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Zhao R, Yang Y, Li S, Chen S, Ding J, Wu Y, Qu M, Di Y. Comparative study of integrated bio-responses in deep-sea and nearshore mussels upon abiotic condition changes: Insight into distinct regulation and adaptation. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106610. [PMID: 38879901 DOI: 10.1016/j.marenvres.2024.106610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/16/2024] [Accepted: 06/12/2024] [Indexed: 06/18/2024]
Abstract
Deep-sea mussels, one of the dominant species in most deep-sea ecosystems, have long been used as model organisms to investigate the adaptations and symbiotic relationships of deep-sea macrofauna under laboratory conditions due to their ability to survive under atmospheric pressure. However, the impact of additional abiotic conditions beyond pressure, such as temperature and light, on their physiological characteristics remains unknown. In this study, deep-sea mussels (Gigantidas platifrons) from cold seep of the South China Sea, along with nearshore mussels (Mytilus coruscus) from the East China Sea, were reared in unfavorable abiotic conditions for up to 8 days. Integrated biochemical indexes including antioxidant defense, immune ability and energy metabolism were investigated in the gill and digestive gland, while cytotoxicity was determined in hemocytes of both types of mussels. The results revealed mild bio-responses in two types of mussels in the laboratory, represented by the effective antioxidant defense with constant total antioxidant capability level and malondialdehyde content. There were also disparate adaptations in deep-sea and nearshore mussels. In deep-sea mussels, significantly increased immune response and energy reservation were observed in gills, together with the elevated cytotoxicity in hemocytes, implying the more severe biological adaptation was required, mainly due to the symbiotic bacteria loss under laboratory conditions. On the contrary, insignificant biological responses were exhibited in nearshore mussels except for the increased energy consumption, indicating the trade-off strategy to use more energy to deal with potential stress. Overall, this comparative study highlights the basal bio-responses of deep-sea and nearshore mussels out of their native environments, providing evidence that short-term culture of both mussels under easily achievable laboratory conditions would not dramatically alter their biological status. This finding will assist in broadening the application of deep-sea mussels as model organism in future research regardless of the specialized research equipment.
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Affiliation(s)
- Ruoxuan Zhao
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Yingli Yang
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Shuimei Li
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Siyu Chen
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Jiawei Ding
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Yusong Wu
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Mengjie Qu
- Ocean College, Zhejiang University, Zhoushan, 316000, China
| | - Yanan Di
- Ocean College, Zhejiang University, Zhoushan, 316000, China.
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Ye LJ, Möller M, Luo YH, Zou JY, Zheng W, Liu J, Li DZ, Gao LM. Variation in gene expression along an elevation gradient of Rhododendron sanguineum var. haemaleum assessed in a comparative transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1133065. [PMID: 37025136 PMCID: PMC10070981 DOI: 10.3389/fpls.2023.1133065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Selection along environmental gradients may play a vital role in driving adaptive evolution. Nevertheless, genomic variation and genetic adaptation along environmental clines remains largely unknown in plants in alpine ecosystems. To close this knowledge gap, we assayed transcriptomic profiles of late flower bud and early leaf bud of Rhododendron sanguineum var. haemaleum from four different elevational belts between 3,000 m and 3,800 m in the Gaoligong Mountains. By comparing differences in gene expression of these samples, a gene co-expression network (WGCNA) was constructed to identify candidate genes related to elevation. We found that the overall gene expression patterns are organ-specific for the flower and leaf. Differentially expressed unigenes were identified in these organs. In flowers, these were mainly related to terpenoid metabolism (RsHMGR, RsTPS), while in leaves mainly related to anthocyanin biosynthesis (RsCHS, RsF3'5'H). Terpenoids are the main components of flower scent (fragrance) likely attracting insects for pollination. In response to fewer pollinators at higher elevation zone, it seems relatively less scent is produced in flower organs to reduce energy consumption. Secondary metabolites in leaves such as anthocyanins determine the plants' alternative adaptive strategy to extreme environments, such as selective pressures of insect herbivory from environmental changes and substrate competition in biosynthesis pathways at high elevations. Our findings indicated that the gene expression profiles generated from flower and leaf organs showed parallel expression shifts but with different functionality, suggesting the existence of flexibility in response strategies of plants exposed to heterogeneous environments across elevational gradients. The genes identified here are likely to be involved in the adaptation of the plants to these varying mountainous environments. This study thus contributes to our understanding of the molecular mechanisms of adaptation in response to environmental change.
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Affiliation(s)
- Lin-Jiang Ye
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Key Laboratory of Plant Resources and Biodiversity of Jiangxi Province, Jingdezhen University, Jingdezhen, Jiangxi, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Michael Möller
- Royal Botanic Garden Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, China
| | - Jia-Yun Zou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wei Zheng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, Yunnan, China
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Wang L, Du M, Wang B, Duan H, Zhang B, Wang D, Li Y, Wang J. Transcriptome analysis of halophyte Nitraria tangutorum reveals multiple mechanisms to enhance salt resistance. Sci Rep 2022; 12:14031. [PMID: 35982183 PMCID: PMC9388663 DOI: 10.1038/s41598-022-17839-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 08/01/2022] [Indexed: 12/05/2022] Open
Abstract
As a typical halophyte, Nitraria tangutorum Bobr. has attracted the interest of many researchers with the excellent salt tolerance. Elucidation of the mechanism of N. tangutorum salinity tolerance will facilitate the genetic improvement of productive plants faced with salinity. To reveal the molecular response to gradually accumulated salt stress in N. tangutorum, RNA-sequencing and analysis of gradually accumulated NaCl treated samples and control samples were performed, and a total of 1419 differentially expressed genes were identified, including 949 down-regulated genes and 470 up-regulated genes. Detailed analysis uncovered that the catabolism of organic compounds mainly based on oxidative phosphorylation genes was up-regulated. Additionally, various antioxidant genes, especially anthocyanin-related genes, were found to help N. tangutorum remove reactive oxygen species. Moreover, the Mitogen activated protein kinase signaling pathway and other signaling pathways co-regulated various salt tolerance activities. Additionally, intracellular ion homeostasis was maintained via regulation of osmotic regulator-related genes, cutin-related genes, and cell elongation-related genes to retain cellular water and reduce ion concentration. In particularly, simultaneous up-regulation in cytoskeleton-related genes, cell wall-related genes, and auxin-related genes, provided evidence of important role of cell expansion in plant salt tolerance. In conclusion, complex regulatory mechanisms modulated by multiple genes might contribute to the salt tolerance by N. tangutorum.
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Affiliation(s)
- Lirong Wang
- Qinghai Provincial Key Laboratory of High-Value Utilization of Characteristic Economic Plants, Qinghai Minzu University, Xining, 810007, China.,Institute of Ecology and Environment of Qinghai-Tibet Plateau, Qinghai Minzu University, Xining, 810007, China
| | - Meng Du
- Qinghai Provincial Key Laboratory of High-Value Utilization of Characteristic Economic Plants, Qinghai Minzu University, Xining, 810007, China
| | - Bo Wang
- College of Forestry, Gansu Agricultural University, Lanzhou, 730000, China
| | - Huirong Duan
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Benyin Zhang
- College of Eco-Environmental Engineering, Qinghai University, Xining, 810016, China
| | - Dong Wang
- Lanzhou Agriculture and Rural Affairs Bureau in Gansu Province, Lanzhou, 730030, China
| | - Yi Li
- College of Forestry, Gansu Agricultural University, Lanzhou, 730000, China.
| | - Jiuli Wang
- Qinghai Provincial Key Laboratory of High-Value Utilization of Characteristic Economic Plants, Qinghai Minzu University, Xining, 810007, China. .,Institute of Ecology and Environment of Qinghai-Tibet Plateau, Qinghai Minzu University, Xining, 810007, China.
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4
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Baratti M, Pinosio S, Gori M, Biricolti S, Chini G, Fratini S, Cannicci S, Caliani I, Oliva M, De Marchi L, Pretti C. Differential gene expression and chemical patterns of an intertidal crab inhabiting a polluted port and an adjacent marine protected area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153463. [PMID: 35101492 DOI: 10.1016/j.scitotenv.2022.153463] [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: 10/15/2021] [Revised: 12/14/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
The acquisition of data to safeguard marine protected areas located close to ports is important in order to develop plans that allow effective protection from pollution as well as sustainable development of the port. The area Secche della Meloria is a Marine Protected Area (MPA-MEL) three miles from Livorno Harbour (LH), which is characterized by a long history of pollution. Here we studied the bioaccumulation and transcriptomic patterns of the marbled crab, Pachygrapsus marmoratus (Fabricius, 1787) (Crustacea; Brachyura, Grapsidae), inhabiting the two selected sites. Results showed that the two crab populations are significantly different in their chemical composition of trace elements and Polyciclic Aromatic Hydrocarbons (PAHs), and gene expression patterns (1280 DEGs). Enrichment analysis indicated that crabs at LH had the highest stress response genes, and they were associated with higher levels of bioaccumulation detected in body tissues. We are confident that the significant differential gene expression profiles observed between crabs, characterized by significant chemical differences, is associated with responses to contaminant exposure.
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Affiliation(s)
- Mariella Baratti
- Institute of Biosciences and Bioresources, IBBR-CNR, Sesto Fiorentino I-50019, Italy.
| | - Sara Pinosio
- Institute of Biosciences and Bioresources, IBBR-CNR, Sesto Fiorentino I-50019, Italy; Institute of Applied Genomics IGA-CNR, Udine I-33100, Italy
| | - Massimo Gori
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Firenze I-50144, Italy
| | - Stefano Biricolti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Firenze I-50144, Italy
| | - Giacomo Chini
- Department of Biology, University of Florence, Sesto Fiorentino I-5001, Italy
| | - Sara Fratini
- Department of Biology, University of Florence, Sesto Fiorentino I-5001, Italy
| | - Stefano Cannicci
- Department of Biology, University of Florence, Sesto Fiorentino I-5001, Italy; The Swire Institute of Marine Science and Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, PR China
| | - Ilaria Caliani
- Department of Physical, Earth and Environmental Sciences, University of Siena, Siena I-53100, Italy
| | - Matteo Oliva
- Interuniversity Consortium of Marine Biology "G. Bacci, CIBM ", Livorno I-57128, Italy
| | - Lucia De Marchi
- Interuniversity Consortium of Marine Biology "G. Bacci, CIBM ", Livorno I-57128, Italy; Departamento de Biologia e CESAM, Universidade de Aveiro, Aveiro 3810-193, Portugal
| | - Carlo Pretti
- Interuniversity Consortium of Marine Biology "G. Bacci, CIBM ", Livorno I-57128, Italy; Department of Veterinary Sciences, University of Pisa, Pisa I-56124, Italy
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5
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Liu J, Zhang D, Zhang L, Wang Z, Shen J. New Insight on Vitality Differences for the Penaeid Shrimp, Fenneropenaeus chinensis, in Low Salinity Environment Through Transcriptomics. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.716018] [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
Excessive rainfall changes salinity in shrimp farming ponds in short period and exerts low salinity stress on the outdoor breeding shrimp under global warming. Fenneropenaeus chinensis can have different performance on vitality in low salinity environments. To reveal mechanisms of vitality difference in shrimp living in low saline environments. This study based on the normal and moribund F. chinensis in 10 ppt salinity environment using high-throughput sequencing identifies 1,429 differentially expressed genes (DEGs), 586 of which are upregulated, while 843 of which are downregulated in the normal group (FCN10) as compared to the moribund group (FCM10). Meanwhile, another transcriptomic analysis is conducted on the normal and moribund shrimp from 25 ppt (FCN25 vs. FCM25) salinity environment as the control, in which 1,311 DEGs (upregulated: 327 genes, downregulated: 984 genes) are identified. In this study, intersective pathways, GO (Gene Ontology) categories and DEGs from the two groups of comparative transcriptome are investigated. The two intersective pathways (Metabolism of xenobiotics by cytochrome P450, Pentose, and glucuronate interconversions) significantly enriched by DEGs are related to detoxification. In these two pathways, there is one vitality regulation-related gene (VRRG), the Dhdh (dihydrodiol dehydrogenase), which is upregulated in both the groups of FCN10 and FCN25 as compared to the groups of FCM10 and FCM25, respectively. Similarly, in the 25 top intersective GO categories, four VRRGs are revealed. Three of them are upregulated (Itgbl, kielin/chordin-like protein, Slc2a8, solute carrier family 2, facilitated glucose transporter member 8-like protein and Cyp3a30, cytochrome P450 3A30-like protein); one of them is downregulated (Slc6a9, sodium-dependent nutrient amino acid transporter 1-like protein isoform X2). These GO categories are related to transmembrane transporter activity of substance, enzyme inhibitor activity, monooxygenase activity. RT-qPCR analysis further verifies the VRRGs. The study gives new insight into understanding the vitality differences for F. chinensis, in low salinity environment. The pathways and DEGs in response to low salinity stress in modulating the vitality of F. chinensis that could serve as tools in future genetic studies and molecular breeding.
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6
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Gao Z, Yao L, Pan L. Gene expression and functional analysis of different heat shock protein (HSPs) in Ruditapes philippinarum under BaP stress. Comp Biochem Physiol C Toxicol Pharmacol 2022; 251:109194. [PMID: 34619354 DOI: 10.1016/j.cbpc.2021.109194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/02/2021] [Accepted: 09/19/2021] [Indexed: 12/21/2022]
Abstract
Heat shock proteins (HSPs) are a class of highly conserved proteins which can protect cells against various types of stress. However, little information on the mechanism involved in the organic contaminants stress response of HSPs is available, especially in marine invertebrates. The present study was conducted to evaluate the responses of HSPs in clams (Ruditapes philippinarum) under Benzo[a] pyrene (BaP) exposure. The clams were exposed to BaP (concentrations: 0, 0.1, 1, 10 μg/L) for 15 days. 6 HSPs mRNA were classified, and the results of tissue distribution indicated that 4 HSPs gene expressed most in the digestive glands. The transcription level of 6 HSPs (HSP22-1, HSP22-2, HSP40A, HSP60, HSP70, HSP90) genes and the aryl hydrocarbon receptor signaling pathway-related genes, and detoxification system-related enzymes activities were analyzed at 0, 1, 3, 6, 10 and 15 days. The activities of phase II detoxification metabolic enzymes and signaling pathway related genes in clams were severely affected by BaP stress and presented significant difference. Our result suggested that HSPs were produced in the presence of BaP and participated in the process of detoxification metabolism to a certain extent. Additionally, the transcription of HSP40A gene may be used as a potential biomarker of BaP exposure due to its evident concentration- and time-dependent expression pattern. Overall, the study investigated the classification of HSPs in R. philippinarum, provided information about the expression profiles of various HSPs after BaP exposure and broadened the understanding mechanism of HSPs in detoxification defense system under PAHs stress in mollusks.
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Affiliation(s)
- Zhongyuan Gao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China
| | - Linlin Yao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China.
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7
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Ip JCH, Leung PTY, Qiu JW, Lam PKS, Wong CKC, Chan LL, Leung KMY. Transcriptomics reveal triphenyltin-induced molecular toxicity in the marine mussel Perna viridis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148040. [PMID: 34091345 DOI: 10.1016/j.scitotenv.2021.148040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Triphenyltin (TPT) is widely used as an active ingredient in antifouling paints and fungicides, and continuous release of this highly toxic endocrine disruptor has caused serious pollution to coastal marine ecosystems and organisms worldwide. Using bioassays and transcriptome sequencing, this study comprehensively investigated the molecular toxicity of TPT chloride (TPTCl) to the marine mussel Perna viridis which is a commercially important species and a common biomonitor for marine pollution in Southeast Asia. Our results indicated that TPTCl was highly toxic to adult P. viridis, with a 96-h LC10 and a 96-h EC10 at 18.7 μg/L and 2.7 μg/L, respectively. A 21-day chronic exposure to 2.7 μg/L TPTCl revealed a strong bioaccumulation of TPT in gills (up to 36.48 μg/g dry weight) and hepatopancreas (71.19 μg/g dry weight) of P. viridis. Transcriptome analysis indicated a time course dependent gene expression pattern in both gills and hepatopancreas. Higher numbers of differentially expressed genes were detected at Day 21 (gills: 1686 genes; hepatopancreas: 1450 genes) and at Day 28 (gills: 628 genes; hepatopancreas: 238 genes) when compared with that at Day 7 (gills: 104 genes, hepatopancreas: 112 genes). Exposure to TPT strongly impaired the endocrine system through targeting on nuclear receptors and putative steroid metabolic genes. Moreover, TPT widely disrupted cellular functions, including lipid metabolism, xenobiotic detoxification, immune response and endoplasmic-reticulum-associated degradation expression, which might have caused the bioaccumulation of TPT in the tissues and aggregation of peptides and proteins in cells that further activated the apoptosis process in P. viridis. Overall, this study has advanced our understanding on both ecotoxicity and molecular toxic mechanisms of TPT to marine mussels, and contributed empirical toxicity data for risk assessment and management of TPT contamination.
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Affiliation(s)
- Jack Chi-Ho Ip
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China; The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China; Department of Biology and Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Kowloon, Hong Kong, China
| | - Priscilla T Y Leung
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Jian-Wen Qiu
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China; Department of Biology and Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Kowloon, Hong Kong, China
| | - Paul K S Lam
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China; Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Hong Kong, China
| | - Chris K C Wong
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China; Department of Biology and Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong Baptist University, Kowloon, Hong Kong, China
| | - Leo L Chan
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Kenneth M Y Leung
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China; Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Hong Kong, China.
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Comparative Genomics Reveals 13 Different Isoforms of Mytimycins (A-M) in Mytilus galloprovincialis. Int J Mol Sci 2021; 22:ijms22063235. [PMID: 33810127 PMCID: PMC8004829 DOI: 10.3390/ijms22063235] [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: 02/01/2021] [Revised: 03/12/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022] Open
Abstract
Mytimycins are cysteine-rich antimicrobial peptides that show antifungal properties. These peptides are part of the immune network that constitutes the defense system of the Mediterranean mussel (Mytilus galloprovincialis). The immune system of mussels has been increasingly studied in the last decade due to its great efficiency, since these molluscs, particularly resistant to adverse conditions and pathogens, are present all over the world, being considered as an invasive species. The recent sequencing of the mussel genome has greatly simplified the genetic study of some of its immune genes. In the present work, we describe a total of 106 different mytimycin variants in 16 individual mussel genomes. The 13 highly supported mytimycin clusters (A–M) identified with phylogenetic inference were found to be subject to the presence/absence variation, a widespread phenomenon in mussels. We also identified a block of conserved residues evolving under purifying selection, which may indicate the “functional core” of the mature peptide, and a conserved set of 10 invariable plus 6 accessory cysteines which constitute a plastic disulfide array. Finally, we extended the taxonomic range of distribution of mytimycins among Mytilida, identifying novel sequences in M. coruscus, M. californianus, P. viridis, L. fortunei, M. philippinarum, M. modiolus, and P. purpuratus.
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Dou M, Jiao YH, Zheng JW, Zhang G, Li HY, Liu JS, Yang WD. De novo transcriptome analysis of the mussel Perna viridis after exposure to the toxic dinoflagellate Prorocentrum lima. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 192:110265. [PMID: 32045784 DOI: 10.1016/j.ecoenv.2020.110265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/23/2020] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
Diarrheic shellfish poisoning (DSP) toxins are produced by harmful microalgae and accumulate in bivalve mollusks, causing various toxicity. These toxic effects appear to abate with increasing DSP concentration and longer exposure time, however, the underlying mechanisms remain unclear. To explore the underlying molecular mechanisms, de novo transcriptome analysis of the digestive gland of Perna viridis was performed after Prorocentrum lima exposure. RNA-seq analysis showed that 1886 and 237 genes were up- and down-regulated, respectively after 6 h exposure to P. lima, while 265 genes were up-regulated and 217 genes were down-regulated after 96 h compared to the control. These differentially expressed genes mainly involved in Nrf2 signing pathways, immune stress, apoptosis and cytoskeleton, etc. Combined with qPCR results, we speculated that the mussel P. viridis might mainly rely on glutathione S-transferase (GST) and ABC transporters to counteract DSP toxins during short-term exposure. However, longer exposure of P. lima could activate the Nrf2 signaling pathway and inhibitors of apoptosis protein (IAP), which in turn reduced the damage of DSP toxins to the mussel. DSP toxins could induce cytoskeleton destabilization and had some negative impact on the immune system of bivalves. Collectively, our findings uncovered the crucial molecular mechanisms and the regulatory metabolic nodes that underpin the defense mechanism of bivalves against DSP toxins and also advanced our current understanding of bivalve defense mechanisms.
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Affiliation(s)
- Min Dou
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, China.
| | - Yu-Hu Jiao
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, China
| | - Jian-Wei Zheng
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Hong-Ye Li
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, China
| | - Jie-Sheng Liu
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, China
| | - Wei-Dong Yang
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, China.
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10
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López-Landavery EA, Amador-Cano G, Alejandri N, Ramirez-Álvarez N, Montelongo I, Díaz F, Galindo-Sánchez CE. Transcriptomic response and hydrocarbon accumulation in the eastern oyster (Crassostrea virginica) exposed to crude oil. Comp Biochem Physiol C Toxicol Pharmacol 2019; 225:108571. [PMID: 31306803 DOI: 10.1016/j.cbpc.2019.108571] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022]
Abstract
The adverse effect of crude oil on marine invertebrates is well known. To have a better understanding of its effects on marine invertebrates, Crassostrea virginica was exposed to different concentrations (50, 100 and 200 μg/L) of a mixture of super-light and light crude oil for two weeks, evaluating the transcriptomic response of the digestive gland using RNA-Seq and their accumulation in soft tissues. A total of 33,469,374 reads were assembled, which resulted in 61,356 genome assemblies ('Genes'). Trinotate was used for transcript annotation. At the end of this process, 86,409 transcripts were maintained, comprising a broad set of enzymes from xenobiotics metabolism, oxidative stress, stress and immune responses, and energetic metabolism. The enrichment analysis revealed a change in biological processes and molecular functions, finding from 100 to 200 μg/L. Moreover, the differential gene expression analysis showed a dose-dependent transcriptional response, generally up to 100 μg/L and in some cases up to 200 μg/L, which suggested that oysters' response decreased after 100 μg/L; the analysis of crude oil presence in soft tissues indicated that C. virginica is a suitable candidate for ecotoxicology. Finally, these results should contribute to expanding current genomic resources for C. virginica. Furthermore, they will help to develop new studies in aquatic toxicology focused on knowledge in depth of metabolic pathways, jointly with other approaches (such as proteomics) to allow obtaining a complete idea about the eastern oyster response to crude oil.
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Affiliation(s)
- Edgar A López-Landavery
- Department of Marine Biotechnology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, BC, Mexico
| | - Gerardo Amador-Cano
- Universidad Tecnológica del Mar de Tamaulipas (UTMART), La Pesca, Soto La Marina, Tamaulipas, Mexico
| | - Naholi Alejandri
- Department of Marine Biotechnology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, BC, Mexico
| | - Nancy Ramirez-Álvarez
- Instituto de Investigaciones Oceanológicas (IIO), Universidad Autónoma de Baja California (UABC), Ensenada, BC, Mexico
| | - Isidro Montelongo
- Universidad Tecnológica del Mar de Tamaulipas (UTMART), La Pesca, Soto La Marina, Tamaulipas, Mexico
| | - Fernando Díaz
- Department of Marine Biotechnology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, BC, Mexico
| | - Clara E Galindo-Sánchez
- Department of Marine Biotechnology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, BC, Mexico.
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11
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Zhang X, Huang H, He Y, Ruan Z, You X, Li W, Wen B, Lu Z, Liu B, Deng X, Shi Q. High-throughput identification of heavy metal binding proteins from the byssus of chinese green mussel (Perna viridis) by combination of transcriptome and proteome sequencing. PLoS One 2019; 14:e0216605. [PMID: 31071150 PMCID: PMC6508894 DOI: 10.1371/journal.pone.0216605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/24/2019] [Indexed: 12/27/2022] Open
Abstract
The Byssus, which is derived from the foot gland of mussels, has been proved to bind heavy metals effectively, but few studies have focused on the molecular mechanisms behind the accumulation of heavy metals by the byssus. In this study, we integrated high-throughput transcriptome and proteome sequencing to construct a comprehensive protein database for the byssus of Chinese green mussel (Perna viridis), aiming at providing novel insights into the molecular mechanisms by which the byssus binds to heavy metals. Illumina transcriptome sequencing generated a total of 55,670,668 reads. After filtration, we obtained 53,047,718 clean reads and subjected them to de novo assembly using Trinity software. Finally, we annotated 73,264 unigenes and predicted a total of 34,298 protein coding sequences. Moreover, byssal samples were analyzed by proteome sequencing, with the translated protein database from the foot transcriptome as the reference for further prediction of byssal proteins. We eventually determined 187 protein sequences in the byssus, of which 181 proteins are reported for the first time. Interestingly, we observed that many of these byssal proteins are rich in histidine or cysteine residues, which may contribute to the byssal accumulation of heavy metals. Finally, we picked one representative protein, Pvfp-5-1, for recombinant protein synthesis and experimental verification of its efficient binding to cadmium (Cd2+) ions.
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Affiliation(s)
- Xinhui Zhang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Huiwei Huang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | | | - Zhiqiang Ruan
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | | | - Bo Wen
- BGI-Shenzhen, BGI, Shenzhen, China
| | - Zizheng Lu
- Shenzhen Horus Marine Technology Co. Ltd., Shenzhen, China
| | - Bing Liu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xu Deng
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- * E-mail: (QS); (XD)
| | - Qiong Shi
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
- Laboratory of Aquatic Bioinformatics, BGI-Zhenjiang Institute of Hydrobiology, BGI Marine, BGI, Zhenjiang, China
- * E-mail: (QS); (XD)
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12
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Li Y, Zhang L, Li R, Zhang M, Li Y, Wang H, Wang S, Bao Z. Systematic identification and validation of the reference genes from 60 RNA-Seq libraries in the scallop Mizuhopecten yessoensis. BMC Genomics 2019; 20:288. [PMID: 30975074 PMCID: PMC6460854 DOI: 10.1186/s12864-019-5661-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/31/2019] [Indexed: 12/15/2022] Open
Abstract
Background Reverse transcription quantitative PCR (RT-qPCR) is widely used for gene expression analysis in various organisms. Its accuracy largely relies on the stability of reference genes, making reference gene selection a vital step in RT-qPCR experiments. However, previous studies in mollusks only focused on the reference genes widely used in vertebrates. Results In this study, we conducted the transcriptome-wide identification of reference genes in the bivalve mollusk Mizuhopecten yessoensis based on 60 transcriptomes covering early development, adult tissues and gonadal development. A total of 964, 1210 and 2097 candidate reference genes were identified, respectively, resulting in a core set of 568 genes. Functional enrichment analysis showed that these genes are significantly overrepresented in Gene Ontology (GO) terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to ribosomes, energy production, etc. Six genes (RS23, EF1A, NDUS4, SELR1, EIF3F, and OLA1) were selected from the candidate genes for RT-qPCR validation, together with 6 commonly used reference genes (ACT, CYTC, HEL, EF1B, GAPDH and RPL16). Stability analyses using geNorm, NormFinder and the comparative delta-Ct method revealed that the new candidate reference genes are more stable than the traditionally used genes, and ACT and CYTC are not recommended under either of the three circumstances. There was a significant correlation between the Ct of RT-qPCR and the log2(TPM) of RNA-Seq data (Ct = − 0.94 log2(TPM) + 29.67, R2 = 0.73), making it easy to estimate the Ct values from transcriptome data prior to RT-qPCR experiments. Conclusion Our study represents the first transcriptome-wide identification of reference genes for early development, adult tissues, and gonadal development in the Yesso scallop and will benefit gene expression studies in other bivalve mollusks. Electronic supplementary material The online version of this article (10.1186/s12864-019-5661-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yajuan Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Ruojiao Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Meiwei Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Yangping Li
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Hao Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, 5 Yushan Road, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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13
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Briones C, Nuñez JJ, Pérez M, Espinoza-Rojas D, Molina-Quiroz C, Guiñez R. De novo male gonad transcriptome draft for the marine mussel Perumytilus purpuratus with a focus on its reproductive-related proteins. J Genomics 2018; 6:127-132. [PMID: 30510598 PMCID: PMC6275399 DOI: 10.7150/jgen.27864] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/04/2018] [Indexed: 12/17/2022] Open
Abstract
Perumytilus purpuratus is a marine mussel considered a bioengineer species with a broad distribution in the Pacific and Atlantic coast of South America. Studies have shown two geographically and genetically differentiated subpopulations at molecular level and in sperm morphological traits. To open avenues for molecular research on P. purpuratus, a global de novo transcriptome from gonadal tissue of mature males was sequenced using the Illumina platform. From a total of 126.38 million reads, 37,765 transcripts were successfully annotated. BUSCO analysis determined a level of 89% completeness for the assembled transcriptome. The functional gene ontology (GO) annotation indicated that, in terms of abundance, the transcripts related with molecular function were the most represented, followed by those related with biological process and cellular components. Additionally, a subset of GO annotations generated using the "sperm" term resulted in a total of 1,294 sequences where the biological process category was the more represented, with transcripts strongly associated to sperm-processes required for fertilization, and with processes where the sperm-egg interaction could be implicated. Our work will contribute to the evolutionary understanding of the molecular mechanisms related to tissue-specific functions. This work reports the first male gonad transcriptome for the mussel P. purpuratus, generating a useful transcriptomic resource for this species and other closely related mytilids.
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Affiliation(s)
- Carolina Briones
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - José J Nuñez
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Montse Pérez
- Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, 36200 Vigo, España
| | | | | | - Ricardo Guiñez
- Instituto de Ciencias Naturales Alexander von Humboldt, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Casilla 170, Antofagasta, Chile
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14
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Chavan P, Kumar R, Joshi H, Kirubagaran R, Venugopalan VP. Multimarker study of the effects of antifouling biocide on benthic organisms: results using Perna viridis as candidate species. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:20407-20418. [PMID: 28685340 DOI: 10.1007/s11356-017-9607-z] [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: 03/28/2017] [Accepted: 06/21/2017] [Indexed: 06/07/2023]
Abstract
Toxic effects of continuous low dose application of the antifouling biocide chlorine on marine benthic organisms were monitored using transplanted green mussels (Perna viridis) and a suite of biomarkers. Caged mussels were deployed in chlorinated and non-chlorinated sections of the cooling system of an operating electric power plant. Biomarkers indicative of general stress, oxidative stress (superoxide dismutase and catalase), and DNA integrity, along with expression of stress proteins, were studied to assess the effects. Deterioration in condition index with corresponding increase in DNA strand breaks was indicative of chlorine stress. Superoxide dismutase enzyme did not show any particular trend, but catalase activity was high during the initial days of exposure at the chlorinated site; later, it became almost equal to that at the control site. Similarly, expressions of stress proteins (HSP60, HSP70, HSP22, GSTS1, and CYP4) showed bell-shaped pattern during the period of study. Positive correlation among the endpoints indicated the utility of the multimarker approach to monitor the effects of continuous low dose chlorination on mussels.
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Affiliation(s)
- Pooja Chavan
- Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, Bhabha Atomic Research Centre, Kalpakkam, 603 102, India
| | - Rajesh Kumar
- Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, Bhabha Atomic Research Centre, Kalpakkam, 603 102, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400 094, India
| | - Hiren Joshi
- Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, Bhabha Atomic Research Centre, Kalpakkam, 603 102, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400 094, India
| | - Ramalingam Kirubagaran
- Marine Biotechnology, ESSO-National Institute of Ocean Technology, Pallikaranai, Chennai, 600 100, India
| | - Vayalam P Venugopalan
- Biofouling and Biofilm Processes Section, Water and Steam Chemistry Division, Bhabha Atomic Research Centre, Kalpakkam, 603 102, India.
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400 094, India.
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15
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Tang W, Xiao Y, Li G, Zheng X, Yin Y, Wang L, Zhu Y. Analysis of digital gene expression profiling in the gonad of male silkworms (Bombyx mori) under fluoride stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 153:127-134. [PMID: 29425843 DOI: 10.1016/j.ecoenv.2018.01.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 01/09/2018] [Accepted: 01/11/2018] [Indexed: 06/08/2023]
Abstract
Fluorine is an essential element, but excessive fluoride can cause serious effects on the respiratory, digestive, and reproductive systems. Fluorine has been suggested to cause reproductive toxicity in vertebrates, but its potential to reproductively affect invertebrates remains unknown. In the present study, the lepidopteran model insect Bombyx mori was used to assess the reproductive toxicity of NaF. The underlying molecular mechanisms were explored by RNA sequencing, and we investigated the testes transcriptomic profile of B. mori treated with NaF via a digital gene expression (DGE) analysis. Among 520 candidate genes, 297 and 223 were identified as significantly upregulated or downregulated, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were carried out on all genes to determine their biological functions and associated processes. The results indicated that numerous differentially expressed genes are involved in the stress response, detoxification, antibacterial, transport, oxidative phosphorylation, and ribosome. The reliability of the data was confirmed by a quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The changed Glutathione S-transferase (GST) activity and glutathione (GSH) content in the NaF-treated groups were increased and reduced respectively. This study reveals that using RNA-sequencing for the transcriptome profiling of B. mori testes can lead to better comprehension of the male reproductive toxicity effects of NaF. Furthermore, we expect that these results will aid future molecular studies on the reproductive toxicity of NaF in other species.
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Affiliation(s)
- Wenchao Tang
- School of Biotechnology, Southwest University, Chongqing 400716, China
| | - Yuanyuan Xiao
- School of Life Sciences, Southwest University, Chongqing 400716, China
| | - Guannan Li
- School of Biotechnology, Southwest University, Chongqing 400716, China
| | - Xi Zheng
- School of Biotechnology, Southwest University, Chongqing 400716, China
| | - Yaru Yin
- School of Biotechnology, Southwest University, Chongqing 400716, China
| | - Lingyan Wang
- School of Biotechnology, Southwest University, Chongqing 400716, China
| | - Yong Zhu
- School of Biotechnology, Southwest University, Chongqing 400716, China.
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16
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Zhang L, Sun W, Zhang Z, Chen H, Jia X, Cai W. Gender-specific metabolic responses in gonad of mussel Perna viridis to triazophos. MARINE POLLUTION BULLETIN 2017; 123:39-46. [PMID: 28938996 DOI: 10.1016/j.marpolbul.2017.09.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/08/2017] [Accepted: 09/14/2017] [Indexed: 06/07/2023]
Abstract
Triazophos, as a lipophilic organophosphate pesticide, displays higher bioaccumulation in the gonads of shellfish. To study the reproductive toxicity of triazophos, we applied metabolomics to characterize the gender-specific metabolic responses in mussel Perna viridis exposed to triazophos. Metabolites were differently altered by triazophos in ovaries of mussel at different concentrations and time intervals, while basically similar metabolic response patterns were observed in male mussels at the two tested concentrations after exposure for 24 and 48h. The significant changes of metabolites in ovaries of mussel exhibited the disturbances in energy metabolism and osmotic regulation, while in male samples triazophos only affected the energy metabolism. Moreover, glycine, sn-glycero-3-phosphocholine, ethanol, aspartate, etc. exhibited consistent variation tendency in both male and female individuals. While the changes of homarine, betaine, taurine, hypotaurine, malonate, β-alanine, succinate, and choline showed obviously gender-specific responses. Overall, this study confirmed the gender-specific responses in gonad of P. viridis to triazophos exposure.
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Affiliation(s)
- Linbao Zhang
- Scientific Observing and Experimental Station of South China Sea Fishery Resources & Environments, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China; Key Laboratory of Fishery Ecology and Environment, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China.
| | - Wei Sun
- Scientific Observing and Experimental Station of South China Sea Fishery Resources & Environments, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China; Key Laboratory of Fishery Ecology and Environment, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Zhe Zhang
- Scientific Observing and Experimental Station of South China Sea Fishery Resources & Environments, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China; Key Laboratory of Fishery Ecology and Environment, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Haigang Chen
- Scientific Observing and Experimental Station of South China Sea Fishery Resources & Environments, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China; Key Laboratory of Fishery Ecology and Environment, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Xiaoping Jia
- Scientific Observing and Experimental Station of South China Sea Fishery Resources & Environments, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China; Key Laboratory of Fishery Ecology and Environment, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Wengui Cai
- Scientific Observing and Experimental Station of South China Sea Fishery Resources & Environments, Ministry of Agriculture, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China; Key Laboratory of Fishery Ecology and Environment, Chinese Academy of Fishery Sciences, Guangzhou 510300, Guangdong Province, PR China; South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China.
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17
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Zheng P, Wang M, Li C, Sun X, Wang X, Sun Y, Sun S. Insights into deep-sea adaptations and host-symbiont interactions: A comparative transcriptome study on Bathymodiolus
mussels and their coastal relatives. Mol Ecol 2017; 26:5133-5148. [DOI: 10.1111/mec.14160] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Ping Zheng
- Key Laboratory of Marine Ecology and Environmental Sciences; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- University of Chinese Academy of Sciences; Beijing China
| | - Minxiao Wang
- Key Laboratory of Marine Ecology and Environmental Sciences; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- Deep Sea Research Center; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
| | - Chaolun Li
- Key Laboratory of Marine Ecology and Environmental Sciences; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- University of Chinese Academy of Sciences; Beijing China
- Deep Sea Research Center; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- Laboratory for Marine Ecology and Environmental Science; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
| | | | - Xiaocheng Wang
- Key Laboratory of Marine Ecology and Environmental Sciences; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- University of Chinese Academy of Sciences; Beijing China
| | - Yan Sun
- Key Laboratory of Marine Ecology and Environmental Sciences; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
| | - Song Sun
- Key Laboratory of Marine Ecology and Environmental Sciences; Institute of Oceanology; Chinese Academy of Sciences; Qingdao China
- University of Chinese Academy of Sciences; Beijing China
- Laboratory for Marine Ecology and Environmental Science; Qingdao National Laboratory for Marine Science and Technology; Qingdao China
- Jiaozhou Bay Marine Ecosystem Research Station; Chinese Academy of Sciences; Qingdao China
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18
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Cappello T, Maisano M, Mauceri A, Fasulo S. 1H NMR-based metabolomics investigation on the effects of petrochemical contamination in posterior adductor muscles of caged mussel Mytilus galloprovincialis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 142:417-422. [PMID: 28454054 DOI: 10.1016/j.ecoenv.2017.04.040] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/13/2017] [Accepted: 04/17/2017] [Indexed: 06/07/2023]
Abstract
Environmental metabolomics is a high-throughout approach that provides a snapshot of the metabolic status of an organism. In order to elucidate the biological effects of petrochemical contamination on aquatic invertebrates, mussels Mytilus galloprovincialis were caged at the "Augusta-Melilli-Priolo" petrochemical area and Brucoli (Sicily, south Italy), chosen as the reference site. After confirming the elevated concentrations of polycyclic aromatic hydrocarbons (PAHs) and mercury (Hg) in Augusta sediments in our previous work (Maisano et al., 2016a), herein an environmental metabolomics approach based on protonic nuclear magnetic resonance (1H NMR), coupled with chemometrics, was applied on the mussel posterior adductor muscle (PAM), the main muscular system in bivalve molluscs. Amino acids, osmolytes, energy storage compounds, tricarboxylic acid cycle intermediates, and nucleotides, were found in PAM NMR spectra. Principal Component Analysis (PCA) indicated that mussels caged at the polluted site clustered separately from mussels from the control area, suggesting a clear differentiation between their metabolic profiles. Specifically, disorders in energy metabolism, alterations in amino acids metabolism, and disturbance in the osmoregulatory processes were observed in mussel PAM. Overall, findings from this work demonstrated the usefulness of applying an active biomonitoring strategy for environmental risk assessment, and the effectiveness of metabolomics in elucidating changes in metabolic pathways of aquatic organisms caged at sites differentially contaminated, and thus its suitability to be applied in ecotoxicological studies.
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Affiliation(s)
- Tiziana Cappello
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy.
| | - Maria Maisano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Angela Mauceri
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Salvatore Fasulo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
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Zhang X, Ruan Z, You X, Wang J, Chen J, Peng C, Shi Q. De novo assembly and comparative transcriptome analysis of the foot from Chinese green mussel (Perna viridis) in response to cadmium stimulation. PLoS One 2017; 12:e0176677. [PMID: 28520756 PMCID: PMC5435178 DOI: 10.1371/journal.pone.0176677] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/14/2017] [Indexed: 12/12/2022] Open
Abstract
The Chinese green mussel, Perna viridis, is a marine bivalve with important economic values as well as biomonitoring roles for aquatic pollution. Byssus, secreted by the foot gland, has been proved to bind heavy metals effectively. In this study, using the RNA sequencing technology, we performed comparative transcriptomic analysis on the mussel feet with or without inducing by cadmium (Cd). Our current work is aiming at providing insights into the molecular mechanisms of byssus binding to heavy metal ions. The transcriptome sequencing generated a total of 26.13-Gb raw data. After a careful assembly of clean data, we obtained a primary set of 105,127 unigenes, in which 32,268 unigenes were annotated. Based on the expression profiles, we identified 9,048 differentially expressed genes (DEGs) between Cd treatment (50 or 100 μg/L) at 48 h and the control, suggesting an extensive transcriptome response of the mussels during the Cd stimulation. Moreover, we observed that the expression levels of 54 byssus protein coding genes increased significantly after the 48-h Cd stimulation. In addition, 16 critical byssus protein coding genes were picked for profiling by quantitative real-time PCR (qRT-PCR). Finally, we reached a primary conclusion that high content of tyrosine (Tyr), cysteine (Cys), histidine (His) residues or the special motif plays an important role in the accumulation of heavy metals in byssus. We also proposed an interesting model for the confirmed byssal Cd accumulation, in which biosynthesis of byssus proteins may play simultaneously critical roles since their transcription levels were significantly elevated.
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Affiliation(s)
- Xinhui Zhang
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Fisheries, BGI, Shenzhen, China
| | - Zhiqiang Ruan
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Fisheries, BGI, Shenzhen, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Fisheries, BGI, Shenzhen, China
| | | | - Jieming Chen
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Fisheries, BGI, Shenzhen, China
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Fisheries, BGI, Shenzhen, China
| | - Qiong Shi
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Fisheries, BGI, Shenzhen, China
- * E-mail:
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Ubrihien RP, Ezaz T, Taylor AM, Stevens MM, Krikowa F, Foster S, Maher WA. The response of Isidorella newcombi to copper exposure: Using an integrated biological framework to interpret transcriptomic responses from RNA-seq analysis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 185:183-192. [PMID: 28236764 DOI: 10.1016/j.aquatox.2017.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/11/2017] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
This study describes the transcriptomic response of the Australian endemic freshwater gastropod Isidorella newcombi exposed to 80±1μg/L of copper for 3days. Analysis of copper tissue concentration, lysosomal membrane destabilisation and RNA-seq were conducted. Copper tissue concentrations confirmed that copper was bioaccumulated by the snails. Increased lysosomal membrane destabilisation in the copper-exposed snails indicated that the snails were stressed as a result of the exposure. Both copper tissue concentrations and lysosomal destabilisation were significantly greater in snails exposed to copper. In order to interpret the RNA-seq data from an ecotoxicological perspective an integrated biological response model was developed that grouped transcriptomic responses into those associated with copper transport and storage, survival mechanisms and cell death. A conceptual model of expected transcriptomic changes resulting from the copper exposure was developed as a basis to assess transcriptomic responses. Transcriptomic changes were evident at all the three levels of the integrated biological response model. Despite lacking statistical significance, increased expression of the gene encoding copper transporting ATPase provided an indication of increased internal transport of copper. Increased expression of genes associated with endocytosis are associated with increased transport of copper to the lysosome for storage in a detoxified form. Survival mechanisms included metabolic depression and processes associated with cellular repair and recycling. There was transcriptomic evidence of increased cell death by apoptosis in the copper-exposed organisms. Increased apoptosis is supported by the increase in lysosomal membrane destabilisation in the copper-exposed snails. Transcriptomic changes relating to apoptosis, phagocytosis, protein degradation and the lysosome were evident and these processes can be linked to the degradation of post-apoptotic debris. The study identified contaminant specific transcriptomic markers as well as markers of general stress. From an ecotoxicological perspective, the use of a framework to group transcriptomic responses into those associated with copper transport, survival and cell death assisted with the complex process of interpretation of RNA-seq data. The broad adoption of such a framework in ecotoxicology studies would assist in comparison between studies and the identification of reliable transcriptomic markers of contaminant exposure and response.
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Affiliation(s)
- Rodney P Ubrihien
- Ecochemistry Laboratory, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
| | - Tariq Ezaz
- Ecochemistry Laboratory, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
| | - Anne M Taylor
- Ecochemistry Laboratory, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
| | - Mark M Stevens
- NSW Department of Primary Industries, Yanco Agricultural Institute, Private Mail Bag, Yanco, NSW, 2703, Australia; Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Australia.
| | - Frank Krikowa
- Ecochemistry Laboratory, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
| | - Simon Foster
- Ecochemistry Laboratory, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
| | - William A Maher
- Ecochemistry Laboratory, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
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Jiang F, Yue X, Wang H, Liu B. Transcriptome profiles of the clam Meretrix petechialis hepatopancreas in response to Vibrio infection. FISH & SHELLFISH IMMUNOLOGY 2017; 62:175-183. [PMID: 28110034 DOI: 10.1016/j.fsi.2017.01.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/23/2016] [Accepted: 01/17/2017] [Indexed: 05/27/2023]
Abstract
Microbial diseases have received much attention due to their enormous destruction of aquaculture, and Vibrio parahaemolyticus is one of the main pathogens that cause bacterial disease in the clam Meretrix petechialis. To better understand the molecular mechanisms of the immune response to Vibrio in M. petechialis, RNA-Seq was applied to explore global expression changes of hepatopancreas from this clam after Vibrio challenge. There were 199,318,966 clean reads obtained by Illumina sequencing, which were further assembled into 214,577 transcripts, and then 147,255 unigenes with an N50 of 1393 bp were identified. Gene ontology (GO) analysis revealed 21 biological process subcategories, 15 cellular component subcategories and 12 molecular function subcategories. A total of 8358 unigenes were mapped onto 267 biological signaling pathways by KEGG, among which there were 16 pathways related to the immune system. In total, 206 differentially expressed genes (DEGs) were identified, including 113 up-regulated unigenes and 93 down-regulated unigenes. In these DEGs, 96 DEGs were annotated in at least one database, accounting for 46.60% of all significant DEGs. To validate the transcriptome dataset, 15 DEGs were selected for real-time qPCR confirmation and the results showed that expression patterns of 13 genes (86.7%) agreed well with the RNA-Seq analysis. Fourteen of the 206 DEGs were annotated to be immune-related genes, and we examined the expression patterns of four immune-related DEGs using clams post immersion challenge. This study enriched the M. petechialis transcriptome database and provided insight into the immune response of M. petechialis against Vibrio infection.
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Affiliation(s)
- Fengjuan Jiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Yue
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Hongxia Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Baozhong Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266000, Qingdao, China.
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Yeung JWY, Zhou GJ, Leung KMY. Sub-lethal effects of cadmium and copper on RNA/DNA ratio and energy reserves in the green-lipped mussel Perna viridis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 132:59-67. [PMID: 27262215 DOI: 10.1016/j.ecoenv.2016.05.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 06/05/2023]
Abstract
This study aims to test if RNA/DNA ratio and various energy reserve parameters (i.e., glycogen, lipid, protein content and total energy reserves) are sensitive biomarkers for indicating stresses induced by metal contaminants in the green-lipped mussel Perna viridis, a common organism for biomonitoring in Southeast Asia. This study was, therefore, designed to examine the effects of cadmium (Cd) and copper (Cu) on these potential biomarkers in two major energy storage tissues, adductor muscle (AM) and hepatopancreas (HP), of P. viridis after sub-lethal exposure to either metal for 10 days. The results showed that neither Cd nor Cu treatments affected the RNA/DNA ratio, glycogen and protein contents in AM and HP. As the most sensitive biomarker in P. viridis, the total lipid content in both AM and HP was significantly decreased in the treatment of 5μg Cu/L and 0.01-0.1μgCd/L, respectively. However, soft-tissue body burdens of Cu or Cd did not significantly correlate with each of the four biomarkers regardless of the tissue type. In addition, AM generally stored more glycogen than HP, whereas HP stored more lipids than AM. We proposed that multiple biomarkers may be employed as an integrated diagnostic tool for monitoring the health condition of the mussels.
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Affiliation(s)
- Jamius W Y Yeung
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Guang-Jie Zhou
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Kenneth M Y Leung
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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23
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Ip JCH, Leung PTY, Ho KKY, Qiu JW, Leung KMY. De novo transcriptome assembly of the marine gastropod Reishia clavigera for supporting toxic mechanism studies. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 178:39-48. [PMID: 27450239 DOI: 10.1016/j.aquatox.2016.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 07/06/2016] [Accepted: 07/14/2016] [Indexed: 06/06/2023]
Abstract
The intertidal whelk Reishia clavigera is commonly used as a biomonitor of chemical contamination in the marine environment along Western Pacific region, and as a model for mechanistic studies of organotin-mediated imposex development. However, limited genomic resources of R. clavigera have restricted its role for the investigation of molecular mechanisms of such endocrine disruptions. This study, therefore, aimed to establish tissue-specific transcriptomes of the digestive gland, gonad, head ganglia, penis and the remaining body part of the male and female R. clavigera. By combining the results, a global transcriptome was obtained. A total of 578,134,720 high-quality filtered reads were obtained using Illumina sequencing. The R. clavigera transcriptome comprised of 38,466 transcripts and 32,798 unigenes with predicted open reading frames. The average length of transcripts was 1,709bp with N50 of 2,236bp. Based on sequence similarity searches against public databases, 28,657 transcripts and 24,403 unigenes had at least one BLAST hit. There were 17,530 transcripts and 14,897 unigenes annotated with at least one Gene Ontology (GO) term. Moreover, 5,776 transcripts and 5,137 unigenes were associated with 333 Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways. The numbers of unigenes were similar among the five target tissues and between sexes, but tissue-specific expression profiles were revealed by multivariate analyses. Based on the functional annotation, putative steroid hormone-associated unigenes were identified. In particular, we highlighted the presence of steroid hormone receptor homologues that could be the targets for mechanistic studies of the organotin-mediated imposex development in marine gastropods. This newly generated transcriptome assembly of R. clavigera provides a valuable molecular resource for ecotoxicological and environmental genomic studies.
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Affiliation(s)
- Jack C H Ip
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Priscilla T Y Leung
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Kevin K Y Ho
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - J W Qiu
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China; Department of Biology, Hong Kong Baptist University, Waterloo Road, Kowloon, Hong Kong, China
| | - Kenneth M Y Leung
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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Immel F, Broussard C, Catherinet B, Plasseraud L, Alcaraz G, Bundeleva I, Marin F. The Shell of the Invasive Bivalve Species Dreissena polymorpha: Biochemical, Elemental and Textural Investigations. PLoS One 2016; 11:e0154264. [PMID: 27213644 PMCID: PMC4877012 DOI: 10.1371/journal.pone.0154264] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 04/11/2016] [Indexed: 11/18/2022] Open
Abstract
The zebra mussel Dreissena polymorpha is a well-established invasive model organism. Although extensively used in environmental sciences, virtually nothing is known of the molecular process of its shell calcification. By describing the microstructure, geochemistry and biochemistry/proteomics of the shell, the present study aims at promoting this species as a model organism in biomineralization studies, in order to establish a bridge with ecotoxicology, while sketching evolutionary conclusions. The shell of D. polymorpha exhibits the classical crossed-lamellar/complex crossed lamellar combination found in several heterodont bivalves, in addition to an external thin layer, the characteristics of which differ from what was described in earlier publication. We show that the shell selectively concentrates some heavy metals, in particular uranium, which predisposes D. polymorpha to local bioremediation of this pollutant. We establish the biochemical signature of the shell matrix, demonstrating that it interacts with the in vitro precipitation of calcium carbonate and inhibits calcium carbonate crystal formation, but these two properties are not strongly expressed. This matrix, although overall weakly glycosylated, contains a set of putatively calcium-binding proteins and a set of acidic sulphated proteins. 2D-gels reveal more than fifty proteins, twenty of which we identify by MS-MS analysis. We tentatively link the shell protein profile of D. polymorpha and the peculiar recent evolution of this invasive species of Ponto-Caspian origin, which has spread all across Europe in the last three centuries.
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Affiliation(s)
- Françoise Immel
- Laboratoire de Biogenèse Membranaire UMR5200, CNRS, Université de Bordeaux, Villenave d'Ornon, France
- Biogéosciences UMR6282, CNRS, Université de Bourgogne Franche-Comté, Dijon, France
- * E-mail: (FI); (FM)
| | - Cédric Broussard
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Descartes, Paris, France
- Plate-forme Protéomique 3P5, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Bastien Catherinet
- Biogéosciences UMR6282, CNRS, Université de Bourgogne Franche-Comté, Dijon, France
| | - Laurent Plasseraud
- ICMUB UMR6302, CNRS, Université de Bourgogne Franche-Comté, Dijon, France
| | - Gérard Alcaraz
- UPSP PROXISS, Département Agronomie Environnement AgroSupDijon, Dijon, France
| | - Irina Bundeleva
- Biogéosciences UMR6282, CNRS, Université de Bourgogne Franche-Comté, Dijon, France
| | - Frédéric Marin
- Biogéosciences UMR6282, CNRS, Université de Bourgogne Franche-Comté, Dijon, France
- * E-mail: (FI); (FM)
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Biodegradation of DDT by Stenotrophomonas sp. DDT-1: Characterization and genome functional analysis. Sci Rep 2016; 6:21332. [PMID: 26888254 PMCID: PMC4758049 DOI: 10.1038/srep21332] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/21/2016] [Indexed: 11/08/2022] Open
Abstract
A novel bacterium capable of utilizing 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) as the sole carbon and energy source was isolated from a contaminated soil which was identified as Stenotrophomonas sp. DDT-1 based on morphological characteristics, BIOLOG GN2 microplate profile, and 16S rDNA phylogeny. Genome sequencing and functional annotation of the isolate DDT-1 showed a 4,514,569 bp genome size, 66.92% GC content, 4,033 protein-coding genes, and 76 RNA genes including 8 rRNA genes. Totally, 2,807 protein-coding genes were assigned to Clusters of Orthologous Groups (COGs), and 1,601 protein-coding genes were mapped to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The degradation half-lives of DDT increased with substrate concentration from 0.1 to 10.0 mg/l, whereas decreased with temperature from 15 °C to 35 °C. Neutral condition was the most favorable for DDT biodegradation. Based on genome annotation of DDT degradation genes and the metabolites detected by GC-MS, a mineralization pathway was proposed for DDT biodegradation in which it was orderly converted into DDE/DDD, DDMU, DDOH, and DDA via dechlorination, hydroxylation, and carboxylation, and ultimately mineralized to carbon dioxide. The results indicate that the isolate DDT-1 is a promising bacterial resource for the removal or detoxification of DDT residues in the environment.
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26
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Patnaik BB, Wang TH, Kang SW, Hwang HJ, Park SY, Park EB, Chung JM, Song DK, Kim C, Kim S, Lee JS, Han YS, Park HS, Lee YS. Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery. PLoS One 2016; 11:e0148622. [PMID: 26872384 PMCID: PMC4752248 DOI: 10.1371/journal.pone.0148622] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/20/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The freshwater mussel Cristaria plicata (Bivalvia: Eulamellibranchia: Unionidae), is an economically important species in molluscan aquaculture due to its use in pearl farming. The species have been listed as endangered in South Korea due to the loss of natural habitats caused by anthropogenic activities. The decreasing population and a lack of genomic information on the species is concerning for environmentalists and conservationists. In this study, we conducted a de novo transcriptome sequencing and annotation analysis of C. plicata using Illumina HiSeq 2500 next-generation sequencing (NGS) technology, the Trinity assembler, and bioinformatics databases to prepare a sustainable resource for the identification of candidate genes involved in immunity, defense, and reproduction. RESULTS The C. plicata transcriptome analysis included a total of 286,152,584 raw reads and 281,322,837 clean reads. The de novo assembly identified a total of 453,931 contigs and 374,794 non-redundant unigenes with average lengths of 731.2 and 737.1 bp, respectively. Furthermore, 100% coverage of C. plicata mitochondrial genes within two unigenes supported the quality of the assembler. In total, 84,274 unigenes showed homology to entries in at least one database, and 23,246 unigenes were allocated to one or more Gene Ontology (GO) terms. The most prominent GO biological process, cellular component, and molecular function categories (level 2) were cellular process, membrane, and binding, respectively. A total of 4,776 unigenes were mapped to 123 biological pathways in the KEGG database. Based on the GO terms and KEGG annotation, the unigenes were suggested to be involved in immunity, stress responses, sex-determination, and reproduction. A total of 17,251 cDNA simple sequence repeats (cSSRs) were identified from 61,141 unigenes (size of >1 kb) with the most abundant being dinucleotide repeats. CONCLUSIONS This dataset represents the first transcriptome analysis of the endangered mollusc, C. plicata. The transcriptome provides a comprehensive sequence resource for the conservation of genetic information in this species and enrichment of the genetic database. The development of molecular markers will assist in the genetic improvement of C. plicata.
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Affiliation(s)
- Bharat Bhusan Patnaik
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Bhubaneswar- 751024, Odisha, India
| | - Tae Hun Wang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Se Won Kang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Hee-Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - So Young Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Eun Bi Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Jong Min Chung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Dae Kwon Song
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Changmu Kim
- National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Soonok Kim
- National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Jun Sang Lee
- Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 200-701, Republic of Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 300 Yongbong-Dong, Buk-gu, Gwangju, 500-757, Republic of Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 305-150, Republic of Korea
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
- * E-mail:
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Mosa KA, Saadoun I, Kumar K, Helmy M, Dhankher OP. Potential Biotechnological Strategies for the Cleanup of Heavy Metals and Metalloids. FRONTIERS IN PLANT SCIENCE 2016; 7:303. [PMID: 27014323 PMCID: PMC4791364 DOI: 10.3389/fpls.2016.00303] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 02/25/2016] [Indexed: 05/18/2023]
Abstract
Global mechanization, urbanization, and various natural processes have led to the increased release of toxic compounds into the biosphere. These hazardous toxic pollutants include a variety of organic and inorganic compounds, which pose a serious threat to the ecosystem. The contamination of soil and water are the major environmental concerns in the present scenario. This leads to a greater need for remediation of contaminated soils and water with suitable approaches and mechanisms. The conventional remediation of contaminated sites commonly involves the physical removal of contaminants, and their disposition. Physical remediation strategies are expensive, non-specific and often make the soil unsuitable for agriculture and other uses by disturbing the microenvironment. Owing to these concerns, there has been increased interest in eco-friendly and sustainable approaches such as bioremediation, phytoremediation and rhizoremediation for the cleanup of contaminated sites. This review lays particular emphasis on biotechnological approaches and strategies for heavy metal and metalloid containment removal from the environment, highlighting the advances and implications of bioremediation and phytoremediation as well as their utilization in cleaning-up toxic pollutants from contaminated environments.
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Affiliation(s)
- Kareem A. Mosa
- Department of Applied Biology, College of Sciences, University of SharjahSharjah, UAE
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar UniversityCairo, Egypt
- *Correspondence: Kareem A. Mosa,
| | - Ismail Saadoun
- Department of Applied Biology, College of Sciences, University of SharjahSharjah, UAE
| | - Kundan Kumar
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K. K. Birla Goa CampusGoa, India
| | - Mohamed Helmy
- The Donnelly Centre for Cellular and Biomedical Research, University of Toronto, TorontoON, Canada
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of MassachusettsAmherst, MA, USA
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28
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Characterization of Physa acuta expressed sequence tags and transcript mining following cadmium exposure. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0334-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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29
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Wong YH, Sun J, He LS, Chen LG, Qiu JW, Qian PY. High-throughput transcriptome sequencing of the cold seep mussel Bathymodiolus platifrons. Sci Rep 2015; 5:16597. [PMID: 26593439 PMCID: PMC4655397 DOI: 10.1038/srep16597] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 10/08/2015] [Indexed: 12/29/2022] Open
Abstract
Bathymodiolid mussels dominate hydrothermal vents, cold methane/sulfide-hydrocarbon seeps, and other sites of organic enrichment. Here, we aimed to explore the innate immune system and detoxification mechanism of the deep sea mussel Bathymodiolus platifrons collected from a methane seep in the South China Sea. We sequenced the transcriptome of the mussels’ gill, foot and mantle tissues and generated a transcriptomic database containing 96,683 transcript sequences. Based on GO and KEGG annotations, we reported transcripts that were related to the innate immune system, heavy metal detoxification and sulfide metabolic genes. Our in-depth analysis on the isoforms of peptidoglycan recognition protein (PGRP) that have different cellular location and potentially differential selectivity towards peptidoglycan (PGN) from gram-positive and gram-negative bacteria were differentially expressed in different tissues. We also reported a potentially novel form of metallothionein and the production of phytochelatin in B. platifrons, which has not been reported in any of its coastal relative Mytilus mussel species. Overall, the present study provided new insights into heavy metal and sulfide metabolism in B. platifrons and can be served as the basis for future molecular studies on host-symbiont interactions in cold seep mussels.
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Affiliation(s)
- Yue Him Wong
- Division of Life Science, School of Science, the Hong Kong University of Science and Technology, Hong Kong S.A.R
| | - Jin Sun
- Department of Biology, Hong Kong Baptist University, Hong Kong S.A.R
| | - Li Sheng He
- Sanya Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Hainan, People Republic of China
| | - Lian Guo Chen
- Division of Life Science, School of Science, the Hong Kong University of Science and Technology, Hong Kong S.A.R
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong S.A.R
| | - Pei-Yuan Qian
- Division of Life Science, School of Science, the Hong Kong University of Science and Technology, Hong Kong S.A.R
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30
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Liu T, Pan L, Jin Q, Cai Y. Differential gene expression analysis of benzo(a)pyrene toxicity in the clam, Ruditapes philippinarum. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 115:126-136. [PMID: 25686690 DOI: 10.1016/j.ecoenv.2015.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/01/2015] [Accepted: 02/04/2015] [Indexed: 06/04/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are known for their carcinogenic, teratogenic and mutagenic properties. Benzo(a)pyrene (BaP) possesses the greatest carcinogenic potential among the various PAHs. In this study, digital gene expression (DGE) was performed to investigate the digestive gland transcriptome profile of the clam Ruditapes philippinarum exposed to BaP. A total of 10,508,312 and 11,414,297 clean reads were generated respectively, from control and BaP exposure DGE libraries. One hundred and forty-five differentially expressed genes were detected after comparing two libraries with 58 up-regulated and 87 down-regulated genes. GO annotation and KEGG pathway analyses were performed on all genes to understand their biological functions and processes. The results showed that numerous enriched differentially expressed genes are related to growth and development, antioxidant metabolism, apoptosis and detoxification metabolism. Quantitative real-time PCR was performed to verify the expressed genes of DGE. Our results provide evidences that RNA-seq is a powerful tool for toxicology and capable of generating novel and valuable information at the transcriptome level for characterizing deleterious effects caused by BaP.
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Affiliation(s)
- Tong Liu
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China.
| | - Qian Jin
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Yuefeng Cai
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
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