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Chen S, Jiang X, Xia L, Chen Z, Zhou K, Yan J, Li P. The identification, adaptive evolutionary analyses and mRNA expression levels of homeobox (hox) genes in the Chinese mitten crab Eriocheir sinensis. BMC Genomics 2023; 24:436. [PMID: 37537567 PMCID: PMC10401747 DOI: 10.1186/s12864-023-09489-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/28/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Arthropods are the largest group in the animal kingdom and are morphologically characterized by heterorhythmic segments. Brachyuran decapod crustaceans undergo brachyurization metamorphosis in the early developmental process, characterized by a reduced abdomen that is folded beneath the cephalothorax and inserted between the pereiopods or in a special cavity. As the main cause of major alterations in the evolution of animal body plans, Hox genes encode transcription factors and are involved in bilaterian anterior-posterior axis patterning. RESULTS We found eight Hox genes (labial, proboscipedia, Deformed, zerknüllt, Sex combs reduced, Antennapedia, Ultrabithorax, fushi tarazu, abdominal-A and Abdominal-B) in Eriocheir sinensis. The phylogenetic topology of 13 arthropod Hox genes was closely related to traditional taxonomic groupings. Genome collinearity analysis was performed using genomic data and chromosomal location data of E. sinensis and Portunus trituratus. We found that their chromosomes were highly collinear, and there was a corresponding collinear relationship between the three Hox genes (lab, ftz and Abd-B). The mRNA expression levels of Scr and Antp fluctuated significantly in different developmental stages of E. sinensis, especially in the brachyurization stages. Evolutionary analysis indicated the presence of positively selected sites in Ubx. CONCLUSIONS In this study, we used genome-wide analysis to identify and analyze all members of the Hox genes in E. sinensis. Our data will contribute to a better understanding of Hox genes in E. sinensis and provide useful molecular evolutionary information for further investigation on their roles in the brachyurization of crabs.
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Affiliation(s)
- Shasha Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Xianfeng Jiang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Longjie Xia
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zhiyi Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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2
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Jaramillo ML, Ammar D, Quispe RL, Bonatto Paese CL, Gruendling AP, Müller YM, Nazari EM. Identification of Hox genes and their expression profiles during embryonic development of the emerging model organism, Macrobrachium olfersii. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:292-300. [PMID: 35037742 DOI: 10.1002/jez.b.23118] [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: 07/07/2021] [Revised: 12/13/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
Hox genes encode transcription factors that specify the body segment identity during development, including crustaceans, such as amphipods and decapods, that possess a remarkable diversity of segments and specialized appendages. In amphipods, alterations of specialized appendages have been obtained using knockout experiment of Hox genes, which suggests that these genes are involved in the evolution of morphology within crustaceans. However, studies of Hox genes in crustaceans have been limited to a few species. Here, we identified the homeodomain of nine Hox genes: labial (lab), proboscipedia (pb), Deformed (Dfd), Sex combs reduced (Scr), fushi tarazu (ftz), Antennapedia (Antp), Ultrabithorax (Ubx), abdominal-A (abdA), and Abdominal-B (AbdB), and evaluated their expression by RT-qPCR and RT-PCR in the ovary, during embryonic development, and at the first larval stage (Zoea I) of the decapod Macrobrachium olfersii. The transcript levels of lab, Dfd, and ftz decreased and transcripts of pb, Scr, Antp, Ubx, abdA, and AbdB increased during embryonic development. Hox genes were expressed in mature ovaries and Zoea I larval stages, except Scr and ftz, respectively. In addition, isoforms of Dfd, Scr, Ubx, and abdA, which have been scarcely reported in crustaceans, were described. New partial sequences of 87 Hox genes from other crustaceans were identified from the GenBank database. Our results are interesting for future studies to determine the specific function of Hox genes and their isoforms in the freshwater prawn M. olfersii and to contribute to the understanding of the diversity and evolution of body plans and appendages in Crustaceans.
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Affiliation(s)
- Michael L Jaramillo
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Dib Ammar
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Ruth L Quispe
- Departamento de Bioquímica, Campus Universitário, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Christian L Bonatto Paese
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Ana P Gruendling
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Yara M Müller
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Evelise M Nazari
- Departamento de Biologia Celular, Embriologia e Genética, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
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Smith G, Manzano-Marín A, Reyes-Prieto M, Antunes CSR, Ashworth V, Goselle ON, Jan AAA, Moya A, Latorre A, Perotti MA, Braig HR. Human follicular mites: Ectoparasites becoming symbionts. Mol Biol Evol 2022; 39:msac125. [PMID: 35724423 PMCID: PMC9218549 DOI: 10.1093/molbev/msac125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 12/13/2022] Open
Abstract
Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans tha continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Here, we describe the profound impact of this transition on the genome and physiology of the mite. Genome sequencing revealed that the permanent host association of D. folliculorum led to an extensive genome reduction through relaxed selection and genetic drift, resulting in the smallest number of protein-coding genes yet identified among panarthropods. Confocal microscopy revealed that this gene loss coincided with an extreme reduction in the number of cells. Single uninucleate muscle cells are sufficient to operate each of the three segments that form each walking leg. While it has been assumed that the reduction of the cell number in parasites starts early in development, we identified a greater total number of cells in the last developmental stage (nymph) than in the terminal adult stage, suggesting that reduction starts at the adult or ultimate stage of development. This is the first evolutionary step in an arthropod species adopting a reductive, parasitic or endosymbiotic lifestyle. Somatic nuclei show underreplication at the diploid stage. Novel eye structures or photoreceptors as well as a unique human host melatonin-guided day/night rhythm are proposed for the first time. The loss of DNA repair genes coupled with extreme endogamy might have set this mite species on an evolutionary dead-end trajectory.
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Affiliation(s)
- Gilbert Smith
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | - Alejandro Manzano-Marín
- Centre for Microbiology and Environmental Systems Science (CMESS), University of Vienna, Vienna, Austria
| | - Mariana Reyes-Prieto
- Institute of Integrative Systems Biology (I2Sysbio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Foundation for the Promotion of Health and Biomedical Research of the Valencian Community (FISABIO), València, Spain
| | | | - Victoria Ashworth
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | - Obed Nanjul Goselle
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | | | - Andrés Moya
- Institute of Integrative Systems Biology (I2Sysbio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Foundation for the Promotion of Health and Biomedical Research of the Valencian Community (FISABIO), València, Spain
- Center for Networked Biomedical Research in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Amparo Latorre
- Institute of Integrative Systems Biology (I2Sysbio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Foundation for the Promotion of Health and Biomedical Research of the Valencian Community (FISABIO), València, Spain
- Center for Networked Biomedical Research in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - M Alejandra Perotti
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Henk R Braig
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
- Institute and Museum of Natural Sciences, National University of San Juan, San Juan, Argentina
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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.
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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
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5
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Novikova EL, Kulakova MA. There and Back Again: Hox Clusters Use Both DNA Strands. J Dev Biol 2021; 9:28. [PMID: 34287306 PMCID: PMC8293171 DOI: 10.3390/jdb9030028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/25/2022] Open
Abstract
Bilaterian animals operate the clusters of Hox genes through a rich repertoire of diverse mechanisms. In this review, we will summarize and analyze the accumulated data concerning long non-coding RNAs (lncRNAs) that are transcribed from sense (coding) DNA strands of Hox clusters. It was shown that antisense regulatory RNAs control the work of Hox genes in cis and trans, participate in the establishment and maintenance of the epigenetic code of Hox loci, and can even serve as a source of regulatory peptides that switch cellular energetic metabolism. Moreover, these molecules can be considered as a force that consolidates the cluster into a single whole. We will discuss the examples of antisense transcription of Hox genes in well-studied systems (cell cultures, morphogenesis of vertebrates) and bear upon some interesting examples of antisense Hox RNAs in non-model Protostomia.
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Affiliation(s)
- Elena L. Novikova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
| | - Milana A. Kulakova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
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6
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Miller SW, Posakony JW. Disparate expression specificities coded by a shared Hox-C enhancer. eLife 2020; 9:39876. [PMID: 32342858 PMCID: PMC7188484 DOI: 10.7554/elife.39876] [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: 07/06/2018] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
Can a single regulatory sequence be shared by two genes undergoing functional divergence? Here we describe a single promiscuous enhancer within the Drosophila Antennapedia Complex, EO053, that directs aspects of the expression of two adjacent genes, pb (a Hox2 ortholog) and zen2 (a divergent Hox3 paralog), with disparate spatial and temporal expression patterns. We were unable to separate the pb-like and zen2-like specificities within EO053, and we identify sequences affecting both expression patterns. Importantly, genomic deletion experiments demonstrate that EO053 cooperates with additional pb- and zen2-specific enhancers to regulate the mRNA expression of both genes. We examine sequence conservation of EO053 within the Schizophora, and show that patterns of synteny between the Hox2 and Hox3 orthologs in Arthropods are consistent with a shared regulatory relationship extending prior to the Hox3/zen divergence. Thus, EO053 represents an example of two genes having evolved disparate outputs while utilizing this shared regulatory region. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Steve W Miller
- Division of Biological Sciences, Section of Cell & Developmental Biology, University of California San Diego, La Jolla, United States
| | - James W Posakony
- Division of Biological Sciences, Section of Cell & Developmental Biology, University of California San Diego, La Jolla, United States
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7
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Gan BL, He RQ, Zhang Y, Wei DM, Hu XH, Chen G. Downregulation of HOXA3 in lung adenocarcinoma and its relevant molecular mechanism analysed by RT-qPCR, TCGA and in silico analysis. Int J Oncol 2018; 53:1557-1579. [PMID: 30066858 PMCID: PMC6086630 DOI: 10.3892/ijo.2018.4508] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/02/2018] [Indexed: 12/11/2022] Open
Abstract
Recent studies have indicated that homeobox A3 (HOXA3) functions as a carcinogen in colon cancer and the methylation level of HOXA3 is significantly increased in lung adenocarcinoma (LUAD) tissues. However, at least to the best of our knowledge, few studies to date have been performed on HOXA3 in non-small cell lung cancer (NSCLC). Therefore, further studies on HOXA3 expression in NSCLC and the potential regulatory mechanisms are urgently required. In this study, HOXA3 expression in 55 tissues of cases of NSCLC and corresponding non-lung cancer tissues was detected by reverse transcription-quantitative PCR (RT-qPCR). In addition, the clinical significance of HOXA3 expression in NSCLC was evaluated using the Cancer Genome Atlas (TCGA) database. Bioinformatics analysis was then performed to elucidate the potential molecular mechanisms of action of HOXA3. Furthermore, the potential target microRNAs (miRNAs or miRs) of HOXA3 were predicted using miRWalk2.0. Based on Gene Expression Omnibus (GEO) and TGCA databases, standardized mean difference (SMD) and sROC methods were used for meta-analyses of the expression of potential target miRNAs of HOXA3 in NSCLC to evaluate their association with HOXA3. The results revealed that the HOXA3 expression levels in NSCLC, LUAD and lung squamous cell carcinoma (LUSC) were 0.1130±0.1398, 0.1295±0.16890 and 0.0906±0.0846, respectively. These values were all decreased compared with the normal tissues (0.1877±0.1975, 0.2337±0.2405 and 0.1249±0.0873, respectively, P<0.05). The TCGA database also revealed the low expression trend of HOXA3. The downregulation of HOXA3 may play an important role in the progression and the poor prognosis of LUAD. The TCGA database also suggested that HOXA3 in LUAD and LUSC tissues exhibited certain mutational levels. In addition, the methylation levels in the NSCLC, LUAD and LUSC tissues significantly increased [NSCLC: fold change (FC), 1.3226; P<0.001; LUAD: FC, 1.2712; P<0.001; and LUSC: FC, 1.3786; P<0.001]. According to the analyses using the Kyoto Encyclopedia of Genes and Genomes (KEGG), we found that the co-expression HOXA3 genes were mainly associated with the focal adhesion signalling pathway and the ECM-receptor interaction signalling pathway. Furthermore, the predicted miRNA, miR-372-3p, exhibited a high expression in both the NSCLC and LUAD tissues (P<0.05). On the whole, the findings of this study indicate that low HOXA3 expression may play a certain role in LUAD; however, its association with LUSC still requires further investigation. HOXA3 function may be achieved through different pathways or target miRNAs. However, the specific underlying mechanisms need to be confirmed through various functional studies.
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Affiliation(s)
- Bin-Liang Gan
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Rong-Quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yu Zhang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Dan-Ming Wei
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Xiao-Hua Hu
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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Kim DH, Lee BY, Kim HS, Jeong CB, Hwang DS, Kim IC, Lee JS. Identification and characterization of homeobox (Hox) genes and conservation of the single Hox cluster (324.6 kb) in the water flea Daphnia magna. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:76-82. [PMID: 29441720 DOI: 10.1002/jez.b.22793] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/19/2018] [Accepted: 01/25/2018] [Indexed: 11/07/2022]
Abstract
We report the complete sequence analysis of the entire complement of eight typical homeobox (Hox) genes (Lab, Pb, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) and two other genes (Hox3 and Ftz) in a 324.6-kb region in the water flea Daphnia magna. In the cluster of D. magna Hox genes, we found one long interspersed nuclear element (LINE)/R2-NeSL between Ubx and Abd-A that was not present in Daphnia pulex Hox genes. In basal expression of Hox genes at different developmental stages, biothorax complex genes (Ubx, Abd-A, and Abd-B) and some antennapedia complex genes (Lab, Scr, Antp) were moderately expressed, but the Hox3 gene was barely expressed. Three homeobox genes (Antp, Ubx, Abd-A) were highly expressed at 6-7 days after release from the brood chamber and/or in the adult stage. The structural array and transcribed orientation of Dm-Hox genes were identical to those of the sister species D. pulex (∼340 kb), indicating that the Hox gene structure in daphnids is highly conserved. However, Dm- and Dp-Hox3, -deformed (Dfd), and -fushi tarazu (Ftz) genes varied from orthologous genes in pancrustacean species.
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Affiliation(s)
- Duck-Hyun 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
| | - Hui-Su Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Dae-Sik Hwang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Il-Chan Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
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Kim HS, Hwang DS, Jeong CB, Au DWT, Lee JS. Identification and conservation of gene loss events of Hox gene clusters in the marine medaka (Oryzias melastigma). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 326:387-393. [PMID: 27966251 DOI: 10.1002/jez.b.22713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/11/2016] [Accepted: 10/17/2016] [Indexed: 11/07/2022]
Abstract
In this study, the identification of the whole Hox gene clusters (46 Hox genes) in the marine medaka Oryzias melastigma was investigated using genome assembly and RNA-seq information. Moreover, the gene loss events of Hox gene clusters, which may occur during fish evolution, were examined for a better understanding of the evolutionary status of the gene lost events of the Hox gene cluster across fish species, particularly in the genus Oryzias.
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Affiliation(s)
- Hui-Su Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Dae-Sik Hwang
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
| | - Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea.,Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul, South Korea
| | - Doris W T Au
- State Key Laboratory on Marine Pollution and Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, People's Republic of China
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon, South Korea
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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.
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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.
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