1
|
Lee YH, Kim MS, Lee Y, Kim DH, Lee JS. Nanoplastics induce epigenetic signatures of transgenerational impairments associated with reproduction in copepods under ocean acidification. JOURNAL OF HAZARDOUS MATERIALS 2023; 449:131037. [PMID: 36842400 DOI: 10.1016/j.jhazmat.2023.131037] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Ocean acidification (OA) is one of many major global climate changes that pose a variety of risks to marine ecosystems in different ways. Meanwhile, there is growing concern about how nanoplastics (NPs) affect marine ecosystems. Combined exposure of marine organisms to OA and NPs is inevitable, but their interactive effects remain poorly understood. In this study, we investigated the multi- and transgenerational toxicity of NPs on copepods under OA conditions for ten generations. The findings revealed that OA and NPs have a synergistic negative effect on copepod reproduction across generations. In particular, the transgenerational groups showed reproductive impairments in the F1 and F2 generations (F1T and F2T), even though they were never exposed to NPs. Moreover, our epigenetic examinations demonstrated that the observed intergenerational reproductive impairments are associated with differential methylation patterns of specific genes, suggesting that the interaction of OA and NPs can pose a significant threat to the sustainability of copepod populations through epigenetic modifications. Overall, our findings provide valuable insight into the intergenerational toxicity and underlying molecular mechanisms of responses to NPs under OA conditions.
Collapse
Affiliation(s)
- Young Hwan Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Yoseop Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
2
|
Kim DH, Jeong H, Kim MS, Kim S, Souissi S, Park HG, Hagiwara A, Lee JS. Identification and characterization of homeobox gene clusters in harpacticoid and calanoid copepods. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:215-224. [PMID: 34855303 DOI: 10.1002/jez.b.23112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/10/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
In this study, we have identified the entire complement of typical homeobox (Hox) genes (Lab, Pb, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) in harpacticoid and calanoid copepods and compared them with the cyclopoid copepod Paracyclopina nana. The harpacticoid copepods Tigriopus japonicus and Tigriopus kingsejongensis have seven Hox genes (Lab, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) and the Pb and Ftz genes are also present in the cyclopoid copepod P. nana. In the Hox gene cluster of the calanoid copepod Eurytemora affinis, all the Hox genes were present linearly in the genome but the Antp gene was duplicated. Of the three representative copepods, the P. nana Hox gene cluster was the most compact due to its small genome size. The Hox gene expression profile patterns in the three representative copepods were stage-specific. The Lab, Dfd, Scr, Pb, Ftz, and Hox3 genes showed a high expression in early developmental stages but Antp, Ubx, Abd-A, and Abd-B genes were mostly expressed in later developmental stages, implying that these Hox genes may be closely associated with the development of segment identity during early development.
Collapse
Affiliation(s)
- Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Haksoo Jeong
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Sanghee Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Sami Souissi
- Laboratoire d'Océanologie et de Géosciences, Station marine de Wimereux, CNRS, UMR 8187 LOG, Université de Lille, Université du Littoral Côte d'Opale, Lille, France
| | - Heum Gi Park
- Department of Marine Resource Development, College of Life Sciences, Gangneung-Wonju National University, Gangneung, South Korea
| | - Atsushi Hagiwara
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
- Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Japan
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon, South Korea
| |
Collapse
|
3
|
Zhang XL, Liu P, Xu SL, Rizo EZ, Zhang Q, Dumont HJ, Han BP. Geographic Variation of Phyllodiaptomus tunguidus Mitogenomes: Genetic Differentiation and Phylogeny. Front Genet 2021; 12:711992. [PMID: 34531896 PMCID: PMC8439380 DOI: 10.3389/fgene.2021.711992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/03/2021] [Indexed: 12/04/2022] Open
Abstract
Phyllodiaptomus tunguidus (Copepoda: Calanoida) is largely endemic to and widespread in freshwater in southern China, where it inhabits a complex landscape from lowland to highland across an elevation gradient of 2000m. A deep genetic differentiation can be expected between its most distant geographic populations. Here, we sequenced nine mitogenomes from diverse populations. All mitogenomes contained 37 genes, including 13 protein-coding genes (PCG), two rRNA genes, 22 tRNA genes and one control region. Their base composition, genetic distance and tRNA structure indeed revealed a wide differentiation between mitogenomes. Two P. tunguidus from Guangxi near Vietnam differed from the other seven by up to 10.1%. Their tRNA-Arg had a complete clover-leaf structure, whereas that of the others did not contain an entire dihydrouridine arm. The nine mitogenomes also differed in the length of rRNA. NJ, ML, and Bayesian analyses all split them into two clades, viz. the two P. tunguidus from Guangxi (Clade 1), and the other seven (Clade 2). Both the structure and phylogeny of the mitogenomes suggest that P. tunguidus has complex geographic origin, and its populations in Clade 1 have long lived in isolation from those in Clade 2. They currently reach the level of subspecies or cryptic species. An extensive phylogenetic analysis of Copepoda further verified that Diaptomidae is the most recently diverging family in Calanoida and that P. tunguidus is at the evolutionary apex of the family.
Collapse
Affiliation(s)
- Xiao-Li Zhang
- Department of Ecology, Jinan University, Guangzhou, China
| | - Ping Liu
- Department of Ecology, Jinan University, Guangzhou, China
| | - Shao-Lin Xu
- Department of Ecology, Jinan University, Guangzhou, China
| | - Eric Zeus Rizo
- Department of Ecology, Jinan University, Guangzhou, China.,Division of Biological Sciences, College of Arts and Sciences, University of the Philippines Visayas, Iloilo, Philippines
| | - Qun Zhang
- Department of Ecology, Jinan University, Guangzhou, China
| | - Henri J Dumont
- Department of Ecology, Jinan University, Guangzhou, China.,Department of Biology, Ghent University, Ghent, Belgium
| | - Bo-Ping Han
- Department of Ecology, Jinan University, Guangzhou, China
| |
Collapse
|
4
|
Park JC, Lee JS. Genome-wide identification of heat shock proteins in harpacticoid, cyclopoid, and calanoid copepods: Potential application in marine ecotoxicology. MARINE POLLUTION BULLETIN 2021; 169:112545. [PMID: 34111604 DOI: 10.1016/j.marpolbul.2021.112545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Constant evolution of omics-technologies has provided access to identification of various important gene families. Recently, genome assemblies on widely used ecotoxicological model species, including rotifers and copepods have been completed and representative detoxification-related gene families have been discovered for biomarker genes. However, despite ubiquitous presence of stress-response proteins, limited information on full genome-wide report on heat shock proteins (Hsps) is available. Various studies have demonstrated multiple cellular functions of Hsps in living organisms as an important biomarker in response to abiotic and biotic stressors, however, full genome-wide identification of Hsps, particularly in aquatic invertebrates, has not been reported. This is the first study to report the entire Hsps and basal gene expression levels in three regional-specific copepods: Tigriopus japonicus and kingsejongensis, Paracyclopina nana, and Eurytemora affnis, and how each Hsp family gene is regulated at a basal level.
Collapse
Affiliation(s)
- Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
5
|
Dur G, Won EJ, Han J, Lee JS, Souissi S. An individual-based model for evaluating post-exposure effects of UV-B radiation on zooplankton reproduction. Ecol Modell 2021. [DOI: 10.1016/j.ecolmodel.2020.109379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
6
|
Byeon E, Yoon C, Lee JS, Lee YH, Jeong CB, Lee JS, Kang HM. Interspecific biotransformation and detoxification of arsenic compounds in marine rotifer and copepod. JOURNAL OF HAZARDOUS MATERIALS 2020; 391:122196. [PMID: 32062345 DOI: 10.1016/j.jhazmat.2020.122196] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/23/2020] [Accepted: 01/26/2020] [Indexed: 06/10/2023]
Abstract
The toxicity of arsenic (As) has been reported to be different depending on their chemical forms. However, its toxicity mechanisms largely remain unknown. In this study, to investigate toxicity mechanism of As in marine zooplanktons, namely, the rotifer Brachionus plicatilis and the copepod Paracyclopina nana, metabolites of As were analyzed by using a high-performance liquid chromatography coupled with inductively coupled plasma mass spectrometry with in vivo toxicity and antioxidant responses in response to inorganic As, including arsenate (AsV) and arsenite (AsIII). While AsIII was more toxic than AsV in both organisms, the rotifer B. plicatilis exhibited stronger tolerance, compared to the copepod P. nana. The As speciation analysis revealed differences in biotransformation processes in two species with B. plicatilis having a more simplified process than P. nana, contributing to a better tolerance against As in the rotifer B. plicatilis compared to P. nana. Moreover, the levels of GSH content and the regulation of omega class glutathione S-transferases were different in response to oxidative stress between B. plicatilis and P. nana. These results suggest that the rotifer B. plicatilis has a unique survival strategy with more efficient biotransformation and antioxidant responses, compared to P. nana, conferring higher tolerance to As.
Collapse
Affiliation(s)
- Eunjin Byeon
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Cheolho Yoon
- Korea Basic Science Institute, Seoul Center, Seoul 02841, South Korea
| | - Jin-Sol Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Young Hwan Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea; Department of Marine Science, College of Nature Science, Incheon National University, Incheon 22012, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Hye-Min Kang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
7
|
Dayras P, Bialais C, Ouddane B, Lee JS, Souissi S. Effects of different routes of exposure to metals on bioaccumulation and population growth of the cyclopoid copepod Paracyclopina nana. CHEMOSPHERE 2020; 248:125926. [PMID: 32006827 DOI: 10.1016/j.chemosphere.2020.125926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/11/2020] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
We examined effects of the three metals cadmium (Cd), copper (Cu), and nickel (Ni) on two subpopulations of the cyclopoid copepod Paracyclopina nana. We sought to investigate the effects of metal exposure on population growth and structure of P. nana and to understand the parameters affecting the metal bioaccumulation in copepods. A first experiment tested the hypothesis of competition between these metals in a mixture using a P. nana mass culture in 10 L beakers with the sublethal concentrations (1/3 of LC50) as determined for E. affinis. A second experiment pursued the same with a P. nana population which was adapted to a higher Cu concentration for several generations (226.9 ± 15.9 μg g-1 dw Cu in copepods) and using the proper sublethal concentrations for P. nana. After 96 h of exposure, results from the first experiment showed a decreasing population growth and instead of an increasing metal accumulation in copepods. Cd also appeared to be more accumulated when it was alone, confirming the hypothesis of metal competition in mixture. Results from the second experiment revealed less marked effects. When metal concentrations increased in the treatment it decreased in copepods, indicating depuration activity in the population already adapted to metal exposure. This paper is the first one investigating the parameters affecting the bioaccumulation capacity of P. nana in response to metals. It offers a better understanding of copepod responses to metal contamination in a complex aquatic environment.
Collapse
Affiliation(s)
- Paul Dayras
- Université de Lille, CNRS, Université du Littoral Côte d'Opale, UMR 8187 LOG, Laboratoire d'Océanologie et de Géosciences, F-62930, Wimereux, France.
| | - Capucine Bialais
- Université de Lille, CNRS, Université du Littoral Côte d'Opale, UMR 8187 LOG, Laboratoire d'Océanologie et de Géosciences, F-62930, Wimereux, France.
| | - Baghdad Ouddane
- Université de Lille, UMR CNRS 8516, Laboratoire LASIR, Equipe Physico-Chimie de l'Environnement, F-59655, Villeneuve d'Ascq Cedex, France.
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea.
| | - Sami Souissi
- Université de Lille, CNRS, Université du Littoral Côte d'Opale, UMR 8187 LOG, Laboratoire d'Océanologie et de Géosciences, F-62930, Wimereux, France.
| |
Collapse
|
8
|
Sun S, Sha Z, Wang Y. The complete mitochondrial genomes of two vent squat lobsters, Munidopsis lauensis and M. verrilli: Novel gene arrangements and phylogenetic implications. Ecol Evol 2019; 9:12390-12407. [PMID: 31788185 PMCID: PMC6875667 DOI: 10.1002/ece3.5542] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/31/2019] [Accepted: 07/19/2019] [Indexed: 12/14/2022] Open
Abstract
Hydrothermal vents are considered as one of the most extremely harsh environments on the Earth. In this study, the complete mitogenomes of hydrothermal vent squat lobsters, Munidopsis lauensis and M. verrilli, were determined through Illumina sequencing and compared with other available mitogenomes of anomurans. The mitogenomes of M. lauensis (17,483 bp) and M. verrilli (17,636 bp) are the largest among all Anomura mitogenomes, while the A+T contents of M. lauensis (62.40%) and M. verrilli (63.99%) are the lowest. The mitogenomes of M. lauensis and M. verrilli display novel gene arrangements, which might be the result of three tandem duplication-random loss (tdrl) events from the ancestral pancrustacean pattern. The mitochondrial gene orders of M. lauensis and M. verrilli shared the most similarities with S. crosnieri. The phylogenetic analyses based on both gene order data and nucleotide sequences (PCGs and rRNAs) revealed that the two species were closely related to Shinkaia crosnieri. Positive selection analysis revealed that eighteen residues in seven genes (atp8, Cytb, nad3, nad4, nad4l, nad5, and nad6) of the hydrothermal vent anomurans were positively selected sites.
Collapse
Affiliation(s)
- Shao'e Sun
- Deep Sea Research CenterInstitute of OceanologyChinese Academy of ScienceQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| | - Zhongli Sha
- Deep Sea Research CenterInstitute of OceanologyChinese Academy of ScienceQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yanrong Wang
- Deep Sea Research CenterInstitute of OceanologyChinese Academy of ScienceQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| |
Collapse
|
9
|
Park JC, Lee MC, Yoon DS, Han J, Park HG, Hwang UK, Lee JS. Genome-wide identification and expression of the entire 52 glutathione S-transferase (GST) subfamily genes in the Cu 2+-exposed marine copepods Tigriopus japonicus and Paracyclopina nana. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 209:56-69. [PMID: 30735907 DOI: 10.1016/j.aquatox.2019.01.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
In this study, the entire glutathione S-transferases (GSTs), the major phase II detoxification enzyme, were identified in two marine copepod species Tigriopus japonicus and Paracyclopina nana. The genome-wide identification of GSTs in T. japonicus and P. nana resulted in 32 and 20 GSTs in total, respectively. Among the identified GSTs, two specific classes of GSTs, specifically sigma and delta/epsilon GSTs were the dominant form of cytosolic GSTs in T. japonicus, while delta/epsilon and mu classes were dominant cytosolic GSTs in P. nana. In addition, Membrane-Associated Proteins in Eicosanoid and Glutathione metabolism (MAPEG) family were found in relatively higher proportion compared to other classes. Moreover, sigma, delta/epsilon, and microsomal GSTs have shown to expand through tandem duplication. To validate the detoxification function of the identified GSTs, both copepods were exposed to copper (Cu2+) and the reactive oxygen species (ROS) level and GST activity were measured. With integration of phylogenetic analysis and xenobiotic-mediated GST mRNA expression patterns along with previous enzymatic activities, the functional divergence among species-specific GST genes was clearly observed. This study covers full identification of GST classes in two marine copepod species and their important role in marine environmental ecotoxicology.
Collapse
Affiliation(s)
- Jun Chul Park
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Chul Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Deok-Seo Yoon
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Heum Gi Park
- Department of Marine Resource Development, College of Life Sciences, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Un-Ki Hwang
- Marine Ecological Risk Assessment Center, West Sea Fisheries Research Institute, National Institute of Fisheries Science, Incheon 46083, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
10
|
Hołyńska M, Wyngaard GA. Towards a phylogeny of
Cyclops
(Copepoda): (in)congruences among morphology, molecules and zoogeography. ZOOL SCR 2019. [DOI: 10.1111/zsc.12342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria Hołyńska
- Museum and Institute of Zoology Polish Academy of Sciences Warszawa Poland
| | - Grace A. Wyngaard
- Department of Biology James Madison University Harrisonburg Virginia
| |
Collapse
|
11
|
Zhou J, Kang HM, Lee YH, Jeong CB, Park JC, Lee JS. Adverse effects of a synthetic pyrethroid insecticide cypermethrin on life parameters and antioxidant responses in the marine copepods Paracyclopina nana and Tigriopus japonicus. CHEMOSPHERE 2019; 217:383-392. [PMID: 30419392 DOI: 10.1016/j.chemosphere.2018.10.217] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
To find the adverse effects induced by cypermethrin, the ecotoxicological model copepods Tigriopus japonicus and Paracyclopina nana were exposed under cypermethrin, which is a widely used type-II pyrethroid insecticide in agriculture. Despite its large-scale application as insecticide in agriculture, little information is available on its adverse effects on aquatic invertebrates. In this study, the toxicity of cypermethrin on two copepods was assessed based on life parameters (growth rate and reproduction), oxidative stress and consequent antioxidant enzymatic activities, and gene expression profiles of antioxidants. The acute toxicity alone demonstrated that P. nana is less tolerant and sensitive against cypermethrin, compared to T. japonicus. However, under chronic exposure, life parameters of both P. nana and T. japonicus were severely affected by cypermethrin. Among antioxidant enzymatic activities, superoxide dismutase (SOD) and glutathione S-transferase (GST), in particular, demonstrated significant increase in response to cypermethrin. Furthermore, temporal-mRNA expression profile showed modulations in antioxidant related genes in response to cypermethrin. Our results provide the underlying toxic mechanism of cypermethrin and the oxidative stress defense mechanism and species-specific tolerance against cypermethrin in two model copepods species.
Collapse
Affiliation(s)
- Jiaying Zhou
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Hye-Min Kang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Young Hwan Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jun Chul Park
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
12
|
Complete mitochondrial genome of the first deep-sea spongicolid shrimp Spongiocaris panglao (Decapoda: Stenopodidea): Novel gene arrangement and the phylogenetic position and origin of Stenopodidea. Gene 2018; 676:123-138. [PMID: 30021129 DOI: 10.1016/j.gene.2018.07.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 07/06/2018] [Accepted: 07/10/2018] [Indexed: 12/17/2022]
Abstract
Stenopodidea Claus, 1872 (Crustacea: Decapoda) is one of the major groups of decapods crustaceans. Hitherto, only one complete mitochondrial genome (mitogenome) from the family Stenopodidae is available for the infraorder Stenopodidea. Here, we determined the complete mitogenome of Spongiocaris panglao de Grave and Saito, 2016 using Illumina sequencing, representing the first species from the family Spongicolidae. The 15,909 bp genome is a circular molecule and consists of 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. Although the overall genome organization is typical for metazoans, the mitogenome of S. panglao shows some derived characters. A + T content of 77.42% in S. pamglao mitogenome is second-highest among the dacapods described to date. The trnR gene exhibit modified secondary structure with the TψC loop completely missing, which might be a putative autapomorphy of S. pamglao mitogenome. Compared with the shallow-water stenopodidean species S. hispidus, the control region of S. pamglao exhibits three characteristics: larger size, higher A + T content, and more tandem repeat sequences. The gene order exhibited difference from the ancestral mitogenome pattern of the Pancrustacea, with 5 tRNA genes rearrangement. The result from BI was agreed with most morphological characters and molecular evidences, revealing that Stenopodidea and Reptantia had the closest relationship, as the sister group of Caridea. Still, the alternative hypothesis supported from ML topology cannot be completely rejected based on the current data. Estimated times revealed that the two stenopodideans families Stenopodidae and Spongicolidae diverged from each other around 122 Mya. The divergence time of spongicolid shrimp is in good agreement with the origin of their hexactinellid hosts (78-144 Mya).
Collapse
|
13
|
Weydmann A, Przyłucka A, Lubośny M, Walczyńska KS, Serrão EA, Pearson GA, Burzyński A. Mitochondrial genomes of the key zooplankton copepods Arctic Calanus glacialis and North Atlantic Calanus finmarchicus with the longest crustacean non-coding regions. Sci Rep 2017; 7:13702. [PMID: 29057900 PMCID: PMC5651803 DOI: 10.1038/s41598-017-13807-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/03/2017] [Indexed: 11/19/2022] Open
Abstract
We determined the nearly complete mitochondrial genomes of the Arctic Calanus glacialis and its North Atlantic sibling Calanus finmarchicus, which are key zooplankton components in marine ecosystems. The sequenced part of C. glacialis mitogenome is 27,342 bp long and consists of two contigs, while for C. finmarchicus it is 29,462 bp and six contigs, what makes them the longest reported copepod mitogenomes. The typical set of metazoan mitochondrial genes is present in these mitogenomes, although the non-coding regions (NCRs) are unusually long and complex. The mitogenomes of the closest species C. glacialis and C. finmarchicus, followed by the North Pacific C. sinicus, are structurally similar and differ from the much more typical of deep-water, Arctic C. hyperboreus. This evolutionary trend for the expansion of NCRs within the Calanus mitogenomes increases mitochondrial DNA density, what resulted in its similar density to the nuclear genome. Given large differences in the length and structure of C. glacialis and C. finmarchicus mitogenomes, we conclude that the species are genetically distinct and thus cannot hybridize. The molecular resources presented here: the mitogenomic and rDNA sequences, and the database of repetitive elements should facilitate the development of genetic markers suitable in pursuing evolutionary research in copepods.
Collapse
Affiliation(s)
- Agata Weydmann
- Institute of Oceanology, Polish Academy of Sciences, Sopot, 81-712, Poland.
- University of Gdansk, Institute of Oceanography, Gdynia, 81-378, Poland.
| | | | - Marek Lubośny
- Institute of Oceanology, Polish Academy of Sciences, Sopot, 81-712, Poland
| | | | - Ester A Serrão
- University of Algarve, CCMAR, CIMAR, Faro, 8005-139, Portugal
| | | | - Artur Burzyński
- Institute of Oceanology, Polish Academy of Sciences, Sopot, 81-712, Poland
| |
Collapse
|
14
|
Lee YH, Kim DH, Kang HM, Wang M, Jeong CB, Lee JS. Adverse effects of methylmercury (MeHg) on life parameters, antioxidant systems, and MAPK signaling pathways in the rotifer Brachionus koreanus and the copepod Paracyclopina nana. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 190:181-189. [PMID: 28734225 DOI: 10.1016/j.aquatox.2017.07.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
To evaluate the adverse effects of MeHg on the rotifer Brachionus koreanus and the copepod Paracyclopina nana, we assessed the effects of MeHg toxicity on life parameters (e.g. growth retardation and fecundity), antioxidant systems, and mitogen-activated protein kinase (MAPK) signaling pathways at various concentrations (1ng/L, 10ng/L, 100ng/L, 500ng/L, and 1000ng/L). MeHg exposure resulted in the growth retardation with the increased ROS levels but decreased glutathione (GSH) levels in a dose-dependent manner in both B. koreanus and P. nana. Antioxidant enzymatic activities (e.g. glutathione S-transferase [GST], glutathione reductase [GR], and glutathione peroxidase [GPx]) in B. koreanus showed more positive responses compared the control but in P. nana, those antioxidant enzymatic activities showed subtle changes due to different no observed effect concentration (NOEC) values among the two species. Expression of antioxidant genes (e.g. superoxide dismutase [SOD], GSTs, glutathione peroxidase [GPx], and catalase [CAT]) also demonstrated similar effects as shown in antioxidant enzymatic activities. In B. koreanus, the level of p-ERK was decreased in the presence of 1000ng/L MeHg, while the levels of p-ERK and p-p38 in P. nana were reduced in the presence of 10ng/L MeHg. However, p-JNK levels were not altered by MeHg in B. koreanus and P. nana, compared to the corresponding controls. In summary, life parameters (e.g. reduced fecundity and survival rate) were closely associated with effects on the antioxidant system in response to MeHg. These observations provide a better understanding on the adverse effects of MeHg on in vivo life parameters and molecular defense mechanisms in B. koreanus and P. nana.
Collapse
Affiliation(s)
- Young Hwan Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Hye-Min Kang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Minghua Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
15
|
Mayor TY, Galimova YA, Sheveleva NG, Sukhanova LV, Kirilchik SV. Molecular phylogenetic analysis of Diacyclops and Acanthocyclops (Copepoda: Cyclopoida) from Lake Baikal based on COI gene. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417020041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Han J, Kim DH, Seo JS, Kim IC, Nelson DR, Puthumana J, Lee JS. Assessing the identity and expression level of the cytochrome P450 20A1 (CYP20A1) gene in the BPA-, BDE-47, and WAF-exposed copepods Tigriopus japonicus and Paracyclopina nana. Comp Biochem Physiol C Toxicol Pharmacol 2017; 193:42-49. [PMID: 28088650 DOI: 10.1016/j.cbpc.2017.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 01/03/2017] [Accepted: 01/07/2017] [Indexed: 01/28/2023]
Abstract
CYP20A1 is a member of the cytochrome P450 (CYP) superfamily, identified as an orphan P450 without any assigned biological function; hence, its continued status as an "orphan" gene. In order to address this shortcoming in our understanding of this superfamily, we sought to characterize the CYP20A1 gene in the copepods Tigriopus japonicus (Tj-CYP20A1) and Paracyclopina nana (Pn-CYP20A1) at their mRNA transcriptional level. We assessed the response of this gene's expression in various developmental stages and in response to treatment with bisphenol A (BPA), 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47), and water accommodated fractions (WAFs) of crude oil. As shown in the vertebrate CYP20A1, both Tj-CYP20A1 and Pn-CYP20A1 contained characteristic conserved motifs and domain regions (I helix, K helix and heme-binding motifs) with unusual amino acid sequences apparent in their gene structure. Also molecular characterization of the putative responsive elements in the promoter regions was performed. We observed transcriptional up-regulation of these genes during post-embryonic developmental stages including sex-specific up-regulation in adults. In addition, concentration- and time-dependent mRNA transcripts in response to xenobiotics (BPA, BDE-47, and WAFs) were seen. This study focuses on the molecular elucidation of CYP20A1 genes and their interactions with xenobiotics in the copepods T. japonicus and P. nana that provides important insight into the biological importance of CYP20A1 in invertebrates.
Collapse
Affiliation(s)
- Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jung Soo Seo
- Pathology Division, National Institute of Fisheries Science, Busan 46083, South Korea
| | - Il-Chan Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, South Korea
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee, Memphis, TN 38163, United States
| | - Jayesh Puthumana
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
17
|
Lee YH, Kang HM, Kim DH, Wang M, Jeong CB, Lee JS. Adverse effects of methylmercury (MeHg) on life parameters, antioxidant systems, and MAPK signaling pathways in the copepod Tigriopus japonicus. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 184:133-141. [PMID: 28131080 DOI: 10.1016/j.aquatox.2017.01.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
Methylmercury (MeHg) is a concerning environmental pollutant that bioaccumulates and biomagnifies in the aquatic food web. However, the effects of MeHg on marine zooplankton are poorly understood even though zooplankton are considered key mediators of the bioaccumulation and biomagnification of MeHg in high-trophic marine organisms. Here, the toxicity of MeHg in the benthic copepod Tigriopus japonicus was assessed, and its adverse effects on growth rate and reproduction were demonstrated. Antioxidant enzymatic activities were increased in the presence of MeHg, indicating that these enzymes play an important role in the defense response to MeHg, which is regulated by a complex mechanism. Subsequent activation of different patterns of mitogen-activated protein kinase (MAPK) pathways was demonstrated, providing a mechanistic approach to understand the signaling pathways involved in the effects of MeHg. Our results provide valuable information for understanding the toxicity of MeHg and the underlying defense mechanism in response to MeHg exposure in marine zooplankton.
Collapse
Affiliation(s)
- Young Hwan Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Hye-Min Kang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Minghua Wang
- Center for Marine Environmental Chemistry and Toxicology, College of the Environment & Ecology, Xiamen University, Xiamen, 361102, China
| | - Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea; Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea.
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, 16419, South Korea.
| |
Collapse
|
18
|
Puthumana J, Lee MC, Han J, Kim HS, Hwang DS, Lee JS. Ecdysone receptor (EcR) and ultraspiracle (USP) genes from the cyclopoid copepod Paracyclopina nana: Identification and expression in response to water accommodated fractions (WAFs). Comp Biochem Physiol C Toxicol Pharmacol 2017; 192:7-15. [PMID: 27890717 DOI: 10.1016/j.cbpc.2016.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/09/2016] [Accepted: 11/22/2016] [Indexed: 01/24/2023]
Abstract
Ecdysteroid hormones are pivotal in the development, growth, and molting of arthropods, and the hormone pathway is triggered by binding ecdysteroid to a heterodimer of the two nuclear receptors; ecdysone receptors (EcR) and ultraspiracle (USP). We have characterized EcR and USP genes, and their 5'-untranslated region (5'-UTR) from the copepod Paracyclopina nana, and studied mRNA transcription levels in post-embryonic stages and in response to water accommodated fractions (WAFs) of crude oil. The open reading frames (ORF) of EcR and USP were 1470 and 1287bp that encoded 490 and 429 amino acids with molecular weight of 121.18 and 105.03kDa, respectively. Also, a well conserved DNA-binding domain (DBD) and ligand-binding domain (LBD) were identified which confirmed by phylogenetic analysis. Messenger RNA transcriptional levels of EcR and USP were developmental stage-specific in early post-embryonic stages (N3-4). However, an evoked expression of USP was observed throughout copepodid stage and in adult females. WAFs (40 and 80%) were acted as an ecdysone agonist in P. nana, and elicited the mRNA transcription levels in adults. Developmental stage-specific transcriptional activation of EcR and USP in response to WAFs was observed. USP gene was down-regulated in the nauplius in response to WAF, whereas up-regulation of USP was observed in the adults. This study represents the first data of molecular elucidation of EcR and USP genes and their regulatory elements from P. nana and the developmental stage specific expression in response to WAFs, which can be used as potential biomarkers for environmental stressors with ecotoxicological evaluations in copepods.
Collapse
MESH Headings
- 5' Untranslated Regions
- Animals
- Arthropod Proteins/genetics
- Arthropod Proteins/metabolism
- Copepoda/drug effects
- Copepoda/genetics
- Copepoda/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Environmental Monitoring/methods
- Gene Expression Regulation, Developmental/drug effects
- Genetic Markers
- Metamorphosis, Biological
- Phylogeny
- Promoter Regions, Genetic
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Steroid/genetics
- Receptors, Steroid/metabolism
- Regulatory Elements, Transcriptional
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic/drug effects
- Water Pollutants, Chemical/toxicity
Collapse
Affiliation(s)
- Jayesh Puthumana
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Chul Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Hui-Su Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Dae-Sik Hwang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
19
|
Jeong CB, Kim DH, Kang HM, Lee YH, Kim HS, Kim IC, Lee JS. Genome-wide identification of ATP-binding cassette (ABC) transporters and their roles in response to polycyclic aromatic hydrocarbons (PAHs) in the copepod Paracyclopina nana. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2017; 183:144-155. [PMID: 28073050 DOI: 10.1016/j.aquatox.2016.12.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 12/26/2016] [Accepted: 12/27/2016] [Indexed: 06/06/2023]
Abstract
The ATP-binding cassette (ABC) protein superfamily is one of the largest gene families and is highly conserved in all domains. The ABC proteins play roles in several biological processes, including multi-xenobiotic resistance (MXR), by functioning as transporters in the cellular membrane. They also mediate the cellular efflux of a wide range of substrates against concentration gradients. In this study, 37 ABC genes belonging to eight distinct subfamilies were identified in the marine copepod Paracyclopina nana and annotated based on a phylogenetic analysis. Also, the functions of P-glycoproteins (P-gp) and multidrug resistance-associated proteins (MRPs), conferring MXR, were verified using fluorescent substrates and specific inhibitors. The activities of MXR-mediated ABC proteins and their transcriptional level were examined in response to polyaromatic hydrocarbons (PAHs), main components of the water-accommodated fraction. This study increases the understanding of the protective role of MXR in response to PAHs over the comparative evolution of ABC gene families.
Collapse
Affiliation(s)
- Chang-Bum Jeong
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, South Korea
| | - Duck-Hyun Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Hye-Min Kang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Young Hwan Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Hui-Su Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Il-Chan Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
20
|
Jeong CB, Kang HM, Lee MC, Kim DH, Han J, Hwang DS, Souissi S, Lee SJ, Shin KH, Park HG, Lee JS. Adverse effects of microplastics and oxidative stress-induced MAPK/Nrf2 pathway-mediated defense mechanisms in the marine copepod Paracyclopina nana. Sci Rep 2017; 7:41323. [PMID: 28117374 PMCID: PMC5259799 DOI: 10.1038/srep41323] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/16/2016] [Indexed: 12/23/2022] Open
Abstract
Microplastic pollution causes a major concern in the marine environment due to their worldwide distribution, persistence, and adverse effects of these pollutants in the marine ecosystem. Despite its global presence, there is still a lack of information on the effect of microplastics on marine organisms at the molecular level. Herein we demonstrated ingestion and egestion of nano- (0.05 μm) and micro-sized (0.5 and 6 μm) polystyrene microbeads in the marine copepod Paracyclopina nana, and examined molecular responses to exposure to microbeads with in vivo endpoints such as growth rate and fecundity. Also, we proposed an adverse outcome pathway for microplastic exposure that covers molecular and individual levels. This study provides the first insight into the mode of action in terms of microplastic-induced oxidative stress and related signaling pathways in P. nana.
Collapse
Affiliation(s)
- Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.,Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, South Korea
| | - Hye-Min Kang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Chul Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Dae-Sik Hwang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Sami Souissi
- Univ. Lille, CNRS, Univ. Littoral Cote d'Opale, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F 62930 Wimereux, France
| | - Su-Jae Lee
- Department of Life Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, South Korea
| | - Kyung-Hoon Shin
- Department of Marine Sciences and Convergent Technology, College of Science &Technology, Hanyang University, Ansan 15588, South Korea
| | - Heum Gi Park
- Department of Marine Resource Development, College of Life Sciences, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| |
Collapse
|
21
|
Lee MC, Puthumana J, Lee SH, Kang HM, Park JC, Jeong CB, Han J, Hwang DS, Seo JS, Park HG, Om AS, Lee JS. BDE-47 induces oxidative stress, activates MAPK signaling pathway, and elevates de novo lipogenesis in the copepod Paracyclopina nana. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 181:104-112. [PMID: 27825063 DOI: 10.1016/j.aquatox.2016.10.025] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 06/06/2023]
Abstract
Brominated flame retardant, 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47), has received grave concerns as a persistent organic pollutant, which is toxic to marine organisms, and a suspected link to endocrine abnormalities. Despite the wide distribution in the marine ecosystem, very little is known about the toxic impairments on marine organisms, particularly on invertebrates. Thus, we examined the adverse effects of BDE-47 on life history trait (development), oxidative markers, fatty acid composition, and lipid accumulation in response to BDE-47-induced stress in the marine copepod Paracyclopina nana. Also, activation level of mitogen-activated protein kinase (MAPK) signaling pathways along with the gene expression profile of de novo lipogenesis (DNL) pathways were addressed. As a result, BDE-47 induced oxidative stress (e.g. reactive oxygen species, ROS) mediated activation of extracellular signal-regulated kinase (ERK) and c-Jun-N-terminal kinase (JNK) signaling cascades in MAPK pathways. Activated MAPK pathways, in turn, induced signal molecules that bind to the transcription factors (TFs) responsible for lipogenesis to EcR, SREBP, ChREBP promoters. Also, the stress stimulated the conversion of saturated fatty acids (SFAs) to polyunsaturated fatty acids (PUFAs), a preparedness of the organism to adapt the observed stress, which could be correlated with the elongase and desaturase gene (e.g. ELO3, Δ5-DES, Δ9-DES) expressions, and then extended to the delayed early post-embryonic development and increased accumulation of lipid droplets in P. nana. This study will provide a better understanding of how BDE-47 effects on marine invertebrates particularly on the copepods, an important link in the marine food chain.
Collapse
Affiliation(s)
- Min-Chul Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jayesh Puthumana
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Seung-Hwi Lee
- Department of Food and Nutrition, College of Health Science, Honam University, Gwangju 62399, South Korea; Department of Food and Nutrition, College of Human Ecology, Hanyang University, Seoul 04763, South Korea
| | - Hye-Min Kang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jun Chul Park
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Dae-Sik Hwang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jung Soo Seo
- Pathology Division, National Institute of Fisheries Science, Busan 46083, South Korea
| | - Heum Gi Park
- Department of Marine Bioscience, College of Life Sciences, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Ae-Son Om
- Department of Food and Nutrition, College of Human Ecology, Hanyang University, Seoul 04763, South Korea.
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
22
|
Dahms HU, Won EJ, Kim HS, Han J, Park HG, Souissi S, Raisuddin S, Lee JS. Potential of the small cyclopoid copepod Paracyclopina nana as an invertebrate model for ecotoxicity testing. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 180:282-294. [PMID: 27770640 DOI: 10.1016/j.aquatox.2016.10.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 06/06/2023]
Abstract
Aquatic invertebrates contribute significantly to environmental impact assessment of contaminants in aquatic ecosystems. Much effort has been made to identify viable and ecologically relevant invertebrate test organisms to meet rigorous regulatory requirements. Copepods, which are ecologically important and widely distributed in aquatic organisms, offer a huge opportunity as test organisms for aquatic toxicity testing. They have a major role not only in the transfer of energy in aquatic food chains, but also as a medium of transfer of aquatic pollutants across the tropic levels. In this regard, a supratidal and benthic harpacticoid copepod Tigriopus japonicus Mori (order Harpacticoida) has shown promising characteristics as a test organism in the field of ecotoxicology. Because there is a need to standardize a battery of test organisms from species in different phylogenetic and critical ecosystem positions, it is important to identify another unrelated planktonic species for wider application and comparison. In this regard, the cyclopoid copepod Paracyclopina nana Smirnov (order Cyclopoida) has emerged as a potential test organism to meet such requirements. Like T. japonicus, it has a number of features that make it a candidate worth consideration in such efforts. Recently, the genomics of P. nana has been unraveled. Data on biochemical and molecular responses of P. nana against exposure to environmental chemicals and other stressors have been collected. Recently, sequences and expression profiles of a number of genes in P. nana encoding for heat shock proteins, xenobiotic-metabolizing enzymes, and antioxidants have been reported. These genes serve as potential biomarkers in biomonitoring of environmental pollutants. Moreover, the application of gene expression techniques and the use of its whole transcriptome have allowed evaluation of transcriptional changes in P. nana with the ultimate aim of understanding the mechanisms of action of environmental stressors. Whole-animal bioassays and gene expression studies indicate that P. nana may serve as an excellent tool to evaluate the impact of diverse disturbances in the marine environment. With a better understanding of toxicological mechanisms, ecotoxicologists will be able to understand defense mechanisms against toxicants in copepods. In this review, we illustrate the potential of P. nana as an alternative as well as a complementary invertebrate model organism for risk assessment of aquatic pollutants.
Collapse
Affiliation(s)
- Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Eun-Ji Won
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Hui-Su Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Heum Gi Park
- Department of Marine Bioscience, College of Life Sciences, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Sami Souissi
- Univ. Lille, CNRS, Univ. Littoral Cote d'Opale, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, 62930 Wimereux, France
| | - Sheikh Raisuddin
- Department of Medical Elementology and Toxicology, Jamia Hamdard, Hamdard University, New Delhi 110062, India
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
23
|
Kim DH, Puthumana J, Kang HM, Lee MC, Jeong CB, Han J, Hwang DS, Kim IC, Lee JW, Lee JS. Adverse effects of MWCNTs on life parameters, antioxidant systems, and activation of MAPK signaling pathways in the copepod Paracyclopina nana. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 179:115-124. [PMID: 27595654 DOI: 10.1016/j.aquatox.2016.08.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 06/06/2023]
Abstract
Engineered multi-walled carbon nanotubes (MWCNTs) have received widespread applications in a broad variety of commercial products due to low production cost. Despite their significant commercial applications, CNTs are being discharged to aquatic ecosystem, leading a threat to aquatic life. Thus, we investigated the adverse effect of CNTs on the marine copepod Paracyclopina nana. Additional to the study on the uptake of CNTs and acute toxicity, adverse effects on life parameters (e.g. growth, fecundity, and size) were analyzed in response to various concentrations of CNTs. Also, as a measurement of cellular damage, oxidative stress-related markers were examined in a time-dependent manner. Moreover, activation of redox-sensitive mitogen-activated protein kinase (MAPK) signaling pathways along with the phosphorylation pattern of extracellular signal-regulated kinase (ERK), p38, and c-Jun-N-terminal kinases (JNK) were analyzed to obtain a better understanding of molecular mechanism of oxidative stress-induced toxicity in the copepod P. nana. As a result, significant inhibition on life parameters and evoked antioxidant systems were observed without ROS induction. In addition, CNTs activated MAPK signaling pathway via ERK, suggesting that phosphorylated ERK (p-ERK)-mediated adverse effects are the primary cause of in vitro and in vivo endpoints in response to CNTs exposure. Moreover, ROS-independent activation of MAPK signaling pathway was observed. These findings will provide a better understanding of the mode of action of CNTs on the copepod P. nana at cellular and molecular level and insight on possible ecotoxicological implications in the marine environment.
Collapse
Affiliation(s)
- Duck-Hyun Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jayesh Puthumana
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Hye-Min Kang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Chul Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Dae-Sik Hwang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Il-Chan Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, South Korea
| | - Jin Wuk Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| |
Collapse
|
24
|
Kim HS, Kim BM, Lee BY, Souissi S, Park HG, Lee JS. Identification of Hox genes and rearrangements within the single homeobox (Hox) cluster (192.8 kb) of the cyclopoid copepod (Paracyclopina nana). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 326:105-9. [PMID: 26833546 DOI: 10.1002/jez.b.22668] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/12/2016] [Indexed: 11/11/2022]
Abstract
We report the first identification of the entire complement of the eight typical homeobox (hox) genes (lab, pb, Dfd, scr, antp, ubx, Abd-A, and Abd-B) and the ftz gene in a 192.8 kb region in the cyclopoid copepod Paracyclopina nana. A Hox3 gene ortholog was not present in the P. nana hox gene cluster, while the P. nana Dfd gene was transcribed in the opposite direction to the Daphnia pulex Dfd gene, but in the same direction as the Dfd genes of the fruit fly Drosophila melanogaster and red flour beetle Tribolium castaneum. The location of the lab and pb genes was switched in the P. nana hox cluster, while the order of the remaining hox genes was generally conserved with those of other arthropods. J. Exp. Zool. (Mol. Dev. Evol.) 9999B:XX-XX, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Hui-Su Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Bo-Mi Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Bo-Young Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Sami Souissi
- Univ. Lille, CNRS, Univ. Littoral Cote d'Opale, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, Wimereux, France
| | - Heum Gi Park
- Department of Marine Bioscience, College of Life Sciences, Gangneung-Wonju National University, Gangneung, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| |
Collapse
|
25
|
Lee BY, Kim HS, Choi BS, Hwang DS, Choi AY, Han J, Won EJ, Choi IY, Lee SH, Om AS, Park HG, Lee JS. RNA-seq based whole transcriptome analysis of the cyclopoid copepod Paracyclopina nana focusing on xenobiotics metabolism. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2015; 15:12-9. [DOI: 10.1016/j.cbd.2015.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 04/16/2015] [Accepted: 04/30/2015] [Indexed: 11/27/2022]
|
26
|
Won EJ, Han J, Lee Y, Kumar KS, Shin KH, Lee SJ, Park HG, Lee JS. In vivo effects of UV radiation on multiple endpoints and expression profiles of DNA repair and heat shock protein (Hsp) genes in the cycloid copepod Paracyclopina nana. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 165:1-8. [PMID: 26001085 DOI: 10.1016/j.aquatox.2015.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/01/2015] [Accepted: 05/02/2015] [Indexed: 06/04/2023]
Abstract
To evaluate the effects of ultraviolet (UV) radiation on energy acquisition and consumption, the copepod Paracyclopina nana was irradiated with several doses (0-3kJ/m(2)) of UV. After UV radiation, we measured the re-brooding success, growth pattern of newly hatched nauplii, ingestion rate, and assimilation of diet. In addition, we checked the modulated patterns of DNA repair and heat shock protein (hsp) chaperoning genes of P. nana. UV-B radiation induced a significant reduction (7-87%) of the re-brooding rate of ovigerous females, indicating that UV-induced egg sac damage is closely correlated with a reduction in the hatching rate of UV-irradiated ovigerous female offspring. Using chlorophyll a and stable carbon isotope incubation experiments, we found a dose-dependent decrease (P<0.05) in food ingestion and the rate of assimilation to the body in response to UV radiation, implying that P. nana has an underlying ability to shift its balanced-energy status from growth and reproduction to DNA repair and adaptation. Also, expression of P. nana base excision repair (BER)-associated genes and hsp chaperoning genes was significantly increased in response to UV radiation in P. nana. These findings indicate that even 1kJ/m(2) of UV radiation induces a reduction in reproduction and growth patterns, alters the physiological balance and inhibits the ability to cope with UV-induced damage in P. nana.
Collapse
Affiliation(s)
- Eun-Ji Won
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Yeonjung Lee
- Department of Marine Sciences and Convergent Technology, College of Science and Technology, Hanyang University, Ansan 426-791, South Korea
| | - K Suresh Kumar
- Department of Marine Sciences and Convergent Technology, College of Science and Technology, Hanyang University, Ansan 426-791, South Korea
| | - Kyung-Hoon Shin
- Department of Marine Sciences and Convergent Technology, College of Science and Technology, Hanyang University, Ansan 426-791, South Korea
| | - Su-Jae Lee
- Department of Life Sciences, College of Natural Sciences, Hanyang University, Seoul 133-791, South Korea
| | - Heum Gi Park
- Department of Marine Resource Development, College of Life Sciences, Gangneung-Wonju National University, Gangneung 210-702, South Korea.
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea.
| |
Collapse
|
27
|
Won EJ, Lee Y, Han J, Hwang UK, Shin KH, Park HG, Lee JS. Effects of UV radiation on hatching, lipid peroxidation, and fatty acid composition in the copepod Paracyclopina nana. Comp Biochem Physiol C Toxicol Pharmacol 2014; 165:60-6. [PMID: 24952335 DOI: 10.1016/j.cbpc.2014.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/26/2014] [Accepted: 06/10/2014] [Indexed: 11/24/2022]
Abstract
To evaluate the effects of UV radiation on the reproductive physiology and macromolecules in marine zooplankton, several doses of UV radiation were used to treat the copepod Paracyclopina nana, and we analyzed in vivo endpoints of their life cycle such as mortality and reproductive parameters with in vitro biochemical biomarkers such as reactive oxygen species (ROS), the modulated enzyme activity of glutathione S-transferase (GST) and superoxide dismutase (SOD), and the production of a byproduct of peroxidation (e.g. malonedialdehyde, MDA). After UV radiation, the survival rate of P. nana was significantly reduced. Also, egg sac damage and a reduction in the hatching rate of offspring were observed in UV-irradiated ovigerous females. According to the assessed biochemical parameters, we found dose-dependent increases in ROS levels and high levels of the lipid peroxidation decomposition product by 2 kJ m(-2), implying that P. nana was under off-balanced status by oxidative stress-mediated cellular damage. Antioxidant enzyme activities of GST and SOD increased over different doses of UV radiation. To measure UV-induced lipid peroxidation, we found a slight reduction in the composition of essential fatty acids such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). These findings indicate that UV radiation can induce oxidative stress-triggered lipid peroxidation with modulation of antioxidant enzyme activity, leading to a significant effect on mortality and reproductive physiology (e.g. fecundity). These results demonstrate the involvement of UV radiation on essential fatty acids and its susceptibility to UV radiation in the copepod P. nana compared to other species.
Collapse
Affiliation(s)
- Eun-Ji Won
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Yeonjung Lee
- Department of Marine Sciences and Convergent Technology, College of Science and Technology, Hanyang University, Ansan 426-791, South Korea
| | - Jeonghoon Han
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Un-Ki Hwang
- Marine Ecological Risk Assessment Center, West Sea Fisheries Research Institute, National Fisheries Research & Development Institute, Incheon 400-420, South Korea
| | - Kyung-Hoon Shin
- Department of Marine Sciences and Convergent Technology, College of Science and Technology, Hanyang University, Ansan 426-791, South Korea
| | - Heum Gi Park
- Department of Marine Resource Development, College of Life Sciences, Gangneung-Wonju National University, Gangneung 210-702, South Korea.
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 440-746, South Korea.
| |
Collapse
|
28
|
Sun WY, Sun SC. A description of the complete mitochondrial genomes of Amphiporus formidabilis, Prosadenoporus spectaculum and Nipponnemertes punctatula (Nemertea: Hoplonemertea: Monostilifera). Mol Biol Rep 2014; 41:5681-92. [PMID: 24939507 DOI: 10.1007/s11033-014-3438-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/27/2014] [Indexed: 11/30/2022]
Abstract
We sequenced the complete mitochondrial genomes (mitogenomes) of three Hoplonemertea species, Amphiporus formidabilis, Prosadenoporus spectaculum and Nipponnemertes punctatula, which are 14,616, 14,655 and 15,354 bp in length, respectively. Each of the three circular mitogenomes consists of 37 typical genes and some non-coding regions. The nucleotide composition of the coding strand is biased toward T, almost a half of total nucleotides in these mitogenomes. There are many poly-T tracts across these mitogenomes, which exhibit T-number variation within different clones of protein-coding genes, mainly resulting from false PCR amplification. The major non-coding regions have tandem repeat motifs and hairpin-like structures that may be associated with the initiation of replication or transcription. Data published to date for nemerteans show that Palaeonemertea species usually bear the largest mitogenomes, while representatives in the more recently derived Distromatonemertea clade bear the smallest ones; and that the gene arrangement of mitogenomes seems to be variable within the phylum Nemertea, but stable within either of Heteronemertea and Hoplonemertea.
Collapse
Affiliation(s)
- Wen-Yan Sun
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | | |
Collapse
|
29
|
Won EJ, Lee JS. Gamma radiation induces growth retardation, impaired egg production, and oxidative stress in the marine copepod Paracyclopina nana. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2014; 150:17-26. [PMID: 24632311 DOI: 10.1016/j.aquatox.2014.02.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 02/16/2014] [Accepted: 02/18/2014] [Indexed: 06/03/2023]
Abstract
Accidental nuclear radioisotope release into the ocean from nuclear power plants is of concern due to ecological and health risks. In this study, we used the marine copepod Paracyclopina nana to examine the effects of radioisotopes on marine organisms upon gamma radiation, and to measure the effects on growth and fecundity, which affect population and community structure. Upon gamma radiation, mortality (LD50 - 96 h=172 Gy) in P. nana was significantly increased in a dose-dependent manner in ovigerous P. nana females. For developmental impairment of gamma-irradiated nauplii, we observed growth retardation; in over 30 Gy-irradiated groups, offspring did not grow to adults. Particularly, over 50 Gy-irradiated ovigerous P. nana females did not have normal bilateral egg sacs, and their offspring did not develop normally to adulthood. Additionally, at over 30 Gy, we found dose-dependent increases in oxidative levels with elevated antioxidant enzyme activities and DNA repair activities. These findings indicate that gamma radiation can induce oxidative stress and DNA damage with growth retardation and impaired reproduction.
Collapse
Affiliation(s)
- Eun-Ji Won
- Department of Biological Sciences, College of Natural Sciences, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Natural Sciences, Sungkyunkwan University, Suwon 440-746, South Korea.
| |
Collapse
|
30
|
Austin CM, Tan MH, Lee YP, Croft LJ, Meekan MG, Pierce SJ, Gan HM. The complete mitogenome of the whale shark parasitic copepodPandarus rhincodonicusnorman, Newbound & Knott (Crustacea; Siphonostomatoida; Pandaridae) – a new gene order for the copepoda. ACTA ACUST UNITED AC 2014; 27:694-5. [DOI: 10.3109/19401736.2014.913147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
31
|
Easton EE, Darrow EM, Spears T, Thistle D. The mitochondrial genomes of Amphiascoides atopus and Schizopera knabeni (Harpacticoida: Miraciidae) reveal similarities between the copepod orders Harpacticoida and Poecilostomatoida. Gene 2014; 538:123-37. [DOI: 10.1016/j.gene.2013.12.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 12/24/2013] [Indexed: 12/15/2022]
|
32
|
Kim S, Lim BJ, Min GS, Choi HG. The complete mitochondrial genome of Arctic Calanus hyperboreus (Copepoda, Calanoida) reveals characteristic patterns in calanoid mitochondrial genome. Gene 2013; 520:64-72. [DOI: 10.1016/j.gene.2012.09.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 09/10/2012] [Accepted: 09/20/2012] [Indexed: 12/13/2022]
|
33
|
Jondeung A, Karinthanyakit W, Kaewkhumsan J. The complete mitochondrial genome of the black mud crab, Scylla serrata (Crustacea: Brachyura: Portunidae) and its phylogenetic position among (pan)crustaceans. Mol Biol Rep 2012; 39:10921-37. [PMID: 23053985 DOI: 10.1007/s11033-012-1992-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
Abstract
The black mud crab, Scylla serrata (Forskål 1775), is the most economically important edible crab in South-East Asia. In the present study, the complete mitochondrial genome of black mud crab, S. serrata, was determined with the sequential polymerase chain reaction and primer walking sequencing. The complete mitochondrial genome was 15,721 bp in length with an A+T content of 69.2 % and contained 37 mitochondrial genes (13 protein coding genes (PCGs), 2 ribosomal RNA genes and 22 transfer RNA genes) and a control region (CR). The analysis of the CR sequence shows that it contains a multitude of repetitive fragments which can fold into hairpin-like or secondary structures and conserved elements as in other arthropods. The gene order of S. serrata mainly retains as the pancrustacean ground pattern, except for a single translocation of trnH. The gene arrangement of S. serrata appears to be a typical feature of portunid crabs. Phylogenetic analyses with concatenated amino acid sequences of 12 PCGs establishes that S. serrata in a well-supported monophyletic Portunidae and is consistent with previous morphological classification. Moreover, the phylogenomic results strongly support monophyletic Pancrustacea (Hexapoda plus "Crustaceans"). Within Pancrustacea, this study identifies Malacostraca + Entomostraca and Branchiopoda as the sister group to Hexapoda, which confirms that "Crustacea" is not monophyletic. Cirripedia + Remipedia appear to be a basal lineage of Pancrustacea. The present study also provides considerable data for the application of both population and phylogenetic studies of other crab species.
Collapse
Affiliation(s)
- Amnuay Jondeung
- Department of Genetics, Kasetsart University, Bangkok, 10900, Thailand.
| | | | | |
Collapse
|
34
|
Liu GH, Wang SY, Huang WY, Zhao GH, Wei SJ, Song HQ, Xu MJ, Lin RQ, Zhou DH, Zhu XQ. The complete mitochondrial genome of Galba pervia (Gastropoda: Mollusca), an intermediate host snail of Fasciola spp. PLoS One 2012; 7:e42172. [PMID: 22844544 PMCID: PMC3406003 DOI: 10.1371/journal.pone.0042172] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 07/04/2012] [Indexed: 11/26/2022] Open
Abstract
Complete mitochondrial (mt) genomes and the gene rearrangements are increasingly used as molecular markers for investigating phylogenetic relationships. Contributing to the complete mt genomes of Gastropoda, especially Pulmonata, we determined the mt genome of the freshwater snail Galba pervia, which is an important intermediate host for Fasciola spp. in China. The complete mt genome of G. pervia is 13,768 bp in length. Its genome is circular, and consists of 37 genes, including 13 genes for proteins, 2 genes for rRNA, 22 genes for tRNA. The mt gene order of G. pervia showed novel arrangement (tRNA-His, tRNA-Gly and tRNA-Tyr change positions and directions) when compared with mt genomes of Pulmonata species sequenced to date, indicating divergence among different species within the Pulmonata. A total of 3655 amino acids were deduced to encode 13 protein genes. The most frequently used amino acid is Leu (15.05%), followed by Phe (11.24%), Ser (10.76%) and IIe (8.346%). Phylogenetic analyses using the concatenated amino acid sequences of the 13 protein-coding genes, with three different computational algorithms (maximum parsimony, maximum likelihood and Bayesian analysis), all revealed that the families Lymnaeidae and Planorbidae are closely related two snail families, consistent with previous classifications based on morphological and molecular studies. The complete mt genome sequence of G. pervia showed a novel gene arrangement and it represents the first sequenced high quality mt genome of the family Lymnaeidae. These novel mtDNA data provide additional genetic markers for studying the epidemiology, population genetics and phylogeographics of freshwater snails, as well as for understanding interplay between the intermediate snail hosts and the intra-mollusca stages of Fasciola spp..
Collapse
Affiliation(s)
- Guo-Hua Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Shu-Yan Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
- College of Animal Science and Technology, Guangxi Univesity, Nanning, Guangxi Zhuang Nationality Autonomous Region, China
| | - Wei-Yi Huang
- College of Animal Science and Technology, Guangxi Univesity, Nanning, Guangxi Zhuang Nationality Autonomous Region, China
| | - Guang-Hui Zhao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
- College of Veterinary Medicine, Northwest A & F University, Yangling, Shaanxi Province, China
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hui-Qun Song
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Min-Jun Xu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Rui-Qing Lin
- Laboratory of Parasitology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Dong-Hui Zhou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan Province, China
- * E-mail:
| |
Collapse
|
35
|
The mitogenome of Gammarus duebeni (Crustacea Amphipoda): A new gene order and non-neutral sequence evolution of tandem repeats in the control region. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2012; 7:201-11. [DOI: 10.1016/j.cbd.2012.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/21/2012] [Accepted: 02/27/2012] [Indexed: 11/23/2022]
|
36
|
Kilpert F, Held C, Podsiadlowski L. Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications. Mol Phylogenet Evol 2012; 64:106-17. [PMID: 22491068 DOI: 10.1016/j.ympev.2012.03.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 03/15/2012] [Accepted: 03/16/2012] [Indexed: 10/28/2022]
Abstract
In this study, we analyse the evolutionary dynamics and phylogenetic implications of gene order rearrangements in five newly sequenced mitochondrial (mt) genomes and four published mt genomes of isopod crustaceans. The sequence coverage is nearly complete for four of the five newly sequenced species, with only the control region and some tRNA genes missing, while in Janira maculosa only two thirds of the genome could be determined. Mitochondrial gene order in isopods seems to be more plastic than that in other crustacean lineages, making all nine known mt gene orders different. Especially the asellote Janira is characterized by many autapomorphies. The following inferred ancestral isopod mt gene order exists slightly modified in modern isopods: nad1, tnrL1, rrnS, control region, trnS1, cob, trnT, nad5, trnF. We consider the inferred gene translocation events leading to gene rearrangements as valuable characters in phylogenetic analyses. In this first study covering major isopod lineages, potential apomorphies were identified, e.g., a shared relative position of trnR in Valvifera. We also report one of the first findings of homoplasy in mitochondrial gene order, namely a shared relative position of trnV in unrelated isopod lineages. In addition to increased taxon sampling secondary structure, modification in tRNAs and GC-skew inversion may be potentially fruitful subjects for future mt genome studies in a phylogenetic context.
Collapse
Affiliation(s)
- Fabian Kilpert
- Institute of Evolutionary Biology and Ecology, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
| | | | | |
Collapse
|
37
|
Yasuike M, Leong J, Jantzen SG, von Schalburg KR, Nilsen F, Jones SRM, Koop BF. Genomic resources for sea lice: analysis of ESTs and mitochondrial genomes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:155-166. [PMID: 21748342 PMCID: PMC3280385 DOI: 10.1007/s10126-011-9398-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 06/22/2011] [Indexed: 05/31/2023]
Abstract
Sea lice are common parasites of both farmed and wild salmon. Salmon farming constitutes an important economic market in North America, South America, and Northern Europe. Infections with sea lice can result in significant production losses. A compilation of genomic information on different genera of sea lice is an important resource for understanding their biology as well as for the study of population genetics and control strategies. We report on over 150,000 expressed sequence tags (ESTs) from five different species (Pacific Lepeophtheirus salmonis (49,672 new ESTs in addition to 14,994 previously reported ESTs), Atlantic L. salmonis (57,349 ESTs), Caligus clemensi (14,821 ESTs), Caligus rogercresseyi (32,135 ESTs), and Lernaeocera branchialis (16,441 ESTs)). For each species, ESTs were assembled into complete or partial genes and annotated by comparisons to known proteins in public databases. In addition, whole mitochondrial (mt) genome sequences of C. clemensi (13,440 bp) and C. rogercresseyi (13,468 bp) were determined and compared to L. salmonis. Both nuclear and mtDNA genes show very high levels of sequence divergence between these ectoparastic copepods suggesting that the different species of sea lice have been in existence for 37-113 million years and that parasitic association with salmonids is also quite ancient. Our ESTs and mtDNA data provide a novel resource for the study of sea louse biology, population genetics, and control strategies. This genomic information provides the material basis for the development of a 38K sea louse microarray that can be used in conjunction with our existing 44K salmon microarray to study host-parasite interactions at the molecular level. This report represents the largest genomic resource for any copepod species to date.
Collapse
Affiliation(s)
- Motoshige Yasuike
- Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, BC V8W 3N5 Canada
- Present Address: Aquatic Genomics Research Center, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama, Kanagawa 236-8648 Japan
| | - Jong Leong
- Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, BC V8W 3N5 Canada
| | - Stuart G. Jantzen
- Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, BC V8W 3N5 Canada
| | | | - Frank Nilsen
- Department of Biology, University of Bergen, 5020 Bergen, Norway
| | - Simon R. M. Jones
- Pacific Biological Station, Fisheries and Oceans Canada, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7 Canada
| | - Ben F. Koop
- Department of Biology, University of Victoria, PO Box 3020 STN CSC, Victoria, BC V8W 3N5 Canada
| |
Collapse
|
38
|
Kim S, Park MH, Jung JH, Ahn DH, Sultana T, Kim S, Park JK, Choi HG, Min GS. The mitochondrial genomes of Cambaroides similis and Procambarus clarkii (Decapoda: Astacidea: Cambaridae): the phylogenetic implications for Reptantia. ZOOL SCR 2012. [DOI: 10.1111/j.1463-6409.2012.00534.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
39
|
Kim S, Kim J, Choi HG, Park JK, Min GS. Complete mitochondrial genome of the northern mauxia shrimpAcetes chinensis(Decapoda, Dendrobranchiata, Sergestoidae). ACTA ACUST UNITED AC 2012; 23:28-30. [DOI: 10.3109/19401736.2011.643878] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
40
|
Bron JE, Frisch D, Goetze E, Johnson SC, Lee CE, Wyngaard GA. Observing copepods through a genomic lens. Front Zool 2011; 8:22. [PMID: 21933388 PMCID: PMC3184258 DOI: 10.1186/1742-9994-8-22] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 09/20/2011] [Indexed: 01/08/2023] Open
Abstract
Background Copepods outnumber every other multicellular animal group. They are critical components of the world's freshwater and marine ecosystems, sensitive indicators of local and global climate change, key ecosystem service providers, parasites and predators of economically important aquatic animals and potential vectors of waterborne disease. Copepods sustain the world fisheries that nourish and support human populations. Although genomic tools have transformed many areas of biological and biomedical research, their power to elucidate aspects of the biology, behavior and ecology of copepods has only recently begun to be exploited. Discussion The extraordinary biological and ecological diversity of the subclass Copepoda provides both unique advantages for addressing key problems in aquatic systems and formidable challenges for developing a focused genomics strategy. This article provides an overview of genomic studies of copepods and discusses strategies for using genomics tools to address key questions at levels extending from individuals to ecosystems. Genomics can, for instance, help to decipher patterns of genome evolution such as those that occur during transitions from free living to symbiotic and parasitic lifestyles and can assist in the identification of genetic mechanisms and accompanying physiological changes associated with adaptation to new or physiologically challenging environments. The adaptive significance of the diversity in genome size and unique mechanisms of genome reorganization during development could similarly be explored. Genome-wide and EST studies of parasitic copepods of salmon and large EST studies of selected free-living copepods have demonstrated the potential utility of modern genomics approaches for the study of copepods and have generated resources such as EST libraries, shotgun genome sequences, BAC libraries, genome maps and inbred lines that will be invaluable in assisting further efforts to provide genomics tools for copepods. Summary Genomics research on copepods is needed to extend our exploration and characterization of their fundamental biological traits, so that we can better understand how copepods function and interact in diverse environments. Availability of large scale genomics resources will also open doors to a wide range of systems biology type studies that view the organism as the fundamental system in which to address key questions in ecology and evolution.
Collapse
Affiliation(s)
- James E Bron
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, Scotland, UK.
| | | | | | | | | | | |
Collapse
|
41
|
Ma K, Feng J, Lin J, Li J. The complete mitochondrial genome of Macrobrachium nipponense. Gene 2011; 487:160-5. [PMID: 21827838 DOI: 10.1016/j.gene.2011.07.017] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Revised: 06/05/2011] [Accepted: 07/09/2011] [Indexed: 11/18/2022]
Abstract
The complete mitochondrial (mt) genome sequence plays an important role in the accurate determination of phylogenetic relationships among metazoans. Herein, we determined the complete mt genome sequence, structure and organization of Macrobrachium nipponense (M. nipponense) (GenBank ID: NC_015073.1) and compared it to that of Macrobrachium lanchesteri (M. lanchesteri) and Macrobrachium rosenbergii (M. rosenbergii). The 15,806 base pair (bp) M. nipponense mt genome, which is comprised of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) and 2 ribosomal RNAs (rRNAs), is slightly larger than that of M. lanchesteri (15,694bp, GenBank ID: NC_012217.1) and M. rosenbergii (15,772bp, GenBank ID: NC_006880.1). The M. nipponense genome contains a high AT content (66.0%), which is a common feature among metazoan mt genomes. Compared with M. lanchesteri and M. rosenbergii, we found a peculiar non-coding region of 950bp with a microsatellite-like (TA)(6) element and many hairpin structures. The 13 PCGs are comprised of a total of 3707 codons, excluding incomplete termination codons, and the most frequently used amino acid is Leu (16.0%). The predicted start codons in the M. nipponense mt genome include ATG, ATC and ATA. Seven PCGs use TAA as a stop codon, whereas two use TAG, three use T and only one uses TA. Twenty-three of the genes are encoded on the L strand, and ND1, ND4, ND5, ND4L, 12S rRNA, 16S rRNA, tRNA(His), tRNA(Pro), tRNA(Phe), tRNA(Val), tRNA(Gln), tRNA(Cys), tRNA(Tyr) and a tRNA(Leu) are encoded on the H strand. The two rRNAs of M. nipponense and M. rosenbergii are encoded on the H strand, whereas the M. lanchesteri rRNAs are encoded on the L stand.
Collapse
Affiliation(s)
- Keyi Ma
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, China.
| | | | | | | |
Collapse
|
42
|
Cheng J, Ma GQ, Miao ZQ, Shui BN, Gao TX. Complete mitochondrial genome sequence of the spinyhead croaker Collichthys lucidus (Perciformes, Sciaenidae) with phylogenetic considerations. Mol Biol Rep 2011; 39:4249-59. [PMID: 21786157 DOI: 10.1007/s11033-011-1211-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 07/14/2011] [Indexed: 11/29/2022]
Abstract
The complete mitochondrial genome of the spinyhead croaker Collichthys lucidus was determined using long-PCR and primer walking methods. It is a circular molecule of 16,451 bp in length with a standard set of 22 tRNAs, 2 rRNAs, 13 protein-coding genes as well as a non-coding control region in the same order as those of the other bony fishes. C. lucidus mitogenome exhibited a clear strand-specific bias in nucleotide composition, as evidence by a GC- skew of the H-strand of -0.319. The strand-specific bias was also reflected in the codon usage of genes oriented in opposite directions. All tRNA genes except for tRNA( Ser(AGY)) harbored the typical cloverleaf secondary structures and possessed anticodons that matched the vertebrate mitochondrial genetic code. Contrary to the typical structure of control region consistig of TAS, central, and CSB domains, there were no central conserved blocks available in C. lucidus mitogenome. Despite extensive studies based on both morphology and molecules, phylogenetic position of C. lucidus with Sciaenidae is still controversial. Our phylogenetic results provided more evidence to support previous morphological studies and consistently placed C. lucidus as a sister taxon to Collichthys niveatus, with both of these taxa forming the monophyletic Collichthys.
Collapse
Affiliation(s)
- Jiao Cheng
- Fisheries College, Ocean University of China, Qingdao, 266003, China
| | | | | | | | | |
Collapse
|
43
|
Lin RQ, Qiu LL, Liu GH, Wu XY, Weng YB, Xie WQ, Hou J, Pan H, Yuan ZG, Zou FC, Hu M, Zhu XQ. Characterization of the complete mitochondrial genomes of five Eimeria species from domestic chickens. Gene 2011; 480:28-33. [DOI: 10.1016/j.gene.2011.03.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2010] [Revised: 02/13/2011] [Accepted: 03/03/2011] [Indexed: 10/18/2022]
|
44
|
Dequard-Chablat M, Sellem CH, Golik P, Bidard F, Martos A, Bietenhader M, di Rago JP, Sainsard-Chanet A, Hermann-Le Denmat S, Contamine V. Two Nuclear Life Cycle-Regulated Genes Encode Interchangeable Subunits c of Mitochondrial ATP Synthase in Podospora anserina. Mol Biol Evol 2011; 28:2063-75. [DOI: 10.1093/molbev/msr025] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
|
45
|
Minxiao W, Song S, Chaolun L, Xin S. Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: useful molecular markers for phylogenetic and population studies. BMC Genomics 2011; 12:73. [PMID: 21269523 PMCID: PMC3041745 DOI: 10.1186/1471-2164-12-73] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 01/27/2011] [Indexed: 11/10/2022] Open
Abstract
Background Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies. Results The mitochondrial genome of C. sinicus is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of C. sinicus include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes atp6 and atp8 relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 C. sinicus mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci. Conclusion The occurrence of the circular subgenomic fragment during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of C. sinicus during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for resolving phylogenetic issues concerning copepods. The variable site maps of C. sinicus mitogenomes provide a solid foundation for population genetic studies.
Collapse
Affiliation(s)
- Wang Minxiao
- KLMEES and JBMERS, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | | | | | | |
Collapse
|
46
|
Ki JS, Hop H, Kim SJ, Kim IC, Park HG, Lee JS. Complete mitochondrial genome sequence of the Arctic gammarid, Onisimus nanseni (Crustacea; Amphipoda): Novel gene structures and unusual control region features. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2010; 5:105-15. [DOI: 10.1016/j.cbd.2010.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 02/04/2010] [Accepted: 02/08/2010] [Indexed: 10/19/2022]
|
47
|
Phylogeny of the freshwater copepod Mesocyclops (Crustacea: Cyclopidae) based on combined molecular and morphological data, with notes on biogeography. Mol Phylogenet Evol 2010; 55:753-64. [DOI: 10.1016/j.ympev.2010.02.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 02/24/2010] [Accepted: 02/25/2010] [Indexed: 11/18/2022]
|
48
|
Hwang DS, Lee KW, Han J, Park HG, Lee J, Lee YM, Lee JS. Molecular characterization and expression of vitellogenin (Vg) genes from the cyclopoid copepod, Paracyclopina nana exposed to heavy metals. Comp Biochem Physiol C Toxicol Pharmacol 2010; 151:360-8. [PMID: 20045491 DOI: 10.1016/j.cbpc.2009.12.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 12/23/2009] [Accepted: 12/24/2009] [Indexed: 11/22/2022]
Abstract
Induction of vitellogenin (Vg) has been used as a biomarker of exposure to heavy metals and endocrine-disruption chemicals (EDCs) in aquatic organisms. Here, we identified the full-length Vg1 and Vg2 sequence from the brackish water copepod, Paracyclopina nana. Vg1 gene contained 5718bp of the open reading frame (ORF) that encoded the putative protein of 1905 amino acids residues, while Vg2 gene consisted of 5442bp of ORF, encoding the putative protein of 1813 amino acids residues. P. nana Vgs showed highly conserved domains in the N-terminal region. The phylogenetic analysis revealed that P. nana Vgs are distinct from other arthropods, such as insects and decapods, as it formed a clade with other copepods, Tigriopus japonicus and salmon louse (Lepeophtheirus salmonis). The expression of Vg transcripts was detectable after the copepodid stages 4-5. Female copepods expressed over 83 times and 223 times more Vg1 and Vg2 transcripts, respectively, than males. When copepods were exposed to heavy metals (0.1mg/L Cd, 0.4mg/L Cu, and 2mg/L AsIII) for 24, 48, 72, and 96h, P. nana Vg transcripts were highly induced in a time-dependent manner. Interestingly, Vg2 gene was more susceptible than Vg1 to trace heavy metal exposure. This finding indicates that P. nana Vgs provide a potential indicator for assessing the toxic effect of heavy metals. In addition, we suggest P. nana as a potential model species for risk-assessment to environmental pollutants in brackish water.
Collapse
Affiliation(s)
- Dae-Sik Hwang
- Department of Molecular and Environmental Bioscience, Graduate School, Hanyang University, Seoul 133-791, South Korea
| | | | | | | | | | | | | |
Collapse
|
49
|
Ki JS, Lee YM, Jung SO, Horiguchi T, Cho HS, Lee JS. Mitochondrial genome of Thais clavigera (Mollusca: Gastropoda): affirmation of the conserved, ancestral gene pattern within the mollusks. Mol Phylogenet Evol 2009; 54:1016-20. [PMID: 20004731 DOI: 10.1016/j.ympev.2009.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 10/28/2009] [Accepted: 12/03/2009] [Indexed: 10/20/2022]
Abstract
Class Gastropoda includes a large number of described species, many with extensively rearranged mitochondrial genomes. We sequenced the mitogenome of the rock shell, Thais clavigera (Gastropoda: Muricidae), an intertidal snail, using long PCR with primers designed on the basis of expressed sequence tags. The mitogenome of T. clavigera consists of 2 rRNAs, 22 tRNAs, and 13 protein-coding genes, but no control region. Structural comparisons revealed that the order Sorbeoconcha, including T. clavigera, have nearly identical mitochondrial gene patterns. However, they have an inversion between a tRNA(Phe)-tRNA(Glu) cluster that comprises 21 genes, but most of the remaining structure is similar to the putative mollusk ground pattern. These findings will provide a better insight into mitochondrial gene rearrangement over the course of gastropod evolution.
Collapse
Affiliation(s)
- Jang-Seu Ki
- Department of Life Science, College of Natural Sciences, Sangmyung University, Seoul 110-743, South Korea
| | | | | | | | | | | |
Collapse
|
50
|
Ki JS, Dahms HU, Hwang JS, Lee JS. The complete mitogenome of the hydrothermal vent crab Xenograpsus testudinatus (Decapoda, Brachyura) and comparison with brachyuran crabs. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2009; 4:290-299. [PMID: 20403751 DOI: 10.1016/j.cbd.2009.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 07/01/2009] [Accepted: 07/09/2009] [Indexed: 11/28/2022]
Abstract
In this study, we analyzed the complete mitochondrial (mt) genome of a hydrothermal vent crab Xenograpsus testudinatus (Decapoda: Brachyura) obtained from the hydrothermal vents off Kueishantao Island, Taiwan, which extend from the deep sea Okinawa Trench. The mitogenome of X. testudinatus was 15,796 bp in length and contained the same 37 genes (e.g. 2 rRNAs, 22 tRNAs, and 13 PCGs) found in other metazoan mitogenomes. Analysis of the structural mt gene order in X. testudinatus revealed that the 13 PCGs, excluding a translocation of ND6-Cyt b cluster, were similarly ordered when compared to the pancrustacean ground pattern; however the tRNAs were severely rearranged. Phylogenetic analysis of decapod mitogenomes showed that the molecular taxonomy of the vent crab was in accordance with its morphological systematics. Together, these findings suggest that the vent crab studied here has little mitochondrial genetic variation when compared with morphologically defined conspecifics from other marine habitats.
Collapse
Affiliation(s)
- Jang-Seu Ki
- National Research Lab of Marine Molecular and Environmental Bioscience, Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 133-791, South Korea
| | - Hans-Uwe Dahms
- National Research Lab of Marine Molecular and Environmental Bioscience, Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 133-791, South Korea
| | - Jiang-Shiou Hwang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 202, Taiwan.
| | - Jae-Seong Lee
- National Research Lab of Marine Molecular and Environmental Bioscience, Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 133-791, South Korea.
| |
Collapse
|