1
|
Zhao X, Guo M, Wang Y, Jin M, Hou N, Wu H. Toxic effects of nanoplastics on biological nitrogen removal in constructed wetlands: Evidence from iron utilization and metabolism. WATER RESEARCH 2024; 256:121577. [PMID: 38593605 DOI: 10.1016/j.watres.2024.121577] [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: 02/01/2024] [Revised: 03/18/2024] [Accepted: 04/05/2024] [Indexed: 04/11/2024]
Abstract
Nanoplastics (NPs) in wastewaters may present a potential threat to biological nitrogen removal in constructed wetlands (CWs). Iron ions are pivotal in microbially mediated nitrogen metabolism, however, explicit evidence demonstrating the impact of NPs on nitrogen removal regulated by iron utilization and metabolism remains unclear. Here, we investigated how NPs disturb intracellular iron homeostasis, consequently interfering with the coupling mechanism between iron utilization and nitrogen metabolism in CWs. Results indicated that microorganisms affected by NPs developed a siderophore-mediated iron acquisition mechanism to compensate for iron loss. This deficiency resulted from NPs internalization limited the activity of the electron transport system and key enzymes involved in nitrogen metabolism. Microbial network analysis further suggested that NPs exposure could potentially trigger destabilization in microbial networks and impair effective microbial communication, and ultimately inhibit nitrogen metabolism. These adverse effects, accompanied by the dominance of Fe3+ over certain electron acceptors engaged in nitrogen metabolism under NPs exposure, were potentially responsible for the observed significant deterioration in nitrogen removal (decreased by 30 %). This study sheds light on the potential impact of NPs on intracellular iron utilization and offers a substantial understanding of the iron-nitrogen coupling mechanisms in CWs.
Collapse
Affiliation(s)
- Xinyue Zhao
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mengran Guo
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yunan Wang
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ming Jin
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ning Hou
- College of Resource and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Haiming Wu
- School of Environmental Science & Engineering, Shandong University, Qingdao 266237, China.
| |
Collapse
|
2
|
Yu H, Li Y, Han W, Bao L, Liu F, Ma Y, Pu Z, Zeng Q, Zhang L, Bao Z, Wang S. Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach. Nat Protoc 2024; 19:1623-1678. [PMID: 38514839 DOI: 10.1038/s41596-024-00966-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 12/20/2023] [Indexed: 03/23/2024]
Abstract
The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.com/yhw320/PanSyn ), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.
Collapse
Affiliation(s)
- Hongwei Yu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
| | - Wentao Han
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Fuyun Liu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuanting Ma
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lingling Zhang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Zhenmin Bao
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
- Laboratory for Marine Fisheries and Aquaculture, Laoshan Laboratory, Qingdao, China
| | - Shi Wang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
| |
Collapse
|
3
|
Liu H, Ding S, Xu Y, Lin J, Jiang K, Zha S, Bao Y. NO production of granulocytes associated with antibacterial immune response in Tegillarca granosa. FISH & SHELLFISH IMMUNOLOGY 2024; 145:109332. [PMID: 38142829 DOI: 10.1016/j.fsi.2023.109332] [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: 10/25/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 12/26/2023]
Abstract
Nitric oxide (NO) is a signaling molecule and immune effector produced by the nitric oxide synthases (NOS), which involved to various physiological processes of animals. In marine bivalves, hemocytes play important roles in antimicrobial innate immune response. Although hemocyte-derived NO has been detected in several bivalves, the immune function of hemocyte-derived NO is not well understood. Here, we investigated the antibacterial response of hemocyte-derived NO in the blood clam Tegillarca granosa. Two types of hemocytes including erythrocytes and granulocytes were isolated by Percoll density gradient centrifugation, their NO production and TgNOS expression level were analyzed. The results showed that NO was mainly produced in granulocytes and almost no detected in erythrocytes. The granulocytes showed significantly higher NO level and TgNOS expression level than the erythrocytes. And the TgNOS expression level was significantly increased in granulocytes after Vibro parahemolyticus challenge. In addition, the NO donor sodium nitroprusside (SNP) significantly increased the NO production of hemocytes to kill pathogenic bacteria. In summary, the results revealed that granulocytes-derived NO play vital roles in the antimicrobial immune response of the blood clam.
Collapse
Affiliation(s)
- Hongxing Liu
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China
| | - Sixuan Ding
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China
| | - Yingbin Xu
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China
| | - Jie Lin
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China
| | - Kaiqi Jiang
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China
| | - Shanjie Zha
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China
| | - Yongbo Bao
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China.
| |
Collapse
|
4
|
Cheng H, Peng Z, Zhao C, Jin H, Bao Y, Liu M. The transcriptomic and biochemical responses of blood clams (Tegillarca granosa) to prolonged intermittent hypoxia. Comp Biochem Physiol B Biochem Mol Biol 2024; 270:110923. [PMID: 37952637 DOI: 10.1016/j.cbpb.2023.110923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
The blood clam (Tegillarca granosa), a marine bivalve of ecological and economic significance, often encounters intermittent hypoxia in mudflats and aquatic environments. To study the response of blood clam foot to prolonged intermittent hypoxia, the clams were exposed to intermittent hypoxia conditions (0.5 mg/L dissolved oxygen, with a 12-h interval) for 31 days. Initially, transcriptomic analysis was performed, uncovering a total of 698 differentially expressed genes (DEGs), with 236 upregulated and 462 downregulated. These genes show enrichments in signaling pathways related to glucose metabolism, sugar synthesis and responses to oxidative stress. Furthermore, the activity of the enzyme glutathione peroxidase (GPx) and the levels of gpx1 mRNA showed gradual increases, reaching their peak on the 13th day of intermittent hypoxia exposure. This observation suggests an indirect protective role of GPx against oxidative stress. The results of this study make a significantly contribute to our broader comprehensive of the physiological, biochemical responses, and molecular reactions governing the organization of foot muscle tissue in marine bivalves exposed to prolonged intermittent hypoxic conditions.
Collapse
Affiliation(s)
- Haoxiang Cheng
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang 315100, China
| | - Zhilan Peng
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai 315604, China
| | - Chenxi Zhao
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai 315604, China
| | - Hongyu Jin
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang 315100, China
| | - Yongbo Bao
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai 315604, China.
| | - Minhai Liu
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai 315604, China.
| |
Collapse
|
5
|
Zhang W, Zhang Y, Shi X, Wang S, Bao Y. Hemoglobin wonders: a fascinating gas transporter dive into molluscs. Crit Rev Biochem Mol Biol 2023; 58:132-157. [PMID: 38189101 DOI: 10.1080/10409238.2023.2299381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
Hemoglobin (Hb) has been identified in at least 14 molluscan taxa so far. Research spanning over 130 years on molluscan Hbs focuses on their genes, protein structures, functions, and evolution. Molluscan Hbs are categorized into single-, two-, and multiple-domain chains, including red blood cell, gill, and extracellular Hbs, based on the number of globin domains and their respective locations. These Hbs exhibit variation in assembly, ranging from monomeric and dimeric to higher-order multimeric forms. Typically, molluscan Hbs display moderately high oxygen affinity, weak cooperativity, and varying pH sensitivity. Hb's potential role in antimicrobial pathways could augment the immune defense of bivalves, which may be a complement to their lack of adaptive immunity. The role of Hb as a respiratory protein in bivalves likely originated from the substitution of hemocyanin. Molluscan Hbs demonstrate adaptive evolution in response to environmental changes via various strategies (e.g. increasing Hb types, multimerization, and amino acid residue substitutions at key sites), enhancing or altering functional properties for habitat adaptation. Concurrently, an increase in Hb assembly diversity, coupled with a downward trend in oxygen affinity, is observed during molluscan differentiation and evolution. Hb in Protobranchia, Heteroconchia, and Pteriomorphia bivalves originated from separate ancestors, with Protobranchia inheriting a relative ancient molluscan Hb gene. In bivalves, extracellular Hbs share a common origin, while gill Hbs likely emerged from convergent evolution. In summary, research on molluscan Hbs offers valuable insights into the origins, biological variations, and adaptive evolution of animal Hbs.
Collapse
Affiliation(s)
- Weifeng Zhang
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Yang Zhang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xizhi Shi
- School of Marine Science, Ningbo University, Ningbo, China
| | - Shi Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China and National Laboratory for Marine Science and Technology (LMBB & LMFSFPP), Qingdao, China
| | - Yongbo Bao
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
| |
Collapse
|
6
|
Gerdol M, Nerelli DE, Martelossi N, Ogawa Y, Fujii Y, Pallavicini A, Ozeki Y. Taxonomic Distribution and Molecular Evolution of Mytilectins. Mar Drugs 2023; 21:614. [PMID: 38132935 PMCID: PMC10744619 DOI: 10.3390/md21120614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023] Open
Abstract
R-type lectins are a widespread group of sugar-binding proteins found in nearly all domains of life, characterized by the presence of a carbohydrate-binding domain that adopts a β-trefoil fold. Mytilectins represent a recently described subgroup of β-trefoil lectins, which have been functionally characterized in a few mussel species (Mollusca, Bivalvia) and display attractive properties, which may fuel the development of artificial lectins with different biotechnological applications. The detection of different paralogous genes in mussels, together with the description of orthologous sequences in brachiopods, supports the formal description of mytilectins as a gene family. However, to date, an investigation of the taxonomic distribution of these lectins and their molecular diversification and evolution was still lacking. Here, we provide a comprehensive overview of the evolutionary history of mytilectins, revealing an ancient monophyletic evolutionary origin and a very broad but highly discontinuous taxonomic distribution, ranging from heteroscleromorphan sponges to ophiuroid and crinoid echinoderms. Moreover, the overwhelming majority of mytilectins display a chimera-like architecture, which combines the β-trefoil carbohydrate recognition domain with a C-terminal pore-forming domain, suggesting that the simpler structure of most functionally characterized mytilectins derives from a secondary domain loss.
Collapse
Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Daniela Eugenia Nerelli
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Nicola Martelossi
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Yukiko Ogawa
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo 859-3298, Japan
| | - Yuki Fujii
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch, Sasebo 859-3298, Japan
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Yasuhiro Ozeki
- Graduate School of NanoBio Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
| |
Collapse
|
7
|
Jin H, Zhang W, Liu H, Bao Y. Genome-wide identification and characteristic analysis of ETS gene family in blood clam Tegillarca granosa. BMC Genomics 2023; 24:700. [PMID: 37990147 PMCID: PMC10664356 DOI: 10.1186/s12864-023-09731-5] [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: 07/18/2023] [Accepted: 10/11/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND ETS transcription factors, known as the E26 transformation-specific factors, assume a critical role in the regulation of various vital biological processes in animals, including cell differentiation, the cell cycle, and cell apoptosis. However, their characterization in mollusks is currently lacking. RESULTS The current study focused on a comprehensive analysis of the ETS genes in blood clam Tegillarca granosa and other mollusk genomes. Our phylogenetic analysis revealed the absence of the SPI and ETV subfamilies in mollusks compared to humans. Additionally, several ETS genes in mollusks were found to lack the PNT domain, potentially resulting in a diminished ability of ETS proteins to bind target genes. Interestingly, the bivalve ETS1 genes exhibited significantly high expression levels during the multicellular proliferation stage and in gill tissues. Furthermore, qRT-PCR results showed that Tg-ETS-14 (ETS1) is upregulated in the high total hemocyte counts (THC) population of T. granosa, suggesting it plays a significant role in stimulating hemocyte proliferation. CONCLUSION Our study significantly contributes to the comprehension of the evolutionary aspects concerning the ETS gene family, while also providing valuable insights into its role in fostering hemocyte proliferation across mollusks.
Collapse
Affiliation(s)
- Hongyu Jin
- School of Marine Sciences, Ningbo University, Ningbo, 315000, China
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Zhejiang, 315100, China
| | - Weiwei Zhang
- School of Marine Sciences, Ningbo University, Ningbo, 315000, China
| | - Hongxing Liu
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Zhejiang, 315100, China.
| | - Yongbo Bao
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Zhejiang, 315100, China.
| |
Collapse
|
8
|
Rogers TF, Simakov O. Emerging questions on the mechanisms and dynamics of 3D genome evolution in spiralians. Brief Funct Genomics 2023; 22:533-542. [PMID: 37815133 PMCID: PMC10658181 DOI: 10.1093/bfgp/elad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/17/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023] Open
Abstract
Information on how 3D genome topology emerged in animal evolution, how stable it is during development, its role in the evolution of phenotypic novelties and how exactly it affects gene expression is highly debated. So far, data to address these questions are lacking with the exception of a few key model species. Several gene regulatory mechanisms have been proposed, including scenarios where genome topology has little to no impact on gene expression, and vice versa. The ancient and diverse clade of spiralians may provide a crucial testing ground for such mechanisms. Sprialians have followed distinct evolutionary trajectories, with some clades experiencing genome expansions and/or large-scale genome rearrangements, and others undergoing genome contraction, substantially impacting their size and organisation. These changes have been associated with many phenotypic innovations in this clade. In this review, we describe how emerging genome topology data, along with functional tools, allow for testing these scenarios and discuss their predicted outcomes.
Collapse
Affiliation(s)
- Thea F Rogers
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, Division of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| |
Collapse
|
9
|
Xie X, Teng W, Yu Z, Li D, Yang M, Zhang H, Zheng J, Li H, Sun Y, Liu X, Zhou Z, Zhang X, Du S, Li Q, Chang Y, Zhang M, Wang Q. Chromosome-level genome assembly of sea scallop Placopecten magellanicus provides insights into the genetic characteristics and adaptive evolution of large scallops. Genomics 2023; 115:110747. [PMID: 37977331 DOI: 10.1016/j.ygeno.2023.110747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 10/30/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Placopecten magellanicus (Gmelin, 1791), a deep-sea Atlantic scallop, holds significant commercial value as a benthic marine bivalve along the northwest Atlantic coast. Recognizing its economic importance, the need to reconstruct its genome assembly becomes apparent, fostering insights into natural resources and generic breeding potential. This study reports a high-quality chromosome-level genome of P. magellanicus, achieved through the integration of Illumina short read sequencing, PacBio HiFi sequencing, and Hi-C sequencing techniques. The resulting assembly spans 1778 Mb with a scaffold N50 of 86.71 Mb. An intriguing observation arises - the genome size of P. magellanicus surpasses that of its Pectinidae family peers by 1.80 to 2.46 times. Within this genome, 28,111 protein-coding genes were identified. Comparative genomic analysis involving five scallop species unveils the critical determinant of this expanded genome: the proliferation of repetitive sequences recently inserted, contributing to its enlarged size. The landscape of whole genome collinearity sheds light on the relationships among scallop species, enhancing our broader understanding of their genomic framework. This genome provides genomic resources for future molecular biology research on scallops and serves as a guide for the exploration of longevity-related genes in scallops.
Collapse
Affiliation(s)
- Xi Xie
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China; Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Dalian, China
| | - Weiming Teng
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Zuoan Yu
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Dacheng Li
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Miao Yang
- Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Sciences, Liaoning Normal University, Dalian, China
| | - Haijiao Zhang
- Dalian Changhai-Yide Aquatic Products Co., LTD, Dalian, China
| | - Jie Zheng
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Hualin Li
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Yongxin Sun
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Xiangfeng Liu
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China
| | - Zunchun Zhou
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China; Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Dalian, China
| | - Xiliang Zhang
- Dalian Changhai-Yide Aquatic Products Co., LTD, Dalian, China
| | - Shaojun Du
- Institute of Marine and Environmental Technology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yaqing Chang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China.
| | - Ming Zhang
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China.
| | - Qingzhi Wang
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian, China; Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Dalian, China.
| |
Collapse
|
10
|
Kim T, Ri S, Ju K, Shi W, Zhou W, Yu Y, Ri S, Ri H, Yun S, Ri J, Liu G. A C-type lectin with a single carbohydrate-recognition domain (CRD) containing unique QPN/WDD motifs from Tegillarca granosa is involved in the innate immune defense. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109093. [PMID: 37722437 DOI: 10.1016/j.fsi.2023.109093] [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: 08/25/2023] [Revised: 09/12/2023] [Accepted: 09/16/2023] [Indexed: 09/20/2023]
Abstract
C-type lectins (CTLs), a superfamily of Ca2+-dependent carbohydrate-recognition proteins, serve as pattern recognition receptors (PRRs) in the immune response of many species. However, little is currently known about the CTLs of the commercially and ecologically important bivalve species, blood clam (Tegillarca granosa). In this study, a CTL (designated as TgCTL-1) with a single carbohydrate-recognition domain (CRD) containing unique QPN/WDD motifs was identified in the blood clam through transcriptome and whole-genome searching. Multiple alignment and phylogenetic analysis strongly suggested that TgCTL-1 was a new member of the CTL superfamily. Expression analysis demonstrated that TgCTL-1 was highly expressed in the hemocytes and visceral mass of the clam under normal condition. In addition, the expression of TgCTL-1 was shown to be significantly up-regulated upon pathogen challenge. Moreover, the recombinant TgCTL-1 (rTgCTL-1) displayed agglutinating and binding activities against both the gram-positive and gram-negative bacteria tested in a Ca2+-dependent manner. Furthermore, it was found that the in vitro phagocytic activity of hemocytes was significantly enhanced by rTgCTL-1. In general, our results showed that TgCTL-1 was an inducible acute-phase secretory protein, playing crucial roles in recognizing, agglutinating, and binding to pathogenic bacteria as well as modulating phagocytic activity of hemocytes in the innate immune defense of blood clam.
Collapse
Affiliation(s)
- Tongchol Kim
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China; College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, North Korea
| | - Sanghyok Ri
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China; College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, North Korea
| | - Kwangjin Ju
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China; College of Aquaculture, Wonsan Fisheries University, Wonsan, 99903, North Korea
| | - Wei Shi
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Weishang Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Yihan Yu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Sangryong Ri
- College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, North Korea
| | - Hyoksong Ri
- College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, North Korea
| | - Songsu Yun
- College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, North Korea
| | - Junjin Ri
- College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, North Korea
| | - Guangxu Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China.
| |
Collapse
|
11
|
Identificaiton and characterization of a novel hemoglobin gene (Tgr-HbIII) from blood clam Tegillarca granosa. Gene 2023; 862:147256. [PMID: 36754178 DOI: 10.1016/j.gene.2023.147256] [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: 10/23/2022] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023]
Abstract
Hemoglobin (Hb) is the major protein component of red blood cells (hemocytes) of the blood clam Tegillarca granosa. Three T. granosa hemoglobin genes have been mentioned in the literature, designated Tgr-HbI, Tgr-HbIIA and Tgr-HbIIB. Previously, our group identified another novel gene, Tgr-HbIII, in the Hb cluster of the chromosome-level genome but the issue of whether this Hb gene expresses functional protein remains unclear. In the current study, phylogenetic analysis revealed that Tgr-HbIII resembles an ancient Hb gene. Sequence alignment and three-dimensional structural modeling results showed that Tgr-HbIII does not bind heme due to the completely different structure at amino acid position 96-100 and replacement of the N100 residue in known Tgr-Hbs with Q100, what causes loss of a single hydrogen bond linking heme with the globin fold. Interface prediction data suggest that Tgr-HbIII forms a homodimer (ΔG = -5.6 kcal/mol) with a similar conformation to the Tgr-HbI homodimer (ΔG = -3.5 kcal/mol). In adult T. granosa, mRNA expression of Tgr-HbIII was lower than that of Tgr-HbIIA and Tgr-HbIIB (up to 100 × ), but comparable to that of Tgr-HbI. Notably, protein expression of Tgr-HbIII was extremely low. Single-cell RNA sequencing analysis of Hb expression showed that all adult hemocytes expressed Tgr-HbI, Tgr-HbIIA and Tgr-HbIIB, while only 43 % (3872 of 8978) expressed Tgr-HbIII. Based on the collective data, we speculate that Tgr-HbIII carried oxygen prior to mutation of N100 to Q100 and subsequently evolved into a known functional remnant of Hb with an adequate mRNA/low protein expression profile. The current study provides a foundation for further research on the origin, evolution and function of molluscan Hbs.
Collapse
|
12
|
Queiroz JPF, Lourenzoni MR, Rocha BAM. Structural evolution of an amphibian-specific globin: A computational evolutionary biochemistry approach. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101055. [PMID: 36566682 DOI: 10.1016/j.cbd.2022.101055] [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: 07/29/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Studies on the globin family are continuously revealing insights into the mechanisms of gene and protein evolution. The rise of a new globin gene type in Pelobatoidea and Neobatrachia (Amphibia:Anura) from an α-globin precursor provides the opportunity to investigate the genetic and physical mechanisms underlying the origin of new protein structural and functional properties. This amphibian-specific globin (globin A/GbA) discovered in the heart of Rana catesbeiana is a monomer. As the ancestral oligomeric state of α-globins is a homodimer, we inferred that the ancestral state was lost somewhere in the GbA lineage. Here, we combined computational molecular evolution with structural bioinformatics to determine the extent to which the loss of the homodimeric state is pervasive in the GbA clade. We also characterized the loci of GbA genes in Bufo bufo. We found two GbA clades in Neobatrachia. One was deleted in Ranidae, but retained and expanded to yield a new globin cluster in Bufonidae species. Loss of the ancestral oligomeric state seems to be pervasive in the GbA clade. However, a taxonomic sampling that includes more Pelobatoidea, as well as early Neobatrachia, lineages would be necessary to determine the oligomeric state of the last common ancestor of all GbA. The evidence presented here points out a possible loss of oligomerization in Pelobatoidea GbA as a result of amino acid substitutions that weaken the homodimeric state. In contrast, the loss of oligomerization in both Neobatrachia GbA clades was linked to independent deletions that disrupted many packing contacts at the homodimer interface.
Collapse
Affiliation(s)
- João Pedro Fernandes Queiroz
- Laboratorio de Biocristalografia - LABIC, Departamento de Bioquimica e Biologia Molecular, Universidade Federal do Ceara, Campus do Pici s.n., bloco 907, Av. Mister Hull, Fortaleza, Ceara, 60440-970, Brazil.
| | - Marcos Roberto Lourenzoni
- Protein Engineering and Health Solutions Group - GEPeSS Fundacao Oswaldo Cruz - Ceara, Eusébio, Ceara, 60175-047, Brazil.
| | - Bruno Anderson Matias Rocha
- Laboratorio de Biocristalografia - LABIC, Departamento de Bioquimica e Biologia Molecular, Universidade Federal do Ceara, Campus do Pici s.n., bloco 907, Av. Mister Hull, Fortaleza, Ceara, 60440-970, Brazil.
| |
Collapse
|
13
|
Yang Q, Xiao G, Chen R, Huang X, Teng S. Immune responses of hemocytes in the blood clam Tegillarca granosa in response to in vivo Vibrio harveyi infection. FISH & SHELLFISH IMMUNOLOGY 2023; 132:108447. [PMID: 36435369 DOI: 10.1016/j.fsi.2022.11.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/13/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
Aquaculture of the blood clam Tegillarca granosa accounts for approximately 50% of Arcidae (ark shell) production in China. Vibrio infection severely threatens the sustainability of the clam aquaculture industry. Exposure to Vibrio induces an immune response in blood clams. However, the underlying mechanism remains poorly understood. In this study, immune responses of hemocytes in blood clams were detected after Vibrio infection; the immersion method was used in vivo to mimic the clam's natural infection process. After 24 h of exposure to Vibrio infection, the Vibrio load in hemolymph fluid in both the treatment Ⅰ (25,033.33 ± 19,563.11 CFU/mL) and treatment Ⅱ (122,163.33 ± 194,409.49 CFU/mL) groups were significantly higher, than that in the control group (13.67 ± 37.73 CFU/mL) (P < 0.05). Correspondingly, the production of intracellular reactive oxygen species was approximately 1.40 (treatment Ⅰ) and 2.12 (treatment Ⅱ) fold higher than that in the control group (P < 0.05), and the induced DNA damage showed a similar trend (P < 0.05). Vibrio infection also significantly increased lysozyme content, adenosine triphosphate content, and peroxidase isozyme activity, in both the serum and hemocyte lysates (P < 0.05). The expression of immune-associated genes (ABCA3, c-Myc, Caspase 3, and HSP70) was upregulated under infection conditions. The phagocytic activity was approximately 1.99 (treatment Ⅰ) and 2.57 (treatment Ⅱ) fold that in control clams (P < 0.05). In addition, the total hemocyte count and red granulocyte percentage both significantly decreased by approximately 75-90% after Vibrio infection. These results provided novel insights into the mechanism of hemocyte immunity in T. granosa against Vibrio infection, which may aid in the future prevention and control of Vibrio infection in vivo.
Collapse
Affiliation(s)
- Qianyuan Yang
- Zhejiang Mariculture Research Institute, Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-Resource, Wenzhou Key Laboratory of Marine Biological Genetics and Breeding, Wenzhou, Zhejiang, 325005, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Guoqiang Xiao
- Zhejiang Mariculture Research Institute, Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-Resource, Wenzhou Key Laboratory of Marine Biological Genetics and Breeding, Wenzhou, Zhejiang, 325005, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Ran Chen
- Zhejiang Mariculture Research Institute, Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-Resource, Wenzhou Key Laboratory of Marine Biological Genetics and Breeding, Wenzhou, Zhejiang, 325005, China
| | - Xiaolin Huang
- Zhejiang Mariculture Research Institute, Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-Resource, Wenzhou Key Laboratory of Marine Biological Genetics and Breeding, Wenzhou, Zhejiang, 325005, China.
| | - Shuangshuang Teng
- Zhejiang Mariculture Research Institute, Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-Resource, Wenzhou Key Laboratory of Marine Biological Genetics and Breeding, Wenzhou, Zhejiang, 325005, China.
| |
Collapse
|
14
|
Wu Z, Tang M, Zhao J, Lin Z, Wang S, Bao Y. Genome-wide identification and immune response analysis of serine protease inhibitor genes in the blood clam Tegillarca granosa. FISH & SHELLFISH IMMUNOLOGY 2022; 131:1234-1244. [PMID: 36417957 DOI: 10.1016/j.fsi.2022.11.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
Serine protease inhibitors (SPIs) are the main regulators of serine protease activities. In this study, we present a genome-wide identification of SPI genes in T. granosa(TgSPI genes)and their expression characteristics in respond to Vibrio stress. A total of 102 TgSPI genes belonging to eight families, including Serpin, TIL (trypsin inhibitor like cysteine rich domain), Kunitz, Kazal, I84, Pacifastin, WAP (whey acidic protein) and A2M (Alpha-2-macroglobulin) were identified, while no genes belonging to Bowman-Birk, amfpi and Antistasin families were identified. The Kazal family has the most TgSPI genes with 38, and 11 TgSPI genes belong to the mollusc-specific I84 family. The TgSPI genes were found to be randomly distributed on 17 chromosomes with 12 tandem duplicate gene pairs. Expression profiles showed that most TgSPI genes were mainly expressed in immune-related tissues such as hepatopancreas, gill and mantle. In the hepatopancreas, most of TgSPI genes were sensitive to Vibrio stress, 28 and 29 TgSPI genes were up-regulated and down-regulated, respectively. Some up-regulated genes with signal peptides, such as the TgSPIs of I84 family, may act as a mechanism to directly prevent Vibrio from invasion. Six Kazal-type TgSPIs (TgSPI29, 45, 49, 50, 51 and 52) were intracellular proteins and their expression was down-regulated in hemocytes after Vibrio stress. This may have boosted protease activity in hemocytes to the point that more hemoglobin derived peptides were produced and secreted into the hemolymph to exert their anti-Vibrio effects. These findings may provide valuable information for further clarifying the roles of SPIs in the immune defense and will benefit future exploration of the immune function of SPIs in molluscs.
Collapse
Affiliation(s)
- Zongming Wu
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China
| | - Mengjie Tang
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China
| | - Jiafeng Zhao
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China
| | - Zhihua Lin
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China
| | - Sufang Wang
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China.
| | - Yongbo Bao
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China.
| |
Collapse
|
15
|
Sun Y, Liu X, Xie X, Bai Y, Wang S, Teng W, Li D, Li H, Yu Z, Zhang M, Zhou Z, Liu X, Nie H, Du S, Li X, Li Q, Wang Q. A high-quality chromosome-level genome assembly of the bivalve mollusk Mactra veneriformis. G3 (BETHESDA, MD.) 2022; 12:jkac229. [PMID: 36165708 PMCID: PMC9635629 DOI: 10.1093/g3journal/jkac229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Mactra veneriformis (Bivalvia: Mactridae) is a bivalve mollusk of major economic importance in China. Decreased natural yields of M. veneriformis have led to an urgent need for genomic resources. To address this problem and the currently limited knowledge of molecular evolution in this genus, we here report a high-quality chromosome-level genome assembly of M. veneriformis. Our approach yielded a 939.32 Mb assembled genome with an N50 contig length of 7,977.84 kb. Hi-C scaffolding of the genome resulted in assembly of 19 pseudochromosomes. Repetitive elements made up ∼51.79% of the genome assembly. A total of 29,315 protein-coding genes (PCGs) were predicted in M. veneriformis. Construction of a genome-level phylogenetic tree demonstrated that M. veneriformis and Ruditapes philippinarum diverged around 231 million years ago (MYA). Inter-species comparisons revealed that 493 gene families have undergone expansion and 449 have undergone contraction in the M. veneriformis genome. Chromosome-based macrosynteny analysis revealed a high degree of synteny between the 19 chromosomes of M. veneriformis and those of Patinopecten yessoensis. These results suggested that M. veneriformis has a similar karyotype to that of P. yessoensis, and that a highly conserved 19-chromosome karyotype was formed in the early differentiation stages of bivalves. In summary, the genomic resources generated in this work serve as a valuable reference for investigating the molecular mechanisms underlying biological functions in M. veneriformis and will facilitate future genetic improvement and disease treatment in this economically important species. Furthermore, the assembled genome greatly improves our understanding of early genomic evolution of the Bivalvia.
Collapse
Affiliation(s)
| | | | | | | | - Shuo Wang
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Weiming Teng
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Dacheng Li
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Hualin Li
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Zuoan Yu
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Ming Zhang
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Zunchun Zhou
- Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China
| | - Xu Liu
- Panjin Guanghe Crab Industry Co., LTD, Panjin 124299, China
| | - Hongtao Nie
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
| | - Shaojun Du
- Department of Biochemistry and Molecular Biology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD 21202, USA
| | - Xiaodong Li
- Key Laboratory of Zoonosis, Aquaculture Department, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China
| | - Qi Li
- Corresponding author: Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Qingzhi Wang
- Corresponding author: Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China.
| |
Collapse
|
16
|
Zhan Y, Zha S, Peng Z, Lin Z, Bao Y. Hypoxia-mediated immunotoxicity in the blood clam Tegillarca granosa. MARINE ENVIRONMENTAL RESEARCH 2022; 177:105632. [PMID: 35439659 DOI: 10.1016/j.marenvres.2022.105632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/09/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
In marine ecosystems, dissolved oxygen (DO) is essential for maintaining intracellular energy balance during aerobic metabolism. Bivalve mollusks are frequently exposed to hypoxia environments due to tides, temperature changes, and anthropogenic activities. The blood clam, Tegillarca granosa, mainly inhabits intertidal mudflats and is more susceptible to low oxygen events. In this study, we investigated the effect of hypoxia on immune responses in clams, and showed that hypoxia exposure reduced total hemocyte counts (THC), hemoglobin concentrations, and intracellular reactive oxygen species (ROS) levels. Also, phagocytic and cell activities of hemocyte were significantly inhibited. Furthermore, immune-related gene expression was also down-regulated. In conclusion, hypoxia greatly affected immune functions in blood clams, and our research provided the foundation for further mechanistic studies on hypoxia tolerance in clams.
Collapse
Affiliation(s)
- Yu Zhan
- School of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China; Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China
| | - Shanjie Zha
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China
| | - Zhilan Peng
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China
| | - Zhihua Lin
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China
| | - Yongbo Bao
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, Zhejiang, 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China.
| |
Collapse
|
17
|
Ri S, Zha S, Kim T, Ju K, Zhou W, Shi W, Wu M, Kim C, Bao Y, Sun C, Liu G. Identification, characterization, and antimicrobial activity of a novel big defensin discovered in a commercial bivalve mollusc, Tegillarca granosa. FISH & SHELLFISH IMMUNOLOGY 2022; 124:174-181. [PMID: 35398526 DOI: 10.1016/j.fsi.2022.04.003] [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: 01/06/2022] [Revised: 03/08/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
Molluscs, the second largest animal phylum on earth, primarily rely on cellular and humoral immune responses to fight against pathogen infection. Although antimicrobial peptides (AMPs) such as big defensin play crucial roles in the humoral immune response, it remains largely unknown in the ecological and economic important blood clam (Tegillarca granosa). In this study, a novel big defensin gene (TgBD) was identified in T. granosa through transcripts and whole genome searching. Bioinformatic analyses were conducted to explore the molecular characteristics of TgBD, and comparisons of TgBD with those reported in other molluscs were performed by multiple alignments and phylogenetic analysis. In addition, the expression patterns of TgBD in various tissues and upon bacterial challenge were investigated while the antimicrobial activity of synthetic N-terminal domain of TgBD was confirmed in vitro by radial diffusion experiment. Results obtained showed TgBD had an open reading frame (ORF) of 369 bp, encoding a prepropeptide containing a signal peptide and a propeptide. Similar to big defensins reported in other species, TgBD consists of a hydrophobic N-terminal domain containing β1-α1-α2-β2 folds and a cysteine-rich cationic C-terminal domain with three disulfide bonds between C1-C5, C2-C4, and C3-C6. Phylogenetic analysis showed that TgBD shared 76.80% similarity to its close relative ark shell (Scapharca broughtoni). In addition, TgBD expression was observed in all tissues investigated under normal conditions and was significantly induced by injection of Vibrio parahaemolyticus. Furthermore, synthetic N-terminal peptide of TgBD exhibited strong antimicrobial activity against Gram-positive bacteria tested. Our results indicated that TgBD is a constitutive and inducible acute phase AMP, which provides a universal and prompt protection for T. granosa.
Collapse
Affiliation(s)
- Sanghyok Ri
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China; College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, D.P.R, North Korea
| | - Shanjie Zha
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, PR China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, PR China
| | - Tongchol Kim
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China; College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, D.P.R, North Korea
| | - Kwangjin Ju
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China; College of Aquaculture, Wonsan Fisheries University, Wonsan, 999093, D.P.R, North Korea
| | - Weishang Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Wei Shi
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Myongsik Wu
- College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, D.P.R, North Korea
| | - Chunmi Kim
- College of Life Science, Kim Hyong Jik University of Education, Pyongyang, 99903, D.P.R, North Korea
| | - Yongbo Bao
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, PR China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, PR China
| | - Changsen Sun
- Zhejiang Key Laboratory of Aquatic Germplasm Resources, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, PR China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, PR China
| | - Guangxu Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, PR China.
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Liu H, Zha S, Zhang W, Yuan W, Lin Z, Bao Y. Genome-wide identification and characteristic analysis of PGRP gene family in Tegillarca granosa reveals distinct immune response of the invasive pathogen. FISH & SHELLFISH IMMUNOLOGY 2022; 121:232-238. [PMID: 35031474 DOI: 10.1016/j.fsi.2022.01.015] [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: 10/18/2021] [Revised: 12/13/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
The peptidoglycan recognition proteins (PGRPs) are conserved innate immune molecular in invertebrates and vertebrates, which play important roles in immune system by recognize the peptidoglycans of bacterial cell walls. Although PGRPs have been extensively characterized in insects, a systematic analysis of PGRPs in bivalves is lacking. In the present study, the phylogenic relationships, gene structures and expression profiles of PGRPs in marine bivalves were analyzed. The results indicated that the most PGRPs of bivalves were predicted to degrade the peptidoglycans and prevent excessive immunostimulation of bacteria. In addition, the results of the present study showed that the protein diversity of PGRPs in most marine bivalves was mainly generated by the alternative splicing of genes, however the alternative splicing of PGRP gene family was absent in Tegillarca granosa. The differences of PGRPs might be related to the genetic and environmental differences of marine bivalves. Spatiotemporal expression profiling in T. granosa suggested that PGRPs play important roles in the immune response of invasive pathogens. The present study describes a comprehensive view of PGRPs in the blood clam T. granosa and provides a foundation for functional characterization of this gene family in innate immune of marine bivalves.
Collapse
Affiliation(s)
- Hongxing Liu
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China; Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China
| | - Shanjie Zha
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China
| | - Weifeng Zhang
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China; School of Marine Science, Ningbo University, Ningbo, 315100, China
| | - Wenbin Yuan
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China; School of Marine Science, Ningbo University, Ningbo, 315100, China
| | - Zhihua Lin
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ninghai, 315604, China
| | - Yongbo Bao
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China.
| |
Collapse
|
20
|
Li A, Dai H, Guo X, Zhang Z, Zhang K, Wang C, Wang X, Wang W, Chen H, Li X, Zheng H, Li L, Zhang G. Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity. Commun Biol 2021; 4:1287. [PMID: 34773106 PMCID: PMC8590024 DOI: 10.1038/s42003-021-02823-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 10/28/2021] [Indexed: 12/27/2022] Open
Abstract
Understanding the roles of genetic divergence and phenotypic plasticity in adaptation is central to evolutionary biology and important for assessing adaptive potential of species under climate change. Analysis of a chromosome-level assembly and resequencing of individuals across wide latitude distribution in the estuarine oyster (Crassostrea ariakensis) revealed unexpectedly low genomic diversity and population structures shaped by historical glaciation, geological events and oceanographic forces. Strong selection signals were detected in genes responding to temperature and salinity stress, especially of the expanded solute carrier families, highlighting the importance of gene expansion in environmental adaptation. Genes exhibiting high plasticity showed strong selection in upstream regulatory regions that modulate transcription, indicating selection favoring plasticity. Our findings suggest that genomic variation and population structure in marine bivalves are heavily influenced by climate history and physical forces, and gene expansion and selection may enhance phenotypic plasticity that is critical for the adaptation to rapidly changing environments.
Collapse
Affiliation(s)
- Ao Li
- grid.9227.e0000000119573309CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - He Dai
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Ximing Guo
- grid.430387.b0000 0004 1936 8796Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, NJ USA
| | - Ziyan Zhang
- grid.9227.e0000000119573309CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Kexin Zhang
- grid.9227.e0000000119573309CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Chaogang Wang
- grid.9227.e0000000119573309CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Xinxing Wang
- grid.9227.e0000000119573309CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- grid.9227.e0000000119573309CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China ,grid.9227.e0000000119573309National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Hongju Chen
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Xumin Li
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Hongkun Zheng
- grid.410751.6Biomarker Technologies Corporation, Beijing, 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, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China. .,University of Chinese Academy of Sciences, Beijing, China. .,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 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, China. .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China. .,National and Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| |
Collapse
|