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Sarmiento ME, Chin KL, Lau NS, Aziah I, Norazmi MN, Acosta A, Ismail N, Yaacob NS. Mitochondrial DNA sequence of the horseshoe crab Tachypleus gigas. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1710-1714. [PMID: 34104748 PMCID: PMC8158250 DOI: 10.1080/23802359.2021.1930213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This paper reports on the complete mitochondrial (mt) genome of a horseshoe crab, Tachypleus gigas (T. gigas), in Kuala Kemaman, Terengganu, Malaysia. Whole-genome sequencing of hemocyte DNA was performed with Illumina HiSeq system and the generated reads were de novo assembled with ABySS 2.1.5 and reassembled using mitoZ against Carcinoscorpius rotundicauda and Limulus polyphemus, resulting in a contig of 15 Kb. Phylogenetic analysis of the assembled mt genome suggests that the Tachypleus gigas is closely related to Tachypleus tridentatus than to Carcinoscorpius rotundicauda.
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Affiliation(s)
- Maria E Sarmiento
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia
| | - Kai Ling Chin
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Nyok Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Ismail Aziah
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia
| | - Mohd Nor Norazmi
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia
| | - Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia
| | - Noraznawati Ismail
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Nik Soriani Yaacob
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia
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2
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Bowden TJ, Kraev I, Lange S. Post-translational protein deimination signatures and extracellular vesicles (EVs) in the Atlantic horseshoe crab (Limulus polyphemus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 110:103714. [PMID: 32335073 DOI: 10.1016/j.dci.2020.103714] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
The horseshoe crab is a living fossil and a species of marine arthropod with unusual immune system properties which are also exploited commercially. Given its ancient status dating to the Ordovician period (450 million years ago), its standing in phylogeny and unusual immunological characteristics, the horseshoe crab may hold valuable information for comparative immunology studies. Peptidylarginine deiminases (PADs) are calcium dependent enzymes that are phylogenetically conserved and cause protein deimination via conversion of arginine to citrulline. This post-translational modification can lead to structural and functional protein changes contributing to protein moonlighting in health and disease. PAD-mediated regulation of extracellular vesicle (EV) release, a critical component of cellular communication, has furthermore been identified to be a phylogenetically conserved mechanism. PADs, protein deimination and EVs have hitherto not been studied in the horseshoe crab and were assessed in the current study. Horseshoe crab haemolymph serum-EVs were found to be a poly-dispersed population in the 20-400 nm size range, with the majority of EVs falling within 40-123 nm. Key immune proteins were identified to be post-translationally deiminated in horseshoe crab haemolymph serum, providing insights into protein moonlighting function of Limulus and phylogenetically conserved immune proteins. KEGG (Kyoto encyclopaedia of genes and genomes) and GO (gene ontology) enrichment analysis of deiminated proteins identified in Limulus revealed KEGG pathways relating to complement and coagulation pathways, Staphylococcus aureus infection, glycolysis/gluconeogenesis and carbon metabolism, while GO pathways of biological and molecular pathways related to a range of immune and metabolic functions, as well as developmental processes. The characterisation of EVs, and post-translational deimination signatures, revealed here in horseshoe crab, contributes to current understanding of protein moonlighting functions and EV-mediated communication in this ancient arthropod and throughout phylogeny.
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Affiliation(s)
- Timothy J Bowden
- Aquaculture Research Institute, School of Food & Agriculture, University of Maine, University of Maine, Orono, ME, USA.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science Technology, Engineering and Mathematics Open University, Milton Keynes, MK7 6AA, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, W1W 6UW, UK.
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3
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Hunt BJ, Mallon EB, Rosato E. In silico Identification of a Molecular Circadian System With Novel Features in the Crustacean Model Organism Parhyale hawaiensis. Front Physiol 2019; 10:1325. [PMID: 31681024 PMCID: PMC6813248 DOI: 10.3389/fphys.2019.01325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/03/2019] [Indexed: 12/25/2022] Open
Abstract
The amphipod Parhyale hawaiensis is a model organism of growing importance in the fields of evolutionary development and regeneration. A small, hardy marine crustacean that breeds year-round with a short generation time, it has simple lab culture requirements and an extensive molecular toolkit including the ability to generate targeted genetic mutant lines. Here we identify canonical core and regulatory clock genes using genomic and transcriptomic resources as a first step in establishing this species as a model in the field of chronobiology. The molecular clock of P. hawaiensis lacks orthologs of the canonical circadian genes cryptochrome 1 and timeless, in common with the mammalian system but in contrast to many arthropods including Drosophila melanogaster. Furthermore the predicted CLOCK peptide is atypical and CRY2 shows an extended 5′ region of unknown function. These results appear to be shared by two other amphipod species.
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Affiliation(s)
- Benjamin James Hunt
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Eamonn B Mallon
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Ezio Rosato
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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4
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Li Y, Han Z, She Q, Zhao Y, Wei H, Dong J, Xu W, Li X, Liang S. Comparative transcriptome analysis provides insights into the molecular basis of circadian cycle regulation in Eriocheir sinensis. Gene 2019; 694:42-49. [DOI: 10.1016/j.gene.2018.12.081] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/05/2018] [Accepted: 12/27/2018] [Indexed: 11/26/2022]
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5
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Liao YY, Xu PW, Kwan KY, Ma ZY, Fang HY, Xu JY, Wang PL, Yang SY, Xie SB, Xu SQ, Qian D, Li WF, Bai LR, Zhou DJ, Zhang YQ, Lei J, Liu K, Li F, Li J, Zhu P, Wang YJ, Wu HP, Xu YH, Huang H, Zhang C, Liu JX, Han JF. Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus. Sci Data 2019; 6:190029. [PMID: 30806641 PMCID: PMC6390705 DOI: 10.1038/sdata.2019.29] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/03/2019] [Indexed: 01/17/2023] Open
Abstract
Chinese horseshoe crabs (Tachypleus tridentatus), ancient marine arthropods dating back to the mid-Palaeozoic Era, have provided valuable resources for the detection of bacterial or fungal contamination. However, excessive exploitation for the amoebocyte lysate of Tachypleus has dramatically decreased the population of the Chinese horseshoe crabs. Thus, we present sequencing, assembly and annotation of T. tridentatus, with the hope of understanding the genomic feature of the living fossil and assisting scientists with the protection of this endangered species. The final genome contained a total size of 1.943 Gb, covering 90.23% of the estimated genome size. The transcriptome of three larval stages was constructed to investigate the candidate gene involved in the larval development and validate annotation. The completeness of the genome and gene models was estimated by BUSCO, reaching 96.2% and 95.4%, respectively. The synonymous substitution distribution of paralogues revealed that T. tridentatus had undergone two rounds of whole-genome duplication. All genomic and transcriptome data have been deposited in public databases, ready to be used by researchers working on horseshoe crabs.
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Affiliation(s)
- Yong Yan Liao
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Peng Wei Xu
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Kit Yue Kwan
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Zhi Yun Ma
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Huai Yi Fang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Jun Yang Xu
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Peng Liang Wang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Shao Yu Yang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Shang Bo Xie
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Shu Qing Xu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Dan Qian
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Wei Feng Li
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Li Rong Bai
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Da Jie Zhou
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Yan Qiu Zhang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Juan Lei
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Ke Liu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Fan Li
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Jian Li
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Peng Zhu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Yu Jun Wang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Hai Ping Wu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - You Hou Xu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Hu Huang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Jin Xia Liu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
| | - Jun Feng Han
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Qinzhou, 53501 Guangxi, China
- Ocean College, Beibu Gluf University, Qinzhou, 535011, Guangxi, China
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6
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Christie AE, Yu A, Pascual MG, Roncalli V, Cieslak MC, Warner AN, Lameyer TJ, Stanhope ME, Dickinson PS, Joe Hull J. Circadian signaling in Homarus americanus: Region-specific de novo assembled transcriptomes show that both the brain and eyestalk ganglia possess the molecular components of a putative clock system. Mar Genomics 2018; 40:25-44. [PMID: 29655930 DOI: 10.1016/j.margen.2018.03.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/05/2018] [Accepted: 03/06/2018] [Indexed: 12/24/2022]
Abstract
Essentially all organisms exhibit recurring patterns of physiology/behavior that oscillate with a period of ~24-h and are synchronized to the solar day. Crustaceans are no exception, with robust circadian rhythms having been documented in many members of this arthropod subphylum. However, little is known about the molecular underpinnings of their circadian rhythmicity. Moreover, the location of the crustacean central clock has not been firmly established, although both the brain and eyestalk ganglia have been hypothesized as loci. The American lobster, Homarus americanus, is known to exhibit multiple circadian rhythms, and immunodetection data suggest that its central clock is located within the eyestalk ganglia rather than in the brain. Here, brain- and eyestalk ganglia-specific transcriptomes were generated and used to assess the presence/absence of transcripts encoding the commonly recognized protein components of arthropod circadian signaling systems in these two regions of the lobster central nervous system. Transcripts encoding putative homologs of the core clock proteins clock, cryptochrome 2, cycle, period and timeless were found in both the brain and eyestalk ganglia assemblies, as were transcripts encoding similar complements of putative clock-associated, clock input pathway and clock output pathway proteins. The presence and identity of transcripts encoding core clock proteins in both regions were confirmed using PCR. These findings suggest that both the brain and eyestalk ganglia possess all of the molecular components needed for the establishment of a circadian signaling system. Whether the brain and eyestalk clocks are independent of one another or represent a single timekeeping system remains to be determined. Interestingly, while most of the proteins deduced from the identified transcripts are shared by both the brain and eyestalk ganglia, assembly-specific isoforms were also identified, e.g., several period variants, suggesting the possibility of region-specific variation in clock function, especially if the brain and eyestalk clocks represent independent oscillators.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
| | - Andy Yu
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Micah G Pascual
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Vittoria Roncalli
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Matthew C Cieslak
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Amanda N Warner
- Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ 85138, USA
| | - Tess J Lameyer
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME 04672, USA
| | - Meredith E Stanhope
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME 04672, USA
| | - Patsy S Dickinson
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME 04672, USA
| | - J Joe Hull
- Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ 85138, USA
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7
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Biscontin A, Wallach T, Sales G, Grudziecki A, Janke L, Sartori E, Bertolucci C, Mazzotta G, De Pittà C, Meyer B, Kramer A, Costa R. Functional characterization of the circadian clock in the Antarctic krill, Euphausia superba. Sci Rep 2017; 7:17742. [PMID: 29255161 PMCID: PMC5735174 DOI: 10.1038/s41598-017-18009-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/05/2017] [Indexed: 11/30/2022] Open
Abstract
Antarctic krill (Euphausia superba) is a key species in Southern Ocean ecosystem where it plays a central role in the Antarctic food web. Available information supports the existence of an endogenous timing system in krill enabling it to synchronize metabolism and behavior with an environment characterized by extreme seasonal changes in terms of day length, food availability, and surface ice extent. A screening of our transcriptome database “KrillDB” allowed us to identify the putative orthologues of 20 circadian clock components. Mapping of conserved domains and phylogenetic analyses strongly supported annotations of the identified sequences. Luciferase assays and co-immunoprecipitation experiments allowed us to define the role of the main clock components. Our findings provide an overall picture of the molecular mechanisms underlying the functioning of the endogenous circadian clock in the Antarctic krill and shed light on their evolution throughout crustaceans speciation. Interestingly, the core clock machinery shows both mammalian and insect features that presumably contribute to an evolutionary strategy to cope with polar environment’s challenges. Moreover, despite the extreme variability characterizing the Antarctic seasonal day length, the conserved light mediated degradation of the photoreceptor EsCRY1 suggests a persisting pivotal role of light as a Zeitgeber.
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Affiliation(s)
- Alberto Biscontin
- Charité-Universitätsmedizin Berlin, Laboratory of Chronobiology, D-10117, Berlin, Germany.,Department of Biology, University of Padova, 35121, Padova, Italy
| | - Thomas Wallach
- Charité-Universitätsmedizin Berlin, Laboratory of Chronobiology, D-10117, Berlin, Germany
| | - Gabriele Sales
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Astrid Grudziecki
- Charité-Universitätsmedizin Berlin, Laboratory of Chronobiology, D-10117, Berlin, Germany
| | - Leonard Janke
- Charité-Universitätsmedizin Berlin, Laboratory of Chronobiology, D-10117, Berlin, Germany
| | - Elena Sartori
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Cristiano Bertolucci
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121, Ferrara, Italy
| | | | | | - Bettina Meyer
- Alfred Wegener Polar Biological Oceanography, 27570, Bremerhaven, Germany.,Carl von Ossietzky University of Oldenburg, Institute for Chemistry and Biology of the Marine Environment, 26129, Oldenburg, Germany.,Helmholtz Institute for Functional Marine Biodiversity Oldenburg (HIFMB), 26129, Oldenburg, Germany
| | - Achim Kramer
- Charité-Universitätsmedizin Berlin, Laboratory of Chronobiology, D-10117, Berlin, Germany.
| | - Rodolfo Costa
- Department of Biology, University of Padova, 35121, Padova, Italy.
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Chahad-Ehlers S, Arthur LP, Lima ALA, Gesto JSM, Torres FR, Peixoto AA, de Brito RA. Expanding the view of Clock and cycle gene evolution in Diptera. INSECT MOLECULAR BIOLOGY 2017; 26:317-331. [PMID: 28234413 DOI: 10.1111/imb.12296] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We expanded the view of Clock (Clk) and cycle (cyc) gene evolution in Diptera by studying the fruit fly Anastrepha fraterculus (Afra), a Brachycera. Despite the high conservation of clock genes amongst insect groups, striking structural and functional differences of some clocks have appeared throughout evolution. Clk and cyc nucleotide sequences and corresponding proteins were characterized, along with their mRNA expression data, to provide an evolutionary overview in the two major groups of Diptera: Lower Diptera and Higher Brachycera. We found that AfraCYC lacks the BMAL (Brain and muscle ARNT-like) C-terminus region (BCTR) domain and is constitutively expressed, suggesting that AfraCLK has the main transactivation function, which is corroborated by the presence of poly-Q repeats and an oscillatory pattern. Our analysis suggests that the loss of BCTR in CYC is not exclusive of drosophilids, as it also occurs in other Acalyptratae flies such as tephritids and drosophilids, however, but it is also present in some Calyptratae, such as Muscidae, Calliphoridae and Sarcophagidae. This indicates that BCTR is missing from CYC of all higher-level Brachycera and that it was lost during the evolution of Lower Brachycera. Thus, we can infer that CLK protein may play the main role in the CLK\CYC transcription complex in these flies, like in its Drosophila orthologues.
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Affiliation(s)
- S Chahad-Ehlers
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - L P Arthur
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - A L A Lima
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - J S M Gesto
- Laboratório de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - F R Torres
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - A A Peixoto
- Laboratório de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - R A de Brito
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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9
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Simpson SD, Ramsdell JS, Watson III WH, Chabot CC. The Draft Genome and Transcriptome of the Atlantic Horseshoe Crab, Limulus polyphemus. Int J Genomics 2017; 2017:7636513. [PMID: 28265565 PMCID: PMC5317147 DOI: 10.1155/2017/7636513] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/28/2016] [Indexed: 01/21/2023] Open
Abstract
The horseshoe crab, Limulus polyphemus, exhibits robust circadian and circatidal rhythms, but little is known about the molecular mechanisms underlying those rhythms. In this study, horseshoe crabs were collected during the day and night as well as high and low tides, and their muscle and central nervous system tissues were processed for genome and transcriptome sequencing, respectively. The genome assembly resulted in 7.4 × 105 contigs with N50 of 4,736, while the transcriptome assembly resulted in 9.3 × 104 contigs and N50 of 3,497. Analysis of functional completeness by the identification of putative universal orthologs suggests that the transcriptome has three times more total expected orthologs than the genome. Interestingly, RNA-Seq analysis indicated no statistically significant changes in expression level for any circadian core or accessory gene, but there was significant cycling of several noncircadian transcripts. Overall, these assemblies provide a resource to investigate the Limulus clock systems and provide a large dataset for further exploration into the taxonomy and biology of the Atlantic horseshoe crab.
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Affiliation(s)
- Stephen D. Simpson
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA
| | - Jordan S. Ramsdell
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA
| | - Winsor H. Watson III
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Christopher C. Chabot
- Department of Biological Sciences, MSC#64, Plymouth State University, Plymouth, NH 03264, USA
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