineralization in invertebrates, to perform whole-genome resequencing of 878 individuals from wild and breeding populations. This study characterized the genetic architecture of biomineralization-controlled growth and ectopic biomineralization. The insulin-like growth factor (IGF) endocrine signal interacted with ancient single-copy transcription factors to form the regulatory network. Moreover, the "cross-phylum" regulation of key long noncoding RNA (lncRNA) in bivalves and mammals indicated the conserved genetic and epigenetic regulation in exo-/endoskeleton growth. Thyroid hormone signal and apoptosis regulation in pearl oysters affected ectopic biomineralization in pearl oyster. These findings provide insights into the mechanism underlying the evolution and regulation of biomineralization in exo-/endoskeleton animals and ectopic biomineralization.
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Affiliation(s)
- Zhe Zheng
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Ruijuan Hao
- Development and Research Center for Biological Marine Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Chuangye Yang
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yu Jiao
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Qingheng Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Ronglian Huang
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yongshan Liao
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | | | - Yao Ming
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lixin Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Weiming He
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ziman Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Chuyi Li
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Qi He
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Kun Chen
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yuewen Deng
- Fisheries College, Guangdong Ocean University, Zhanjiang, China.,Development and Research Center for Biological Marine Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China.,Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, China.,Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, China
| | - Xiaodong Du
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
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16
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Guo Y, Meng L, Wang M, Zhong Z, Li D, Zhang Y, Li H, Zhang H, Seim I, Li Y, Jiang A, Ji Q, Su X, Chen J, Fan G, Li C, Liu S. Hologenome analysis reveals independent evolution to chemosymbiosis by deep-sea bivalves. BMC Biol 2023; 21:51. [PMID: 36882766 PMCID: PMC9993606 DOI: 10.1186/s12915-023-01551-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Bivalves have independently evolved a variety of symbiotic relationships with chemosynthetic bacteria. These relationships range from endo- to extracellular interactions, making them ideal for studies on symbiosis-related evolution. It is still unclear whether there are universal patterns to symbiosis across bivalves. Here, we investigate the hologenome of an extracellular symbiotic thyasirid clam that represents the early stages of symbiosis evolution. RESULTS We present a hologenome of Conchocele bisecta (Bivalvia: Thyasiridae) collected from deep-sea hydrothermal vents with extracellular symbionts, along with related ultrastructural evidence and expression data. Based on ultrastructural and sequencing evidence, only one dominant Thioglobaceae bacteria was densely aggregated in the large bacterial chambers of C. bisecta, and the bacterial genome shows nutritional complementarity and immune interactions with the host. Overall, gene family expansions may contribute to the symbiosis-related phenotypic variations in different bivalves. For instance, convergent expansions of gaseous substrate transport families in the endosymbiotic bivalves are absent in C. bisecta. Compared to endosymbiotic relatives, the thyasirid genome exhibits large-scale expansion in phagocytosis, which may facilitate symbiont digestion and account for extracellular symbiotic phenotypes. We also reveal that distinct immune system evolution, including expansion in lipopolysaccharide scavenging and contraction of IAP (inhibitor of apoptosis protein), may contribute to the different manners of bacterial virulence resistance in C. bisecta. CONCLUSIONS Thus, bivalves employ different pathways to adapt to the long-term co-existence with their bacterial symbionts, further highlighting the contribution of stochastic evolution to the independent gain of a symbiotic lifestyle in the lineage.
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Affiliation(s)
- Yang Guo
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lingfeng Meng
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minxiao Wang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Zhaoshan Zhong
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Denghui Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Yaolei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Hanbo Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Huan Zhang
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, 210046, China
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Yuli Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Aijun Jiang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Qianyue Ji
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Xiaoshan Su
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Chaolun Li
- Center of Deep-Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- College of Marine Science, University of Chinese Academy of Sciences, Qingdao, 266400, China.
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
- Qingdao Key Laboratory of Marine Genomics, BGI-qingdao, Qingdao, China.
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17
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Chen J, Qiu J, Yang C, Liao Y, He M, Mkuye R, Li J, Deng Y, Du X. Integrated transcriptomic and metabolomic analysis sheds new light on adaptation of Pinctada fucata martensii to short-term hypoxic stress. MARINE POLLUTION BULLETIN 2023; 187:114534. [PMID: 36587532 DOI: 10.1016/j.marpolbul.2022.114534] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/19/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Analyses of the transcriptome and metabolome were conducted to clarify alterations of key genes and metabolites in pearl oysters following exposure to short-term hypoxic treatment. We totally detected 209 DEGs between the control and hypoxia groups. Enrichment analysis indicated the enrichment of GO terms including "oxidation-reduction process", "ECM organization", "chaperone cofactor-dependent protein refolding", and "ECM-receptor interaction" KEGG pathway by the DEGs. In addition, between the two groups, a total of 28 SDMs were identified, which were implicated in 13 metabolic pathways, such as "phenylalanine metabolism", "D-amino acid metabolism", and "aminoacyl-tRNA biosynthesis". Results suggest that pearl oysters are exposed to oxidative stress and apoptosis under short-term hypoxia. Also, pearl oysters might adapt to short-term hypoxic treatment by increasing antioxidant activity, modulating immune and biomineralization activities, maintaining protein homeostasis, and reorganizing the cytoskeleton. The results of our study help unveil the mechanisms by which pearl oysters respond adaptively to short-term hypoxia.
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Affiliation(s)
- Jiayi Chen
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Jinyu Qiu
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Chuangye Yang
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China; Guangdong Marine Ecology Early Warning and Monitoring Laboratory, Zhanjiang 524088, China.
| | - Yongshan Liao
- Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China
| | - Maoxiao He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Robert Mkuye
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Junhui Li
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yuewen Deng
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China; Guangdong Marine Ecology Early Warning and Monitoring Laboratory, Zhanjiang 524088, China
| | - Xiaodong Du
- Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy culture, Zhanjiang, 524088, China; Guangdong Marine Ecology Early Warning and Monitoring Laboratory, Zhanjiang 524088, China
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18
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Shen C, Liang H, Guo Z, Zhang M. Members of the histone-derived antimicrobial peptide family from the pearl oyster Pinctada fucata martensii: Inhibition of bacterial growth. FISH & SHELLFISH IMMUNOLOGY 2023; 132:108439. [PMID: 36423807 DOI: 10.1016/j.fsi.2022.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Because it is difficult to isolate standard antimicrobial peptides (AMPs) using traditional biochemical approaches, we designed, synthesized, and evaluated a series of structurally altered histone-derived AMPs (HDAPs) from the pearl oyster Pinctada fucata martensii using molecular cloning approaches. Four histone-homolog genes (PmH2A, PmH2B, PmH3, and PmH4-1) were identified, of which PmH2A and PmH2B had yet to be described. PmH2A and PmH2B were therefore cloned using Rapid Amplification of cDNA Ends (RACE) and characterized. Constitutive PmH2A and PmH2B mRNA expression was detected in all six pearl oyster tissues tested, with comparatively greater transcript abundance in the gonads. Because α-helical content, hydrophilicity index, and the presence of a proline hinge may be the three important factors influencing the antimicrobial efficacy of HDAPs, we synthesized a series of eight N- and C-terminally truncated or amino acid-substituted synthetic candidate HDAP analogs derived from PmH2A, PmH2B, PmH3, and PmH4-1. Only the PmH2A- and PmH4-derived AMPs inhibited bacterial growth. The PmH2A-derived AMPs were α-helical proteins, while the PmH4-derived AMPs were extended strand/random coil proteins. Our results suggested that having an α-helical structure was particularly important for the antibacterial efficacy of the PmH2A-derived peptides; amphipathic structures (hydrophilic index, 0.3 to -0.3) may enhance the antimicrobial function of both the PmH2A- and PmH4-derived peptides. The high antibacterial efficacy of one of the HDAP analogs studied, PmH2A-AMP (5-13) [KLLK]3, indicated that this protein may represent a promising candidate for the treatment of bacterial infections in aquaculture mollusk species. This first study of HDAPs from the pearl oyster P. f. martensii provides new insights into the design and function of highly effective antimicrobial peptides.
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Affiliation(s)
- Chenghao Shen
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, PR China
| | - Haiying Liang
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, PR China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, Guangdong, 524088, PR China.
| | - Zhijie Guo
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, PR China
| | - Meizhen Zhang
- Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, PR China
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Wang J, Xu Q, Chen M, Chen Y, Wang C, Chen N. Chromosome-level genome assembly of the Pacific geoduck Panopea generosa reveals major inter- and intrachromosomal rearrangements and substantial expansion of the copine gene family. Gigascience 2022; 12:giad105. [PMID: 38116826 PMCID: PMC10729735 DOI: 10.1093/gigascience/giad105] [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: 10/18/2022] [Revised: 06/19/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
The Pacific geoduck Panopea generosa (class Bivalvia, order Adapedonta, family Hiatellidae, genus Panopea) is the largest known burrowing bivalve with considerable commercial value. Pacific geoduck and other geoduck clams play important roles in maintaining ecosystem health for their filter feeding habit and coupling pelagic and benthic processes. Here, we report a high-quality chromosome-level genome assembly of P. generosa to characterize its phylogeny and molecular mechanisms of its life strategies. The assembled P. generosa genome consists of 19 chromosomes with a size of 1.47 Gb, a contig N50 length of 1.6 Mb, and a scaffold N50 length of 73.8 Mb. The BUSCO test of the genome assembly showed 93.0% completeness. Constructed chromosome synteny revealed many occurrences of inter- and intrachromosomal rearrangements between P. generosa and Sinonovacula constricta. Of the 35,034 predicted protein-coding genes, 30,700 (87.6%) could be functionally annotated in public databases, indicating the high quality of genome annotation. Comparison of gene copy numbers of gene families among P. generosa and 11 selected species identified 507 rapidly expanded P. generosa gene families that are functionally enriched in immune and gonad development and may be involved in its complex survival strategies. In particular, genes carrying the copine domains underwent additional duplications in P. generosa, which might be important for neuronal development and immune response. The availability of a fully annotated chromosome-level genome provides a valuable dataset for genetic breeding of P. generosa.
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Affiliation(s)
- Jing Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Qing Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Min Chen
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chunde Wang
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao 266109, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6 , Canada
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20
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Lu X, Zhang M, Yang S, Deng Y, Jiao Y. Transcriptome analysis reveals the diverse response of pearl oyster Pinctada fucata martensii after different PAMP stimulation. FISH & SHELLFISH IMMUNOLOGY 2022; 131:881-890. [PMID: 36374639 DOI: 10.1016/j.fsi.2022.10.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Bivalves have evolved effective strategies to combat different pathogens in the environment. They rely on innate immunity to deal with the invasion of various bacteria, viruses, and other microorganisms. However, the molecular mechanisms underlying the responses remain largely unknown. Herein, we constructed 21 transcriptomes of the hemocytes after lipopolysaccharide (LPS), peptidoglycan (PGN) and polyinosinic-polycytidylic acid (poly(I:C)) stimulation to investigate the molecular mechanisms underlying adaptations and plastic responses to different pathogen-related molecular patterns (PAMPs) in pearl oyster Pinctada fucata martensii. Transcriptome analysis revealed 1986-3427 responsive genes enriched in the major immune and cell cycle-related pathways at different times after PAMP stimulation, and the expression patterns of genes under these pathways are complex and diverse. Moreover, "lysosomes" were enriched 6 h after LPS and PGN stimulation, while "peroxisomes" were only enriched in poly(I:C) group. These results suggest different response strategies of pearl oyster to different PAMPs. Furthermore, we identified 261 pattern-recognition receptors (PRRs) including 4 retinoic acid-inducible gene I-like receptors, 38 NOD-like receptors, 83 Toll-like receptors, and 136 C-type lectins in the genome of P. f. martensii. The diverse expression patterns of these PRRs after different PAMP stimulation indicated that pearl oyster evolved complex and specific recognition systems due to tandem repeat and diverse domain combination, which may help pearl oyster cope with the different pathogens in the environment. The present study improved our understanding of the molecular response of pearl oyster to different PAMP stimulation.
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Affiliation(s)
- Xiaowen Lu
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Ming Zhang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Shuai Yang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yuewen Deng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China; Guangdong Marine Ecology Early Warning and Monitoring Laboratory, Zhanjiang, 524088, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
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21
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Takeuchi T, Suzuki Y, Watabe S, Nagai K, Masaoka T, Fujie M, Kawamitsu M, Satoh N, Myers EW. A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster. DNA Res 2022; 29:dsac035. [PMID: 36351462 PMCID: PMC9646362 DOI: 10.1093/dnares/dsac035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 07/30/2023] Open
Abstract
Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes 14 pairs of long scaffolds (>38 Mb) corresponding to chromosomes (2n = 28). The accuracy of the assembly, as measured by an analysis of k-mers, is estimated to be 99.99997%. Moreover, the haplotypes contain 95.2% and 95.9%, respectively, complete and single-copy BUSCO genes, demonstrating the high quality of the assembly. Transposons comprise 53.3% of the assembly and are a major contributor to structural variations. Despite overall collinearity between haplotypes, one of the chromosomal scaffolds contains megabase-scale non-syntenic regions, which necessarily have never been detected and resolved in conventional haplotype-merged assemblies. These regions encode expanded gene families of NACHT, DZIP3/hRUL138-like HEPN, and immunoglobulin domains, multiplying the immunity gene repertoire, which we hypothesize is important for the innate immune capability of pearl oysters. The pearl oyster genome provides insight into remarkable haplotype diversity in animals.
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Affiliation(s)
| | - Yoshihiko Suzuki
- Present address: Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shugo Watabe
- Kitasato University School of Marine Biosciences, Sagamihara, Kanagawa, Japan
| | - Kiyohito Nagai
- Pearl Research Institute, K. MIKIMOTO & CO., LTD, Shima, Mie, Japan
| | - Tetsuji Masaoka
- Aquatic Breeding Division, Aquaculture Research Department, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Tamaki, Mie, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Eugene W Myers
- Algorithms for Eco and Evo Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
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22
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Boutet I, Alves Monteiro HJ, Baudry L, Takeuchi T, Bonnivard E, Billoud B, Farhat S, Gonzales‐Araya R, Salaun B, Andersen AC, Toullec J, Lallier FH, Flot J, Guiglielmoni N, Guo X, Li C, Allam B, Pales‐Espinosa E, Hemmer‐Hansen J, Moreau P, Marbouty M, Koszul R, Tanguy A. Chromosomal assembly of the flat oyster ( Ostrea edulis L.) genome as a new genetic resource for aquaculture. Evol Appl 2022; 15:1730-1748. [PMID: 36426129 PMCID: PMC9679248 DOI: 10.1111/eva.13462] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 12/01/2022] Open
Abstract
The European flat oyster (Ostrea edulis L.) is a native bivalve of the European coasts. Harvest of this species has declined during the last decades because of the appearance of two parasites that have led to the collapse of the stocks and the loss of the natural oyster beds. O. edulis has been the subject of numerous studies in population genetics and on the detection of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated immune responses to these parasites at the molecular and cellular levels. Several genetic improvement programs have been initiated especially for parasite resistance. Within the framework of a European project (PERLE 2) that aims to produce genetic lines of O. edulis with hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species in the foreshore, obtaining a reference genome becomes essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome-level genome assembly and annotation for the European flat oyster, generated by combining PacBio, Illumina, 10X linked, and Hi-C sequencing. The finished assembly is 887.2 Mb with a scaffold-N50 of 97.1 Mb scaffolded on the expected 10 pseudochromosomes. Annotation of the genome revealed the presence of 35,962 protein-coding genes. We analyzed in detail the transposable element (TE) diversity in the flat oyster genome, highlighted some specificities in tRNA and miRNA composition, and provided the first insight into the molecular response of O. edulis to M. refringens. This genome provides a reference for genomic studies on O. edulis to better understand its basic physiology and as a useful resource for genetic breeding in support of aquaculture and natural reef restoration.
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Affiliation(s)
- Isabelle Boutet
- Sorbonne Université, CNRS, UMR 7144Station Biologique de RoscoffRoscoffFrance
| | | | - Lyam Baudry
- Institut PasteurUnité Régulation Spatiale des Génomes, CNRSParisFrance
| | - Takeshi Takeuchi
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Eric Bonnivard
- Sorbonne Université, CNRS, UMR 7144Station Biologique de RoscoffRoscoffFrance
| | - Bernard Billoud
- Sorbonne Université, CNRSUMR 8227, Station Biologique de RoscoffRoscoffFrance
| | - Sarah Farhat
- Marine Animal Disease Laboratory, School of Marine and Atmospheric SciencesStony Brook UniversityStony BrookNew YorkUSA
| | | | - Benoit Salaun
- Centre Régional de la Conchyliculture Bretagne NordMorlaixFrance
| | - Ann C. Andersen
- Sorbonne Université, CNRS, UMR 7144Station Biologique de RoscoffRoscoffFrance
| | - Jean‐Yves Toullec
- Sorbonne Université, CNRS, UMR 7144Station Biologique de RoscoffRoscoffFrance
| | - François H. Lallier
- Sorbonne Université, CNRS, UMR 7144Station Biologique de RoscoffRoscoffFrance
| | - Jean‐François Flot
- Evolutionary Biology and EcologyUniversité Libre de BruxellesBrusselsBelgium
| | - Nadège Guiglielmoni
- Evolutionary Biology and EcologyUniversité Libre de BruxellesBrusselsBelgium
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal SciencesRutgers UniversityPort NorrisNew JerseyUSA
| | - Cui Li
- Department of Marine Organism Taxonomy and Phylogeny, Institute of OceanologyChinese Academy of SciencesQingdaoChina
| | - Bassem Allam
- Marine Animal Disease Laboratory, School of Marine and Atmospheric SciencesStony Brook UniversityStony BrookNew YorkUSA
| | - Emmanuelle Pales‐Espinosa
- Marine Animal Disease Laboratory, School of Marine and Atmospheric SciencesStony Brook UniversityStony BrookNew YorkUSA
| | - Jakob Hemmer‐Hansen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Pierrick Moreau
- Institut PasteurUnité Régulation Spatiale des Génomes, CNRSParisFrance
| | - Martial Marbouty
- Institut PasteurUnité Régulation Spatiale des Génomes, CNRSParisFrance
| | - Romain Koszul
- Institut PasteurUnité Régulation Spatiale des Génomes, CNRSParisFrance
| | - Arnaud Tanguy
- Sorbonne Université, CNRS, UMR 7144Station Biologique de RoscoffRoscoffFrance
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23
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Xu Y, Dong X, Ma S, Luo C, Xu J. Massive expansion of P-selectin genes in two Venerida species, Sinonovacula constricta and Mercenaria mercenaria: evidence from comparative genomics of Bivalvia. BMC Genomics 2022; 23:662. [PMID: 36123645 PMCID: PMC9484242 DOI: 10.1186/s12864-022-08861-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/25/2022] [Indexed: 12/02/2022] Open
Abstract
Background P-selectin is a molecule participating in the inflammatory response through mediating cellular adhesion and essential for wound repair. However, studies regarding P-selectin in Bivalvia are rare. This study identified 90 P-selectin genes among nine bivalve genomes and classified them into 4 subfamilies according to phylogenetic analysis. Results Notable P-selectin gene expansion was observed in two Venerida species, Sinonovacula constricta and Mercenaria mercenaria. The synteny analysis revealed that P-selectin gene expansion was mostly caused by tandem duplication. In addition, the expression profiles of P-selectin genes in S. constricta showed that many P-selectins were specifically highly expressed in the gills, and the P-selectin expression patterns changed dramatically under low salt stress and ammonia nitrogen stress. Conclusions The massive expansion of P-selectins may facilitate the tolerance to environmental stresses. This study sheds light on the characterizations and expression profiles of P-selectin genes in Bivalvia and provides an integrated framework for further investigation of the role of P-selectins in the environmental tolerance of bivalves. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08861-6.
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Affiliation(s)
- Yuanfeng Xu
- School of Marine Sciences, Ningbo University, Ningbo, 315020, China
| | - Xumeng Dong
- School of Marine Sciences, Ningbo University, Ningbo, 315020, China
| | - Shuonan Ma
- School of Marine Sciences, Ningbo University, Ningbo, 315020, China.
| | - Cheng Luo
- School of Marine Sciences, Ningbo University, Ningbo, 315020, China
| | - Jilin Xu
- School of Marine Sciences, Ningbo University, Ningbo, 315020, China.
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24
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Xiong P, Yao G, Zhang H, He M. Molecular cloning and functional characterization of KCNQ1 in shell biomineralisation of pearl oyster Pinctada fucata martensii. Gene X 2022; 821:146285. [PMID: 35176427 DOI: 10.1016/j.gene.2022.146285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/20/2021] [Accepted: 02/03/2022] [Indexed: 11/28/2022] Open
Abstract
KCNQ1, a voltage-gated potassium ion channel, plays an important role in various physiological processes, including osteoblast differentiation in higher animals. However, its function in lower invertebrates such as marine shellfish remains poorly understood. Pearl oysters, such as P. fucata martensii, are ideal for studying biomineralisation. In this study, a full-length cDNA of KCNQ1 from P. fucata martensii (PfKCNQ1) was obtained, and its function in shell formation was investigated. The full-length 3945 bp cDNA of PfKCNQ1 included an open reading frame (ORF) of 1944 bp encoding a polypeptide of 647 amino acids. Multiple sequence alignment revealed high homology with KCNQ1 from other species, with six transmembrane domains (S1 - S6) and a pore (P) region. Expression pattern analysis showed that PfKCNQ1 was expressed in all tested tissues, with highest expression in mantle and heart, and shell notching induced PfKCNQ1 expression. Silencing PfKCNQ1 expression inhibited PfKCNQ1 expression and downregulated four biomineralisation-related genes (Shematrin, Pif80, N16 and MSI60). Disordered crystals or "hollows" were visible in the shell ultrastructure by scanning electron microscopy following PfKCNQ1 knockdown. The results suggested that PfKCNQ1 may participate in or regulate biomineralisation and shell formation in pearl oyster.
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Affiliation(s)
- Panpan Xiong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gaoyou Yao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Innovation Academy of South China Sea Ecology and Environmental, Engineering, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Maoxian He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China; Innovation Academy of South China Sea Ecology and Environmental, Engineering, Chinese Academy of Sciences, Guangzhou 510301, China.
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25
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Lai Z, Zhao W, Lu Y, Wu L, Yang C, Wang Q. Characterization of transcription factor activator pretein-1 (AP-1) and its association with cold tolerance in Pinctada fucata martensii. FISH & SHELLFISH IMMUNOLOGY 2022; 124:572-578. [PMID: 35483598 DOI: 10.1016/j.fsi.2022.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
AP-1 is an important transcription factor for cell proliferation/differentiation and animal immunity/development; however, its role in research in shellfish is poorly understood. Here, the cDNA of AP-1 gene from Pinctada fucata martensii was characterized. Its expression was detected in all six examined tissues, and a high level was observed in the gill and hepatopancreas. Analysis of the developmental transcriptomes showed that the PmAP-1 gene expression levels were high during D-stage larval and spat stages. The gene also exhibited a significantly high expression under cold tolerance stress. SNP analysis of the exon region and 5' flanking region of PmAP-1 revealed 19 SNPs of which 8 showed significant differences between cold tolerance selection line and base stock. Furthermore, three haplotypes generated by the SNPs of PmAP-1 were significantly associated with cold tolerance, respectively.These results suggest that the PmAP-1 gene plays an important role in the response of P. f. martensii to low temperature stress. These SNPs and haplotypes of PmAP-1 may be related to the cold tolerance of P. f. martensii, and could be candidate markers potentially for further selective breeding.
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Affiliation(s)
- Zhuoxin Lai
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Wei Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yingying Lu
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Lingjun Wu
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chuangye Yang
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China
| | - Qingheng Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China.
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26
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Chen J, Zhai Z, Lu L, Li S, Guo D, Bai L, Yu D. Identification and Characterization of miRNAs and Their Predicted mRNAs in the Larval Development of Pearl Oyster Pinctada fucata. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:303-319. [PMID: 35353261 DOI: 10.1007/s10126-022-10105-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
As an important economic shellfish, the pearl oyster, Pinctada fucata, and its larvae are an ideal model for studying molecular mechanisms of larval development in invertebrates. Larval development directly affects the quantity and quality of pearl oysters. MicroRNAs (miRNAs) may play important roles in development, but the effects of miRNA expression on P. fucata early development remain unknown. In this study, miRNA and mRNA transcriptomics of seven different P. fucata developmental stages were analyzed using Illumina RNA sequencing. A total of 329 miRNAs, including 87 known miRNAs and 242 novel miRNAs, and 33,550 unigenes, including 26,333 known genes and 7217 predicted new genes, were identified in these stages. A cluster analysis showed that the difference in the numbers of miRNAs was greatest between fertilized eggs and trochophores. In addition, the integrated mRNA transcriptome was used to predict target genes for differentially expressed miRNAs between adjacent developmental stages, and the target genes were subjected to a gene ontology enrichment analysis. Using the gene ontology annotation, 100 different expressed genes and 95 differentially expressed miRNAs were identified as part of larval development regulation. Real-time PCR was used to identify eight mRNAs and three miRNAs related to larval development. The present findings will be helpful for further clarifying the regulatory mechanisms of miRNA in invertebrate larval development.
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Affiliation(s)
- Jian Chen
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi, Qinzhou, 535011, People's Republic of China
| | - Ziqin Zhai
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi, Qinzhou, 535011, People's Republic of China
| | - Lili Lu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi, Qinzhou, 535011, People's Republic of China
| | - Suping Li
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi, Qinzhou, 535011, People's Republic of China
| | - Dan Guo
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi, Qinzhou, 535011, People's Republic of China
| | - Lirong Bai
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi, Qinzhou, 535011, People's Republic of China.
| | - Dahui Yu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi, Qinzhou, 535011, People's Republic of China.
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27
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Zeng D, Guo X. Mantle Transcriptome Provides Insights into Biomineralization and Growth Regulation in the Eastern Oyster (Crassostrea virginica). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:82-96. [PMID: 34989931 DOI: 10.1007/s10126-021-10088-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Growth of the eastern oyster Crassostrea virginica, a major aquaculture species in the USA, is highly variable and not well understood at molecular levels. As growth of mollusks is confined in shells constructed by the mantle, mantle transcriptomes of large (fast-growing) and small (slow-growing) eastern oysters were sequenced and compared in this study. Transcription was observed for 31,186 genes, among which 104 genes were differentially expressed between the large and small oysters, including 48 upregulated and 56 downregulated in large oysters. Differentially expressed genes (DEGs) included genes from diverse pathways highlighting the complexity of shell formation and growth regulations. Seventeen of the 48 upregulated DEGs were related to shell matrix formation, most of which were upregulated in large oysters, indicating that large oysters are more active in biomineralization and shell formation. Genomic and transcriptomic analyses identified 22 genes encoding novel polyalanine containing proteins (Pacps) with characteristic motifs for matrix function that are tandemly duplicated on one chromosome, all specifically expressed in mantle and at higher levels in large oysters, suggesting that these expanded Pacps play important roles in shell formation and growth. Analysis of sequence variation identified 244,964 SNPs with 328 associated with growth. This study provides novel candidate genes and markers for shell formation and growth, and suggests that genes related to shell formation are important for the complex regulation of growth in the eastern oyster and possibly other bivalve mollusks. Results of this study show that both transcriptional modulation and functional polymorphism are important in determining growth.
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Affiliation(s)
- Dan Zeng
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, New Jersey, 08349, USA
- College of Life and Environmental Science, Hunan University of Arts and Science, 3150 Dongting Road, Wuling District, Changde, Hunan, 415000, China
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, New Jersey, 08349, USA.
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28
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Evensen KG, Robinson WE, Krick K, Murray HM, Poynton HC. Comparative phylotranscriptomics reveals putative sex differentiating genes across eight diverse bivalve species. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 41:100952. [PMID: 34952324 DOI: 10.1016/j.cbd.2021.100952] [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: 08/31/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Mollusks, especially bivalves, exhibit a great diversity of sex determining mechanisms, including both genetic and environmental sex determination. Some bivalve species can be gonochoristic (separate sexes), while others are hermaphroditic (sequential or simultaneous). Several models have been proposed for specific bivalve species, utilizing information gained from gene expression data, as well as limited RAD-seq data (e.g., from Crassostrea gigas). However, these mechanisms are not as well studied as those in model organisms (e.g., Mus musculus, Drosophila melanogaster, Caenorhabditis elegans) and many genes involved in sex differentiation are not well characterized. We used phylotranscriptomics to better understand which possible sex differentiating genes are in bivalves and how these genes relate to similar genes in diverse phyla. We collected RNAseq data from eight phylogenetically diverse bivalve species: Argopecten irradians, Ensis directus, Geukensia demissa, Macoma tenta, Mercenaria mercenaria, Mya arenaria, Mytilus edulis, and Solemya velum. Using these data, we assembled representative transcriptomes for each species. We then searched for candidate sex differentiating genes using BLAST and confirmed the identity of nine genes using phylogenetics analyses from nine phyla. To increase the confidence of identification, we included ten bivalve genomes in our analyses. From the analysis of doublesex and mab-3 related transcription factor (DMRT) genes, we confirmed the identify of a Mollusk-specific sex determining DMRT gene: DMRT1L. Based on gene expression data from M. edulis and previous research, DMRT1L and FoxL2 are key genes for male and female development, respectively.
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Affiliation(s)
- K Garrett Evensen
- School for the Environment, University of Massachusetts Boston, 100 William T Morrissey Blvd, Boston, MA 02125, United States of America
| | - William E Robinson
- School for the Environment, University of Massachusetts Boston, 100 William T Morrissey Blvd, Boston, MA 02125, United States of America
| | - Keegan Krick
- School for the Environment, University of Massachusetts Boston, 100 William T Morrissey Blvd, Boston, MA 02125, United States of America
| | - Harry M Murray
- Department of Fisheries and Oceans Canada, 80 East White Hills Road, St John's, NL A1C 5X1, Canada
| | - Helen C Poynton
- School for the Environment, University of Massachusetts Boston, 100 William T Morrissey Blvd, Boston, MA 02125, United States of America.
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29
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McCartney MA, Auch B, Kono T, Mallez S, Zhang Y, Obille A, Becker A, Abrahante JE, Garbe J, Badalamenti JP, Herman A, Mangelson H, Liachko I, Sullivan S, Sone ED, Koren S, Silverstein KAT, Beckman KB, Gohl DM. The genome of the zebra mussel, Dreissena polymorpha: a resource for comparative genomics, invasion genetics, and biocontrol. G3 (BETHESDA, MD.) 2022; 12:6460334. [PMID: 34897429 PMCID: PMC9210306 DOI: 10.1093/g3journal/jkab423] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023]
Abstract
The zebra mussel, Dreissena polymorpha, continues to spread from its native range in Eurasia to Europe and North America, causing billions of dollars in damage and dramatically altering invaded aquatic ecosystems. Despite these impacts, there are few genomic resources for Dreissena or related bivalves. Although the D. polymorpha genome is highly repetitive, we have used a combination of long-read sequencing and Hi-C-based scaffolding to generate a high-quality chromosome-scale genome assembly. Through comparative analysis and transcriptomics experiments, we have gained insights into processes that likely control the invasive success of zebra mussels, including shell formation, synthesis of byssal threads, and thermal tolerance. We identified multiple intact steamer-like elements, a retrotransposon that has been linked to transmissible cancer in marine clams. We also found that D. polymorpha have an unusual 67 kb mitochondrial genome containing numerous tandem repeats, making it the largest observed in Eumetazoa. Together these findings create a rich resource for invasive species research and control efforts.
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Affiliation(s)
- Michael A McCartney
- Department of Fisheries, Wildlife and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, St. Paul, MN 55108, USA
| | - Benjamin Auch
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | - Thomas Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sophie Mallez
- Department of Fisheries, Wildlife and Conservation Biology, Minnesota Aquatic Invasive Species Research Center, University of Minnesota, St. Paul, MN 55108, USA
| | - Ying Zhang
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Angelico Obille
- Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Aaron Becker
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, Minneapolis, MN 55455, USA
| | - John Garbe
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA
| | | | - Adam Herman
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | | - Eli D Sone
- Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada.,Department of Materials Science & Engineering, University of Toronto, Toronto, ON M5S 3E4 Canada.,Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Kevin A T Silverstein
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, MN 55455, USA.,Department of Genetics, Cell Biology, and Developmental Biology, University of Minnesota, Minneapolis, MN 55455, USA
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30
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Whaite A, Klein A, Mitu S, Wang T, Elizur A, Cummins S. The byssal-producing glands and proteins of the silverlip pearl oyster Pinctada maxima (Jameson, 1901). BIOFOULING 2022; 38:186-206. [PMID: 35282730 DOI: 10.1080/08927014.2022.2049256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Pinctada maxima are most well known for their production of high-quality natural pearls. They also generate another natural material, the byssus, an adhesive thread critical for steadfast attachment underwater. Herein, P. maxima byssal threads were analysed via proteotranscriptomics to reveal 49 proteins. Further characterisation was undertaken on five highly expressed genes: glycine-rich thread protein (GRT; also known as PUF3), apfp1/perlucin-like protein (Pmfp1); peroxidase; thrombospondin 1, and Balbiani ring 3 (BR3), which showed localised tissue expression. The spatial distribution of GRT and Pmfp1 via immunodetection combined with histology helped to identify glandular regions of the foot that contribute to byssal thread production: the byssal gland, the duct gland, and two thread-forming glands of basophilic and acidophilic serous-like cells. This work advanced primary knowledge on the glands involved in the creation of byssal threads and the protein composition of the byssus for P. maxima, providing a platform for the design of marine biopolymers.
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Affiliation(s)
- Alessandra Whaite
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Anne Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Shahida Mitu
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Tianfang Wang
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Abigail Elizur
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
| | - Scott Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia
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31
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Zhang Y, Mao F, Xiao S, Yu H, Xiang Z, Xu F, Li J, Wang L, Xiong Y, Chen M, Bao Y, Deng Y, Huo Q, Zhang L, Liu W, Li X, Ma H, Zhang Y, Mu X, Liu M, Zheng H, Wong NK, Yu Z. Comparative Genomics Reveals Evolutionary Drivers of Sessile Life and Left-right Shell Asymmetry in Bivalves. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1078-1091. [PMID: 35091095 DOI: 10.1016/j.gpb.2021.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/13/2021] [Accepted: 11/01/2021] [Indexed: 02/05/2023]
Abstract
Bivalves are species-rich mollusks with prominent protective roles in coastal ecosystems. Across these ancient lineages, colony-founding larvae anchor themselves either by byssus production or by cemented attachment. The latter mode of sessile life is strongly molded by left-right shell asymmetry during larval development of Ostreoida oysters such as Crassostrea hongkongensis. Here, we sequenced the genome of C. hongkongensis in high resolution and compared it to reference bivalve genomes to unveil genomic determinants driving cemented attachment and shell asymmetry. Importantly, loss of the homeobox gene Antennapedia (Antp) and broad expansion of lineage-specific extracellular gene families are implicated in a shift from byssal to cemented attachment in bivalves. Comparative transcriptomic analysis shows a conspicuous divergence between left-right asymmetrical C. hongkongensis and symmetrical Pinctada fucata in their expression profiles. Especially, a couple of orthologous transcription factor genes and lineage-specific shell-related gene families including that encoding tyrosinases are elevated, and may cooperatively govern asymmetrical shell formation in Ostreoida oysters.
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Affiliation(s)
- Yang Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Fan Mao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shu Xiao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Haiyan Yu
- Biomarker Technologies Corporation, Beijing 101301, China
| | - Zhiming Xiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Fei Xu
- CAS Key Laboratory of Experimental Marine Biology, Center for Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jun Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Lili Wang
- Biomarker Technologies Corporation, Beijing 101301, China
| | - Yuanyan Xiong
- State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Mengqiu Chen
- State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yongbo Bao
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Yuewen Deng
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Quan Huo
- Hebei Key Laboratory of Applied Chemistry, College of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066044, China
| | - Lvping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Wenguang Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing 101301, China
| | - Haitao Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yuehuan Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xiyu Mu
- Biomarker Technologies Corporation, Beijing 101301, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing 101301, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing 101301, China.
| | - Nai-Kei Wong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Department of Pharmacology, Shantou University Medical College, Shantou 515041, China.
| | - Ziniu Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
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32
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Song N, Li J, Li B, Pan E, Gao J, Ma Y. In vitro crystallization of calcium carbonate mediated by proteins extracted from P. placenta shells. CrystEngComm 2022. [DOI: 10.1039/d2ce00692h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ASM extracted from the shells of P. placenta can stabilize ACC and inhibit secondary nucleation for 10 hours, and an explosive secondary nucleation and quick crystal growth from 50 nm to 10 μm can be finished on the shell surface in one hour.
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Affiliation(s)
- Ningjing Song
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Jiangfeng Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Baosheng Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Ercai Pan
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Juan Gao
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Yurong Ma
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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33
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Chen H, Wang M, Zhang H, Wang H, Zhou L, Zhong Z, Cao L, Lian C, Sun Y, Li C. microRNAs facilitate comprehensive responses of Bathymodiolinae mussel against symbiotic and nonsymbiotic bacteria stimulation. FISH & SHELLFISH IMMUNOLOGY 2021; 119:420-431. [PMID: 34687882 DOI: 10.1016/j.fsi.2021.10.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/08/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
Bathymodiolinae mussels are dominant species in cold seeps and hydrothermal vents and could harbor endosymbionts in gill bacteriocytes. However, mechanisms underlying the symbiosis have remained largely undisclosed for years. In the present study, the global expression pattern of immune-related genes and miRNAs were surveyed in Gigantidas platifrons during bacterial challenges using enriched symbiotic methane oxidation bacteria MOBs or nonsymbiotic Vibrio. As a result, multiple pattern recognition receptors were found differentially expressed at 12 h and 24 h post bacteria challenges and distinctly clustered between stimulations. Dozens of immune effectors along with signal transducers were also modulated simultaneously during MOB or Vibrio challenge. A total of 459 miRNAs were identified in the gill while some were differentially expressed post MOB or nonsymbiotic bacteria challenge. A variety of immune-related genes were annotated as target genes of aforesaid differentially expressed miRNAs. As a result, biological processes including the immune recognition, lysosome activity and bacteria engulfment were suggested to be dynamically modulated by miRNAs in either symbiotic or nonsymbiotic bacteria challenge. It was suggested that G. platifrons mussels could maintain a robust immune response against invading pathogens while establishing symbiosis with chemosynthetic bacteria with the orchestra of immune-related genes and miRNAs.
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Affiliation(s)
- Hao Chen
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Minxiao Wang
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Huan Zhang
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Hao Wang
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Li Zhou
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhaoshan Zhong
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Lei Cao
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chao Lian
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yan Sun
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Chaolun Li
- Center of Deep Sea Research, And CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 10049, China.
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34
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Christiansen H, Heindler FM, Hellemans B, Jossart Q, Pasotti F, Robert H, Verheye M, Danis B, Kochzius M, Leliaert F, Moreau C, Patel T, Van de Putte AP, Vanreusel A, Volckaert FAM, Schön I. Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. BMC Genomics 2021; 22:625. [PMID: 34418978 PMCID: PMC8380342 DOI: 10.1186/s12864-021-07917-3] [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: 04/02/2021] [Accepted: 07/26/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. RESULTS In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. CONCLUSIONS Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.
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Affiliation(s)
- Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.
| | - Franz M Heindler
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Bart Hellemans
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Quentin Jossart
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Henri Robert
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Marie Verheye
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Bruno Danis
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Marc Kochzius
- Marine Biology Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Frederik Leliaert
- Marine Biology Research Group, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Camille Moreau
- Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Université de Bourgogne Franche-Comté (UBFC) UMR CNRS 6282 Biogéosciences, Dijon, France
| | - Tasnim Patel
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Anton P Van de Putte
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Marine Biology Laboratory, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ann Vanreusel
- Marine Biology Research Group, Ghent University, Ghent, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Isa Schön
- OD Nature, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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35
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Gerdol M, La Vecchia C, Strazzullo M, De Luca P, Gorbi S, Regoli F, Pallavicini A, D’Aniello E. Evolutionary History of DNA Methylation Related Genes in Bivalvia: New Insights From Mytilus galloprovincialis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA methylation is an essential epigenetic mechanism influencing gene expression in all organisms. In metazoans, the pattern of DNA methylation changes during embryogenesis and adult life. Consequently, differentiated cells develop a stable and unique DNA methylation pattern that finely regulates mRNA transcription during development and determines tissue-specific gene expression. Currently, DNA methylation remains poorly investigated in mollusks and completely unexplored in Mytilus galloprovincialis. To shed light on this process in this ecologically and economically important bivalve, we screened its genome, detecting sequences homologous to DNA methyltransferases (DNMTs), methyl-CpG-binding domain (MBD) proteins and Ten-eleven translocation methylcytosine dioxygenase (TET) previously described in other organisms. We characterized the gene architecture and protein domains of the mussel sequences and studied their phylogenetic relationships with the ortholog sequences from other bivalve species. We then comparatively investigated their expression levels across different adult tissues in mussel and other bivalves, using previously published transcriptome datasets. This study provides the first insights on DNA methylation regulators in M. galloprovincialis, which may provide fundamental information to better understand the complex role played by this mechanism in regulating genome activity in bivalves.
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36
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He X, Wu F, Zhang L, Li L, Zhang G. Comparative and evolutionary analyses reveal conservation and divergence of the notch pathway in lophotrochozoa. Sci Rep 2021; 11:11378. [PMID: 34059772 PMCID: PMC8166818 DOI: 10.1038/s41598-021-90800-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/17/2021] [Indexed: 01/03/2023] Open
Abstract
Lophotrochozoan species exhibit wide morphological diversity; however, the molecular basis underlying this diversity remains unclear. Here, we explored the evolution of Notch pathway genes across 37 metazoan species via phylogenetic and molecular evolutionary studies with emphasis on the lophotrochozoans. We displayed the components of Notch pathway in metazoans and found that Delta and Hes/Hey-related genes, as well as their functional domains, are duplicated in lophotrochozoans. Comparative transcriptomics analyses allow us to pinpoint sequence divergence of multigene families in the Notch signalling pathway. We identified the duplication mechanism of a mollusc-specific gene, Delta2, and found it displayed complementary expression throughout development. Furthermore, we found the functional diversification not only in expanded genes in the Notch pathway (Delta and Hes/Hey-related genes), but also in evolutionary conservative genes (Notch, Presenilin, and Su(H)). Together, this comprehensive study demonstrates conservation and divergence within the Notch pathway, reveals evolutionary relationships among metazoans, and provides evidence for the occurrence of developmental diversity in lophotrochozoans, as well as a basis for future gene function studies.
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Affiliation(s)
- Xin He
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fucun Wu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China.
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Linlin Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China.
| | - Li Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
| | - Guofan Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, China
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37
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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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38
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Rosani U, Bortoletto E, Bai CM, Novoa B, Figueras A, Venier P, Fromm B. Digging into bivalve miRNAomes: between conservation and innovation. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200165. [PMID: 33813895 PMCID: PMC8059956 DOI: 10.1098/rstb.2020.0165] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2021] [Indexed: 12/17/2022] Open
Abstract
Bivalves are a diverse mollusc group of economic and ecological importance. An evident resilience to pollution, parasites and extreme environments makes some bivalve species important models for studying adaptation and immunity. Despite substantial progress in sequencing projects of bivalves, information on non-coding genes and gene-regulatory aspects is still lacking. Here, we review the current repertoire of bivalve microRNAs (miRNAs), important regulators of gene expression in Metazoa. We exploited available short non-coding RNA (sncRNA) data for Pinctada martensii, Crassostrea gigas, Corbicula fluminea, Tegillarca granosa and Ruditapes philippinarum, and we produced new sncRNA data for two additional bivalves, the Mediterranean mussel Mytilus galloprovincialis and the blood clam Scapharca broughtonii. We found substantial heterogeneity and incorrect annotations of miRNAs; hence, we reannotated conserved miRNA families using recently established criteria for bona fide microRNA annotation. We found 106 miRNA families missing in the previously published bivalve datasets and 89 and 87 miRNA complements were identified in the two additional species. The overall results provide a homogeneous and evolutionarily consistent picture of miRNAs in bivalves and enable future comparative studies. The identification of two bivalve-specific miRNA families sheds further light on the complexity of transcription and its regulation in bivalve 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)
- Umberto Rosani
- Department of Biology, University of Padova, 35121 Padova, Italy
| | | | - Chang-Ming Bai
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture; Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266237, People's Republic of China
| | - Beatriz Novoa
- Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
| | - Antonio Figueras
- Institute of Marine Research (IIM), Spanish National Research Council (CSIC), Eduardo Cabello, 6, 36208 Vigo, Spain
| | - Paola Venier
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
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39
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Cao Y, Tian R, Shi S, Du X, Jiao Y. Characterization and expression analysis of tandemly duplicated nicotinic acetylcholine receptors in pearl oysters after stimulation of pathogen-related molecular patterns. Comp Biochem Physiol B Biochem Mol Biol 2021; 256:110615. [PMID: 33974989 DOI: 10.1016/j.cbpb.2021.110615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 04/22/2021] [Accepted: 05/06/2021] [Indexed: 10/21/2022]
Abstract
Nicotinic acetylcholine receptors (nAChRs) are a class of ligand-gated ion channels that participate in signal transduction and are reported to play an important role in the immunomodulation of vertebrates and invertebrates. Previous studies have shown that the nAChRs in mollusks have undergone large-scale expansion after tandem repeats and retrotransposition, with the most expansion observed in bivalves. This study characterized the sequence of a tandem repeat nAChR unique to several bivalve mollusks and investigated its functions in Pinctada fucata martensii. Firstly, phylogenetic analysis revealed that the tandem arrays of nAChRs existed before bivalve differentiation and m ost tandem-replicated nAChR genes have a conserved genomic structure and domain combination. In present study, five tandemly duplicated nAChR genes were cloned from P. f. martensii and designated as PmnAChR-1 to PmnAChR-5. qRT-PCR analysis revealed that five PmnAChRs were specifically expressed in adult gills. In addition, after PAMP stimulation, the expression of PmnAChRs in hemocytes of P. f. martensii were strongly induced but exhibited different responses to different stimuli. PmnAChR-1, PmnAChR-4, and PmnAChR-5 exhibited strong and wide responsiveness to lipopolysaccharide (LPS) stimulation but had no response to peptidoglycan (PGN) stimulation. PmnAChR-2 expression was notably upregulated at 6 h after PGN challenge but had no response to LPS stimulation. Polyinosinic-polycytidylic acid challenge upregulated nearly all PmnAChRs, except for PmnAChR-5. Furthermore, Pm-miR-873-3p, Pm-miR-4577, Pm-miR-103a-3p, and Pm-miR-6753-3p were identified as the regulatory miRNA of PmnAChR-1, PmnAChR-3, PmnAChR-4, and PmnAChR-5, respectively. These findings suggested that these tandem arrays of nAChRs are unique to bivalves, and the tandem duplication of nAChR genes may be involved in the immune regulation process after pathogen stimulation.
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Affiliation(s)
- Yanfei Cao
- Fishery College, Guangdong Ocean University, Zhanjiang 524025, China
| | - Rongrong Tian
- Fishery College, Guangdong Ocean University, Zhanjiang 524025, China
| | - Shangli Shi
- Fishery College, Guangdong Ocean University, Zhanjiang 524025, China
| | - Xiaodong Du
- Fishery College, Guangdong Ocean University, Zhanjiang 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang 524088, China.
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40
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Wang Z, Liang X, Li G, Liufu B, Lin K, Li J, Wang J, Wang B. Molecular Characterization of Complement Component 3 (C3) in the Pearl Oyster Pinctada fucata Improves Our Understanding of the Primitive Complement System in Bivalve. Front Immunol 2021; 12:652805. [PMID: 33953719 PMCID: PMC8089394 DOI: 10.3389/fimmu.2021.652805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022] Open
Abstract
As the central component in the complement system, complement component 3 (C3) plays essential roles in both the innate and adaptive immune responses. Here, a C3 gene (designated as pf-C3) was obtained from the pearl oyster Pinctada fucata by RT-PCR and rapid amplification of cDNA ends (RACE). The pf-C3 cDNA consists of 5,634 bp with an open reading frame (ORF) of 5,193 bp encoding a protein of 1,730 amino acids with a 19 residue signal peptide. The deduced pf-C3 protein possessed the characteristic structural features present in its homologs and contained the A2M_N_2, ANATO, A2M, A2M_comp, A2M_recep, and C345C domains, as well as the C3 convertase cleavage site, thioester motif, and conserved Cys, His, and Glu residues. Phylogenetic analysis revealed that pf-C3 is closely related to the C3s from other mollusks. Pf-C3 mRNA was expressed in all examined tissues including gill, digestive gland, adductor muscle, mantle and foot, while the highest expression was found in the digestive gland. Following the challenge with Vibrio alginolyticus, pf-C3 expression was significantly induced in hemocytes. Luciferase reporter assays indicated that pf-C3a could activate the NF-κB signal pathway in HEK293T cells. Further knockdown of pf-C3 by specific siRNA could significantly reduce the phagocytosis of V. alginolyticus by hemocytes in vitro. These results would help increase understanding of the function of C3 in the invertebrate immune system and therefore provide new insights into the roles of the primitive complement system in invertebrates.
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Affiliation(s)
- Zhongliang Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Ocean University, Zhanjiang, China
| | - Xueru Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Guiying Li
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Bai Liufu
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Kaiqi Lin
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Jinfeng Li
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Jing Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Bei Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Guangdong Ocean University, Zhanjiang, China
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41
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Lai Z, Adzigbli L, Chen Q, Hao R, Liao Y, Deng Y, Wang Q. Identification and Allelic Variants Associated With Cold Tolerance of PmPIAS in Pinctada fucata martensii. Front Physiol 2021; 12:634838. [PMID: 33737883 PMCID: PMC7960669 DOI: 10.3389/fphys.2021.634838] [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: 11/29/2020] [Accepted: 01/15/2021] [Indexed: 01/06/2023] Open
Abstract
The protein inhibitor of activated STAT (PIAS) functions in diverse aspects, including immune response, cell apoptosis, cell differentiation, and proliferation. In the present study, the PIAS in the pearl oyster Pinctada fucata martensii was characterized. The sequence features of PmPIAS were similar to that of other PIAS sequences with PIAS typical domains, including SAP, Pro-Ile-Asn-Ile-Thr (PINIT), RLD domain, AD, and S/T-rich region. Homologous analysis showed that PmPIAS protein sequence showed the conserved primary structure compared with other species. Ribbon representation of PIAS protein sequences also showed a conserved structure among species, and the PINIT domain and RLD domain showed the conserved structure compared with the sequence of Homo sapiens. The expression pattern of PmPIAS in different tissues showed significant high expression in the gonad. PmPIAS also exhibited a significantly higher expression in the 1 and 2 days after cold tolerance stress (17°C) and showed its potential in the cold tolerance. The SNP analysis of the exon region of PmPIAS obtained 18 SNPs, and among them, 11 SNPs showed significance among different genotypes and alleles between cold tolerance selection line and base stock, which showed their potential in the breeding for cold tolerance traits.
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Affiliation(s)
- Zhuoxin Lai
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Linda Adzigbli
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Qingyue Chen
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Ruijuan Hao
- Development and Research Center for Biological Marine Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Yongshan Liao
- Fisheries College, Guangdong Ocean University, Zhanjiang, China.,Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, China.,Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, China
| | - Yuewen Deng
- Fisheries College, Guangdong Ocean University, Zhanjiang, China.,Development and Research Center for Biological Marine Resources, Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Qingheng Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang, China.,Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, China.,Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, China
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42
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Yang C, Zeng Y, Liao Y, Deng Y, Du X, Wang Q. Integrated GC-MS- and LC-MS-Based Untargeted Metabolomics Studies of the Effect of Vitamin D3 on Pearl Production Traits in Pearl Oyster Pinctada fucata martensii. Front Mol Biosci 2021; 8:614404. [PMID: 33748187 PMCID: PMC7973263 DOI: 10.3389/fmolb.2021.614404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/14/2021] [Indexed: 12/24/2022] Open
Abstract
Pearl oyster Pinctada fucata martensii is widely recognized for biomineralization and has been cultured for high-quality marine pearl production. To ascertain how dietary vitamin D3 (VD3) levels affect the features of pearl production by P. f. martensii and discover the mechanisms regulating this occurrence, five experimental diets with variable levels of VD3 were used with inclusion levels of 0, 500, 1,000, 3,000, and 10,000 IU/kg. The distinct inclusion levels were distributed into five experimental groups (EG1, EG2, EG3, EG4, and EG5). All the experimental groups were reared indoors except the control group (CG) reared at the sea. Pearl oysters, one year and a half old, were used in the grafting operation to culture pearls. During the growing period that lasted 137 days, EG3 had the highest survival rate, retention rate, and high-quality pearl rate. A similar trend was found for EG3 and CG with significantly higher pearl thickness and nacre deposition rates than other groups, but no significant differences were observed between them. A metabolomics profiling using GC–MS and LC–MS of pearl oysters fed with low quantities of dietary VD3 and optimal levels of dietary VD3 revealed 135 statistically differential metabolites (SDMs) (VIP > 1 and p < 0.05). Pathway analysis indicated that SDMs were involved in 32 pathways, such as phenylalanine metabolism, histidine metabolism, glycerophospholipid metabolism, alanine aspartate and glutamate metabolism, arginine and proline metabolism, glycerolipid metabolism, amino sugar and nucleotide sugar metabolism, and tyrosine metabolism. These results provide a theoretical foundation for understanding the impacts of VD3 on pearl production traits in pearl oyster and reinforce forthcoming prospects and application of VD3 in pearl oyster in aquaculture rearing conditions.
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Affiliation(s)
- Chuangye Yang
- Fisheries College, Guangdong Ocean University, Zhanjiang, China.,Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, China.,Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, China.,Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, China
| | - Yetao Zeng
- Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Yongshan Liao
- Fisheries College, Guangdong Ocean University, Zhanjiang, China.,Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, China.,Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, China
| | - Yuewen Deng
- Fisheries College, Guangdong Ocean University, Zhanjiang, China.,Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, China.,Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, China.,Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, China
| | - Xiaodong Du
- Fisheries College, Guangdong Ocean University, Zhanjiang, China.,Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, China.,Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, China.,Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, China
| | - Qingheng Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang, China.,Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, China.,Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, China.,Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, China
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43
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Smith CH. A High-Quality Reference Genome for a Parasitic Bivalve with Doubly Uniparental Inheritance (Bivalvia: Unionida). Genome Biol Evol 2021; 13:evab029. [PMID: 33570560 PMCID: PMC7937423 DOI: 10.1093/gbe/evab029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/16/2022] Open
Abstract
From a genomics perspective, bivalves (Mollusca: Bivalvia) have been poorly explored with the exception for those of high economic value. The bivalve order Unionida, or freshwater mussels, has been of interest in recent genomic studies due to their unique mitochondrial biology and peculiar life cycle. However, genomic studies have been hindered by the lack of a high-quality reference genome. Here, I present a genome assembly of Potamilus streckersoni using Pacific Bioscience single-molecule real-time long reads and 10X Genomics-linked read sequencing. Further, I use RNA sequencing from multiple tissue types and life stages to annotate the reference genome. The final assembly was far superior to any previously published freshwater mussel genome and was represented by 2,368 scaffolds (2,472 contigs) and 1,776,755,624 bp, with a scaffold N50 of 2,051,244 bp. A high proportion of the assembly was comprised of repetitive elements (51.03%), aligning with genomic characteristics of other bivalves. The functional annotation returned 52,407 gene models (41,065 protein, 11,342 tRNAs), which was concordant with the estimated number of genes in other freshwater mussel species. This genetic resource, along with future studies developing high-quality genome assemblies and annotations, will be integral toward unraveling the genomic bases of ecologically and evolutionarily important traits in this hyper-diverse group.
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Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas, Austin, Texas, USA
- Biology Department, Baylor University, Waco, Texas, USA
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44
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Rezende BS, Spotorno-Oliveira P, D'ávila S, Maia LF, Cappa de Oliveira LF. Evidence of a Biogenic Mineralization Process in Vermetid Feeding Mucus as Revealed by Raman Spectroscopy and Scanning Electron Microscopy. MALACOLOGIA 2021. [DOI: 10.4002/040.063.0206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Beatriz Seixas Rezende
- Museu de Malacologia Prof. Maury Pinto de Oliveira, Universidade Federal de Juiz de Fora, MG, Brazil
| | - Paula Spotorno-Oliveira
- Programa de Pós-Graduação em Oceanologia, Universidade Federal do Rio Grande - FURG, Rio Grande, RS, Brazil
| | - Sthefane D'ávila
- Museu de Malacologia Prof. Maury Pinto de Oliveira, Universidade Federal de Juiz de Fora, MG, Brazil
| | - Lenize Fernandes Maia
- Núcleo de Espectroscopia e Estrutura Molecular, Instituto de Ciências Exatas, Universidade Federal de Juiz de Fora, MG, Brazil
| | - Luiz Fernando Cappa de Oliveira
- Núcleo de Espectroscopia e Estrutura Molecular, Instituto de Ciências Exatas, Universidade Federal de Juiz de Fora, MG, Brazil
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45
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Liu C, Zhang R. Biomineral proteomics: A tool for multiple disciplinary studies. J Proteomics 2021; 238:104171. [PMID: 33652138 DOI: 10.1016/j.jprot.2021.104171] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/06/2021] [Accepted: 02/21/2021] [Indexed: 12/11/2022]
Abstract
The hard tissues of animals, such as skeletons and teeth, are constructed by a biologically controlled process called biomineralization. In invertebrate animals, biominerals are considered important for their evolutionary success. These biominerals are hieratical biocomposites with excellent mechanical properties, and their formation has intrigued researchers for decades. Although proteins account for ~5 wt% of biominerals, they are critical players in biomineralization. With the development of high-throughput analysis methods, such as proteomics, biomineral protein data are rapidly accumulating, thus necessitating a refined model for biomineralization. This review focuses on biomineral proteomics in invertebrate animals to highlight the diversity of biomineral proteins (generally 40-80 proteins), and the results indicate that biomineralization includes thermodynamic crystal growth as well as intense extracellular matrix activity and/or vesicle transport. Biominerals have multiple functions linked to biological immunity and antipathogen activity. A comparison of proteomes across species and biomineral types showed that von Willebrand factor type A and epidermal growth factor, which frequently couple with other extracellular domains, are the most common domains. Combined with species-specific repetitive low complexity domains, shell matrix proteins can be employed to predict biomineral types. Furthermore, this review discusses the applications of biomineral proteomics in diverse fields, such as tissue regeneration, developmental biology, archeology, environmental science, and material science.
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Affiliation(s)
- Chuang Liu
- College of Oceanography, Hohai University, Xikang Road, Nanjing, Jiangsu 210098, China.
| | - Rongqing Zhang
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, 705 Yatai Road, Jiaxing 314006, PR China; College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, China.
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46
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Liu F, Li Y, Yu H, Zhang L, Hu J, Bao Z, Wang S. MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca. Nucleic Acids Res 2021; 49:D988-D997. [PMID: 33219670 PMCID: PMC7779068 DOI: 10.1093/nar/gkaa918] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/16/2020] [Accepted: 10/03/2020] [Indexed: 12/11/2022] Open
Abstract
Mollusca represents the second largest animal phylum but remains poorly explored from a genomic perspective. While the recent increase in genomic resources holds great promise for a deep understanding of molluscan biology and evolution, access and utilization of these resources still pose a challenge. Here, we present the first comprehensive molluscan genomics database, MolluscDB (http://mgbase.qnlm.ac), which compiles and integrates current molluscan genomic/transcriptomic resources and provides convenient tools for multi-level integrative and comparative genomic analyses. MolluscDB enables a systematic view of genomic information from various aspects, such as genome assembly statistics, genome phylogenies, fossil records, gene information, expression profiles, gene families, transcription factors, transposable elements and mitogenome organization information. Moreover, MolluscDB offers valuable customized datasets or resources, such as gene coexpression networks across various developmental stages and adult tissues/organs, core gene repertoires inferred for major molluscan lineages, and macrosynteny analysis for chromosomal evolution. MolluscDB presents an integrative and comprehensive genomics platform that will allow the molluscan community to cope with ever-growing genomic resources and will expedite new scientific discoveries for understanding molluscan biology and evolution.
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Affiliation(s)
- Fuyun Liu
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China
| | - Yuli Li
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Hongwei Yu
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding and Sars-Fang Centre, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.,Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
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47
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Cao Y, Tian R, Jiao Y, Zheng Z, Wang Q, Deng Y, Du X. Novel nicotinic acetylcholine receptor involved in immune regulation in pearl oyster (Pinctada fucata martensii). Comp Biochem Physiol B Biochem Mol Biol 2021; 252:110512. [DOI: 10.1016/j.cbpb.2020.110512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/16/2020] [Accepted: 09/29/2020] [Indexed: 01/31/2023]
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48
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Song H, Guo X, Sun L, Wang Q, Han F, Wang H, Wray GA, Davidson P, Wang Q, Hu Z, Zhou C, Yu Z, Yang M, Feng J, Shi P, Zhou Y, Zhang L, Zhang T. The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia. BMC Biol 2021; 19:15. [PMID: 33487168 PMCID: PMC7831173 DOI: 10.1186/s12915-020-00943-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/17/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Inhibitors of apoptosis (IAPs) are critical regulators of programmed cell death that are essential for development, oncogenesis, and immune and stress responses. However, available knowledge regarding IAP is largely biased toward humans and model species, while the distribution, function, and evolutionary novelties of this gene family remain poorly understood in many taxa, including Mollusca, the second most speciose phylum of Metazoa. RESULTS Here, we present a chromosome-level genome assembly of an economically significant bivalve, the hard clam Mercenaria mercenaria, which reveals an unexpected and dramatic expansion of the IAP gene family to 159 members, the largest IAP gene repertoire observed in any metazoan. Comparative genome analysis reveals that this massive expansion is characteristic of bivalves more generally. Reconstruction of the evolutionary history of molluscan IAP genes indicates that most originated in early metazoans and greatly expanded in Bivalvia through both lineage-specific tandem duplication and retroposition, with 37.1% of hard clam IAPs located on a single chromosome. The expanded IAPs have been subjected to frequent domain shuffling, which has in turn shaped their architectural diversity. Further, we observed that extant IAPs exhibit dynamic and orchestrated expression patterns among tissues and in response to different environmental stressors. CONCLUSIONS Our results suggest that sophisticated regulation of apoptosis enabled by the massive expansion and diversification of IAPs has been crucial for the evolutionary success of hard clam and other molluscan lineages, allowing them to cope with local environmental stresses. This study broadens our understanding of IAP proteins and expression diversity and provides novel resources for studying molluscan biology and IAP function and evolution.
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Affiliation(s)
- Hao Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ, USA
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Qianghui Wang
- Novogene Bioinformatics Institute, Beijing, 100029, China
| | - Fengming Han
- Novogene Bioinformatics Institute, Beijing, 100029, China
| | - Haiyan Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | | | | | - Qing Wang
- University of the Chinese Academy of Sciences, Beijing, 100049, China
- Research and Development Center for Efficient Utilization of Coastal Bioresources, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
| | - Zhi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Cong Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenglin Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Meijie Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie Feng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Pu Shi
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Libin Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
- CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
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Xiong X, Li C, Zheng Z, Du X. Novel globular C1q domain-containing protein (PmC1qDC-1) participates in shell formation and responses to pathogen-associated molecular patterns stimulation in Pinctada fucata martensii. Sci Rep 2021; 11:1105. [PMID: 33441832 PMCID: PMC7806589 DOI: 10.1038/s41598-020-80295-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/18/2020] [Indexed: 12/13/2022] Open
Abstract
The C1q protein, which contains the globular C1q (gC1q) domain, is involved in the innate immune response, and is found abundantly in the shell, and it participates in the shell formation. In this study, a novel gC1q domain-containing gene was identified from Pinctada fucata martensii (P. f. martensii) and designated as PmC1qDC-1. The full-length sequence of PmC1qDC-1 was 902 bp with a 534 bp open reading frame (ORF), encoding a polypeptide of 177 amino acids. Quantitative real-time PCR (qRT-PCR) result showed that PmC1qDC-1 was widely expressed in all tested tissues, including shell formation-associated tissue and immune-related tissue. PmC1qDC-1 expression was significantly high in the blastula and gastrula and especially among the juvenile stage, which is the most important stage of dissoconch shell formation. PmC1qDC-1 expression was located in the outer epithelial cells of mantle pallial and mantle edge and irregular crystal tablets were observed in the nacre upon knockdown of PmC1qDC-1 expression at mantle pallial. Moreover, the recombined protein PmC1qDC-1 increased the rate of calcium carbonate precipitation. Besides, PmC1qDC-1 expression was significantly up-regulated in the mantle pallial at 6 h and was significantly up-regulated in the mantle edge at 12 h and 24 h after shell notching. The expression level of PmC1qDC-1 in mantle edge was significantly up-regulated at 48 h after LPS stimulation and was significantly up-regulated at 12 h, 24 h and 48 h after poly I:C stimulation. Moreover, PmC1qDC-1 expression was significantly up-regulated in hemocytes at 6 h after lipopolysaccharide (LPS) and poly I:C challenge. These findings suggest that PmC1qDC-1 plays a crucial role both in the shell formation and the innate immune response in pearl oysters, providing new clues for understanding the shell formation and defense mechanism in mollusk.
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Affiliation(s)
- Xinwei Xiong
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Chuyi Li
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Zhe Zheng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China.
- Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China.
- Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, 524088, China.
| | - Xiaodong Du
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China.
- Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China.
- Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
- Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, 524088, China.
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50
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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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