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Rosani U. Tracing RNA viruses associated with Nudibranchia gastropods. PeerJ 2022; 10:e13410. [PMID: 35586129 PMCID: PMC9109684 DOI: 10.7717/peerj.13410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/19/2022] [Indexed: 01/14/2023] Open
Abstract
Background Nudibranchia is an under-studied taxonomic group of gastropods, including more than 3,000 species with colourful and extravagant body shapes and peculiar predatory and defensive strategies. Although symbiosis with bacteria has been reported, no data are available for the nudibranch microbiome nor regarding viruses possibly associated with these geographically widespread species. Methods Based on 47 available RNA sequencing datasets including more than two billion reads of 35 nudibranch species, a meta-transcriptome assembly was constructed. Taxonomic searches with DIAMOND, RNA-dependent-RNA-polymerase identification with palmscan and viral hallmark genes identification by VirSorter2 in combination with CheckV were applied to identify genuine viral genomes, which were then annotated using CAT. Results A total of 20 viral genomes were identified as bona fide viruses, among 552 putative viral contigs resembling both RNA viruses of the Negarnaviricota, Pisuviricota, Kitrinoviricota phyla and actively transcribing DNA viruses of the Cossaviricota and Nucleocytoviricota phyla. The 20 commonly identified viruses showed similarity with RNA viruses identified in other RNA-seq experiments and can be putatively associated with bacteria, plant and arthropod hosts by co-occurence analysis. The RNA samples having the highest viral abundances showed a heterogenous and mostly sample-specific distribution of the identified viruses, suggesting that nudibranchs possess diversified and mostly unknown viral communities.
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2
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Lee CA, Romanova EV, Southey BR, Gillette R, Sweedler JV. Comparative Analysis of Neuropeptides in Homologous Interneurons and Prohormone Annotation in Nudipleuran Sea Slugs. Front Physiol 2022; 12:809529. [PMID: 35002782 PMCID: PMC8735849 DOI: 10.3389/fphys.2021.809529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023] Open
Abstract
Despite substantial research on neuronal circuits in nudipleuran gastropods, few peptides have been implicated in nudipleuran behavior. In this study, we expanded the understanding of peptides in this clade, using three species with well-studied nervous systems, Hermissenda crassicornis, Melibe leonina, and Pleurobranchaea californica. For each species, we performed sequence homology analysis of de novo transcriptome predictions to identify homologs to 34 of 36 prohormones previously characterized in the gastropods Aplysia californica and Lymnaea stagnalis. We then used single-cell mass spectrometry to characterize peptide profiles in homologous feeding interneurons: the multifunctional ventral white cell (VWC) in P. californica and the small cardioactive peptide B large buccal (SLB) cells in H. crassicornis and M. leonina. The neurons produced overlapping, but not identical, peptide profiles. The H. crassicornis SLB cells expressed peptides from homologs to the FMRFamide (FMRFa), small cardioactive peptide (SCP), LFRFamide (LFRFa), and feeding circuit activating peptides prohormones. The M. leonina SLB cells expressed peptides from homologs to the FMRFa, SCP, LFRFa, and MIP-related peptides prohormones. The VWC, previously shown to express peptides from the FMRFa and QNFLa (a homolog of A. californica pedal peptide 4) prohormones, was shown to also contain SCP peptides. Thus, each neuron expressed peptides from the FMRFa and SCP families, the H. crassicornis and M. leonina SLB cells expressed peptides from the LFRFa family, and each neuron contained peptides from a prohormone not found in the others. These data suggest each neuron performs complex co-transmission, which potentially facilitates a multifunctional role in feeding. Additionally, the unique feeding characteristics of each species may relate, in part, to differences in the peptide profiles of these neurons. These data add chemical insight to enhance our understanding of the neuronal basis of behavior in nudipleurans and other gastropods.
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Affiliation(s)
- Colin A Lee
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Elena V Romanova
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, United States.,Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Rhanor Gillette
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, United States.,Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Jonathan V Sweedler
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, United States.,Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States
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3
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Karmeinski D, Meusemann K, Goodheart JA, Schroedl M, Martynov A, Korshunova T, Wägele H, Donath A. Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia. BMC Ecol Evol 2021; 21:226. [PMID: 34963462 PMCID: PMC8895541 DOI: 10.1186/s12862-021-01944-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/23/2021] [Indexed: 11/24/2022] Open
Abstract
Background The soft-bodied cladobranch sea slugs represent roughly half of the biodiversity of marine nudibranch molluscs on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as targets for drug discovery), the evolutionary history of cladobranch sea slugs is not yet fully understood. Results To enlarge the current knowledge on the phylogenetic relationships, we generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa (Berthella plumula and Polycera quadrilineata). We complemented our taxon sampling with previously published transcriptome data, resulting in a final data set covering 56 species from all but one accepted cladobranch superfamilies. We assembled all transcriptomes using six different assemblers, selecting those assemblies that provided the largest amount of potentially phylogenetically informative sites. Quality-driven compilation of data sets resulted in four different supermatrices: two with full coverage of genes per species (446 and 335 single-copy protein-coding genes, respectively) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximal statistical support for all major splits and phylogenetic relationships at the family level. Besides the questionable position of Noumeaella rubrofasciata, rendering the Facelinidae as polyphyletic, the only notable discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal. Conclusions Our data matrices and the inferred trees can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The placement of E. pulchra, however, proves challenging, even with large data sets and various optimization strategies. Moreover, quartet mapping results show that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01944-0.
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Affiliation(s)
- Dario Karmeinski
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change/ZFMK, Museum Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Karen Meusemann
- Leibniz Institute for the Analysis of Biodiversity Change/ZFMK, Museum Koenig, Adenauerallee 160, 53113, Bonn, Germany.,Australian National Insect Collection, National Research Collections Australia, Commonwealth Scientific and Industrial Research Organisation (CSIRO), National Facilities and Collections, Clunies Ross Street, Acton, Canberra, ACT, 2601, Australia
| | - Jessica A Goodheart
- Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, 92037, USA
| | - Michael Schroedl
- SNSB-Bavarian State Collection of Zoology, Münchhausenstr. 21, 81247, Munich, Germany.,GeoBioCenter LMU und Biozentrum, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Alexander Martynov
- Zoological Museum of the Moscow State University, Bolshaya Nikitskaya Str. 6, 125009, Moscow, Russia
| | - Tatiana Korshunova
- Koltzov Institute of Developmental Biology, Vavilova Str. 26, 119334, Moscow, Russia
| | - Heike Wägele
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change/ZFMK, Museum Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change/ZFMK, Museum Koenig, Adenauerallee 160, 53113, Bonn, Germany.
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4
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Rolón-Martínez S, Habib MR, Mansour TA, Díaz-Ríos M, Rosenthal JJC, Zhou XN, Croll RP, Miller MW. FMRF-NH 2 -related neuropeptides in Biomphalaria spp., intermediate hosts for schistosomiasis: Precursor organization and immunohistochemical localization. J Comp Neurol 2021; 529:3336-3358. [PMID: 34041754 PMCID: PMC8273141 DOI: 10.1002/cne.25195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 11/10/2022]
Abstract
Freshwater snails of the genus Biomphalaria serve as intermediate hosts for the digenetic trematode Schistosoma mansoni, the etiological agent for the most widespread form of intestinal schistosomiasis. As neuropeptide signaling in host snails can be altered by trematode infection, a neural transcriptomics approach was undertaken to identify peptide precursors in Biomphalaria glabrata, the major intermediate host for S. mansoni in the Western Hemisphere. Three transcripts that encode peptides belonging to the FMRF-NH2 -related peptide (FaRP) family were identified in B. glabrata. One transcript encoded a precursor polypeptide (Bgl-FaRP1; 292 amino acids) that included eight copies of the tetrapeptide FMRF-NH2 and single copies of FIRF-NH2 , FLRF-NH2 , and pQFYRI-NH2 . The second transcript encoded a precursor (Bgl-FaRP2; 347 amino acids) that comprised 14 copies of the heptapeptide GDPFLRF-NH2 and 1 copy of SKPYMRF-NH2 . The precursor encoded by the third transcript (Bgl-FaRP3; 287 amino acids) recapitulated Bgl-FaRP2 but lacked the full SKPYMRF-NH2 peptide. The three precursors shared a common signal peptide, suggesting a genomic organization described previously in gastropods. Immunohistochemical studies were performed on the nervous systems of B. glabrata and B. alexandrina, a major intermediate host for S. mansoni in Egypt. FMRF-NH2 -like immunoreactive (FMRF-NH2 -li) neurons were located in regions of the central nervous system associated with reproduction, feeding, and cardiorespiration. Antisera raised against non-FMRF-NH2 peptides present in the tetrapeptide and heptapeptide precursors labeled independent subsets of the FMRF-NH2 -li neurons. This study supports the participation of FMRF-NH2 -related neuropeptides in the regulation of vital physiological and behavioral systems that are altered by parasitism in Biomphalaria.
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Affiliation(s)
- Solymar Rolón-Martínez
- Institute of Neurobiology and Department of Anatomy and Neurobiology, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | - Mohamed R Habib
- Medical Malacology Laboratory, Theodor Bilharz Research Institute, Giza, Egypt
| | - Tamer A Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Clinical Pathology, School of Medicine, University of Mansoura, Mansoura, Egypt
| | | | | | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Roger P Croll
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Mark W Miller
- Institute of Neurobiology and Department of Anatomy and Neurobiology, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
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Dong N, Bandura J, Zhang Z, Wang Y, Labadie K, Noel B, Davison A, Koene JM, Sun HS, Coutellec MA, Feng ZP. Ion channel profiling of the Lymnaea stagnalis ganglia via transcriptome analysis. BMC Genomics 2021; 22:18. [PMID: 33407100 PMCID: PMC7789530 DOI: 10.1186/s12864-020-07287-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/28/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). However, its usefulness is restricted by a limited availability of transcriptome data. While sequence information for the L. stagnalis CNS transcripts has been obtained from EST libraries and a de novo RNA-seq assembly, the quality of these assemblies is limited by a combination of low coverage of EST libraries, the fragmented nature of de novo assemblies, and lack of reference genome. RESULTS In this study, taking advantage of the recent availability of a preliminary L. stagnalis genome, we generated an RNA-seq library from the adult L. stagnalis CNS, using a combination of genome-guided and de novo assembly programs to identify 17,832 protein-coding L. stagnalis transcripts. We combined our library with existing resources to produce a transcript set with greater sequence length, completeness, and diversity than previously available ones. Using our assembly and functional domain analysis, we profiled L. stagnalis CNS transcripts encoding ion channels and ionotropic receptors, which are key proteins for CNS function, and compared their sequences to other vertebrate and invertebrate model organisms. Interestingly, L. stagnalis transcripts encoding numerous putative Ca2+ channels showed the most sequence similarity to those of Mus musculus, Danio rerio, Xenopus tropicalis, Drosophila melanogaster, and Caenorhabditis elegans, suggesting that many calcium channel-related signaling pathways may be evolutionarily conserved. CONCLUSIONS Our study provides the most thorough characterization to date of the L. stagnalis transcriptome and provides insights into differences between vertebrates and invertebrates in CNS transcript diversity, according to function and protein class. Furthermore, this study provides a complete characterization of the ion channels of Lymnaea stagnalis, opening new avenues for future research on fundamental neurobiological processes in this model system.
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Affiliation(s)
- Nancy Dong
- Department of Physiology, University of Toronto, 3308 MSB, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Julia Bandura
- Department of Physiology, University of Toronto, 3308 MSB, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Zhaolei Zhang
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Yan Wang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, M1C 1A4, Canada
| | - Karine Labadie
- Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, BP5706, 91057, Evry, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry, Université Paris-Saclay, 91057, Evry, France
| | - Angus Davison
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK, NG7 2RD, UK
| | - Joris M Koene
- Department of Ecological Science, Faculty of Science, Vrije Universiteit, Amsterdam, The Netherlands
| | - Hong-Shuo Sun
- Department of Physiology, University of Toronto, 3308 MSB, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Department of Surgery, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | | | - Zhong-Ping Feng
- Department of Physiology, University of Toronto, 3308 MSB, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
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Watson WH, Nash A, Lee C, Patz MD, Newcomb JM. The Distribution and Possible Roles of Small Cardioactive Peptide in the Nudibranch Melibe leonina. Integr Org Biol 2020; 2:obaa016. [PMID: 33791559 PMCID: PMC7671164 DOI: 10.1093/iob/obaa016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The neuropeptide small cardioactive peptide (SCP) plays an integrative role in exciting various motor programs involved in feeding and locomotion in a number of gastropod species. In this study, immunohistochemistry, using monoclonal antibodies against SCPB, was used to localize SCPB-like-immunoreactive neurons in the central nervous system, and map their connections to various tissues, in the nudibranch, Melibe leonina. Approximately 28-36 SCPB-like-immunoreactive neurons were identified in the M. leonina brain, as well as one large neuron in each of the buccal ganglia. The neuropil of the pedal ganglia contained the most SCPB-like-immunoreactive varicosities, although only a small portion of these were due to SCPB-like-immunoreactive neurons in the same ganglion. This suggests that much of the SCPB-like immunoreactivity in the neuropil of the pedal ganglia was from neurons in other ganglia that projected through the pedal-pedal connectives or the connectives from the cerebral and pleural ganglia. We also observed extensive SCPB innervation along the length of the esophagus. Therefore, we investigated the impact of SCPB on locomotion in intact animals, as well as peristaltic contractions of the isolated esophagus. Injection of intact animals with SCPB at night led to a significant increase in crawling and swimming, compared to control animals injected with saline. Furthermore, perfusion of isolated brains with SCPB initiated expression of the swim motor program. Application of SCPB to the isolated quiescent esophagus initiated rhythmic peristaltic contractions, and this occurred in preparations both with and without the buccal ganglia being attached. All these data, taken together, suggest that SCPB could be released at night to arouse animals and enhance the expression of both feeding and swimming motor programs in M. leonina.
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Affiliation(s)
- W H Watson
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - A Nash
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - C Lee
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - M D Patz
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - J M Newcomb
- Department of Biology and Health Science, New England College, Henniker, NH 03242, USA
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7
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Klein AH, Ballard KR, Storey KB, Motti CA, Zhao M, Cummins SF. Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Brief Funct Genomics 2020; 18:377-394. [PMID: 31609407 DOI: 10.1093/bfgp/elz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/06/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.
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Affiliation(s)
- Anne H Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kaylene R Ballard
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville Queensland 4810, Australia
| | - Min Zhao
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
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Abstract
The neurotransmitter gamma-aminobutyric acid (GABA) is widely distributed in the mammalian central nervous system, where it acts as a major mediator of synaptic inhibition. GABA also serves as a neurotransmitter in a range of invertebrate phyla, including arthropods, echinoderms, annelids, nematodes, and platyhelminthes. This article reviews evidence supporting the neurotransmitter role of GABA in gastropod molluscs, with an emphasis on its presence in identified neurons and well-characterized neural circuits. The collective findings indicate that GABAergic signaling participates in the selection and specification of motor programs, as well as the bilateral coordination of motor circuits. While relatively few in number, GABAergic neurons can influence neural circuits via inhibitory, excitatory, and modulatory synaptic actions. GABA's colocalization with peptidergic and classical neurotransmitters can broaden its integrative capacity. The functional properties of GABAergic neurons in simpler gastropod systems may provide insight into the role of this neurotransmitter phenotype in more complex brains.
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Key Words
- BCI, buccal-cerebral interneuron
- CBC, cerebral-buccal connective
- CBI, cerebral-buccal interneuron
- CNS, central nervous system
- CPG, central pattern generator
- Cr-Aint, cerebral A interneuron
- DA, dopamine
- EPSP, excitatory postsynaptic potential
- FCAP, feeding circuit activating peptide
- GABA, gamma-aminobutyric acid
- GABAli, GABA-like immunoreactivity
- IPSP, inhibitory postsynaptic potential
- PKC, protein kinase C
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Affiliation(s)
- MARK W. MILLER
- Institute of Neurobiology and Department of Anatomy and Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico 00901
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Tamvacakis AN, Senatore A, Katz PS. Single neuron serotonin receptor subtype gene expression correlates with behaviour within and across three molluscan species. Proc Biol Sci 2018; 285:rspb.2018.0791. [PMID: 30135151 DOI: 10.1098/rspb.2018.0791] [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: 04/09/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022] Open
Abstract
The marine mollusc, Pleurobranchaea californica varies daily in whether it swims and this correlates with whether serotonin (5-HT) enhances the strength of synapses made by the swim central pattern generator neuron, A1/C2. Another species, Tritonia diomedea, reliably swims and does not vary in serotonergic neuromodulation. A third species, Hermissenda crassicornis, never produces this behaviour and lacks the neuromodulation. We found that expression of particular 5-HT receptor subtype (5-HTR) genes in single neurons correlates with swimming. Orthologues to seven 5-HTR genes were identified from whole-brain transcriptomes. We isolated individual A1/C2 neurons and sequenced their RNA or measured 5-HTR gene expression using absolute quantitative PCR. A1/C2 neurons isolated from Pleurobranchaea that produced a swim motor pattern just prior to isolation expressed 5-HT2a and 5-HT7 receptor genes, as did all Tritonia samples. These subtypes were absent from A1/C2 isolated from Pleurobranchaea that did not swim on that day and from Hermissenda A1/C2 neurons. Expression of other receptors was not correlated with swimming. This suggests that these 5-HTRs may mediate the modulation of A1/C2 synaptic strength and play an important role in swimming. Furthermore, it suggests that regulation of receptor expression could underlie daily changes in behaviour as well as evolution of behaviour.
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Affiliation(s)
- A N Tamvacakis
- Neuroscience Institute, Georgia State University, Atlanta, GA, USA
| | - A Senatore
- Biology Department, University of Toronto, Mississauga, Toronto, Ontario, Canada
| | - P S Katz
- Biology Department, University of Massachusetts at Amherst, Amherst, MA, USA
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Green DJ, Huang RC, Sudlow L, Hatcher N, Potgieter K, McCrohan C, Lee C, Romanova EV, Sweedler JV, Gillette MLU, Gillette R. cAMP, Ca 2+, pH i, and NO Regulate H-like Cation Channels That Underlie Feeding and Locomotion in the Predatory Sea Slug Pleurobranchaea californica. ACS Chem Neurosci 2018; 9:1986-1993. [PMID: 30067017 PMCID: PMC6128535 DOI: 10.1021/acschemneuro.8b00187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A systems approach to regulation of neuronal excitation in the mollusc Pleurobranchaea has described novel interactions of cyclic AMP-gated cation current (INa,cAMP), Ca2+, pHi, and NO. INa,cAMP appears in many neurons of feeding and locomotor neuronal networks. It is likely one of the family of hyperpolarization-activated, cyclic-nucleotide-gated currents (h-current) of vertebrate and invertebrate pacemaker networks. There are two isoforms. Ca2+ regulates both voltage dependence and depolarization-sensitive inactivation in both isoforms. The Type 1 INa,cAMP of the feeding network is enhanced by intracellular acidification. A direct dependence of INa,cAMP on cAMP allows the current to be used as a reporter on cAMP concentrations in the cell, and from there to the intrinsic activities of the synthetic adenyl cyclase and the degradative phosphodiesterase. Type 2 INa,cAMP of the locomotor system is activated by serotonergic inputs, while Type 1 of the feeding network is thought to be regulated peptidergically. NO synthase activity is high in the CNS, where it differs from standard neuronal NO synthase in not being Ca2+ sensitive. NO acidifies pHi, potentiating Type 1, and may act to open proton channels. A cGMP pathway does not mediate NO effects as in other systems. Rather, nitrosylation likely mediates its actions. An integrated model of the action of cAMP, Ca2+, pHi, and NO in the feeding network postulates that NO regulates proton conductance to cause neuronal excitation in the cell body on the one hand, and relief of activity-induced hyperacidification in fine dendritic processes on the other.
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Affiliation(s)
- Daniel J Green
- Neuroscience Program , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Rong-Chi Huang
- Department of Molecular & Integrative Physiology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Leland Sudlow
- Department of Molecular & Integrative Physiology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Nathan Hatcher
- Department of Molecular & Integrative Physiology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Kurt Potgieter
- Department of Molecular & Integrative Physiology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Catherine McCrohan
- School of Biological Sciences , University of Manchester , Manchester M13 9PT , United Kingdom
| | - Colin Lee
- Neuroscience Program , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Elena V Romanova
- Beckman Institute for Advanced Science and Technology and Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Jonathan V Sweedler
- Beckman Institute for Advanced Science and Technology and Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Martha L U Gillette
- Department of Cell & Developmental Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Rhanor Gillette
- Department of Molecular & Integrative Physiology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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COOK GEOFFREYM, GRUEN ANNAE, MORRIS JOHN, PANKEY MSABRINA, SENATORE ADRIANO, KATZ PAULS, WATSON WINSORH, NEWCOMB JAMESM. Sequences of Circadian Clock Proteins in the Nudibranch Molluscs Hermissenda crassicornis, Melibe leonina, and Tritonia diomedea. THE BIOLOGICAL BULLETIN 2018; 234:207-218. [PMID: 29949437 PMCID: PMC6180908 DOI: 10.1086/698467] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
While much is known about the genes and proteins that make up the circadian clocks in vertebrates and several arthropod species, much less is known about the clock genes in many other invertebrates, including nudibranchs. The goal of this project was to identify the RNA and protein products of putative clock genes in the central nervous system of three nudibranchs, Hermissenda crassicornis, Melibe leonina, and Tritonia diomedea. Using previously published transcriptomes (Hermissenda and Tritonia) and a new transcriptome (Melibe), we identified nudibranch orthologs for the products of five canonical clock genes: brain and muscle aryl hydrocarbon receptor nuclear translocator like protein 1, circadian locomotor output cycles kaput, non-photoreceptive cryptochrome, period, and timeless. Additionally, orthologous sequences for the products of five related genes-aryl hydrocarbon receptor nuclear translocator like, photoreceptive cryptochrome, cryptochrome DASH, 6-4 photolyase, and timeout-were determined. Phylogenetic analyses confirmed that the nudibranch proteins were most closely related to known orthologs in related invertebrates, such as oysters and annelids. In general, the nudibranch clock proteins shared greater sequence similarity with Mus musculus orthologs than Drosophila melanogaster orthologs, which is consistent with the closer phylogenetic relationships recovered between lophotrochozoan and vertebrate orthologs. The suite of clock-related genes in nudibranchs includes both photoreceptive and non-photoreceptive cryptochromes, as well as timeout and possibly timeless. Therefore, the nudibranch clock may resemble the one exhibited in mammals, or possibly even in non-drosopholid insects and oysters. The latter would be evidence supporting this as the ancestral clock for bilaterians.
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Key Words
- ARNTL, aryl hydrocarbon receptor nuclear translocator like
- BMAL1, brain and muscle aryl hydrocarbon receptor nuclear translocator like protein 1
- CLOCK, circadian locomotor output cycles kaput
- CNS, central nervous system
- CRY DASH, cryptochrome DASH
- FAD, flavin adenine dinucleotide
- G+I, gamma-distributed and invariant
- ML, maximum likelihood
- MSA, multiple sequence alignments
- NCBI, National Center for Biotechnology Information
- NPCRY, non-photoreceptive cryptochrome
- PAC, Per-Arnt-Sim-associated C-terminal
- PAS, Per-Arnt-Sim
- PCRY, photoreceptive cryptochrome
- PHR, 6-4 photolyase
- TSA, transcriptome shotgun assembly
- bHLH, basic helix-loop-helix
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Affiliation(s)
- GEOFFREY M. COOK
- Department of Biology and Health Science, New England College, Henniker, New Hampshire 03242
| | - ANNA E. GRUEN
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - JOHN MORRIS
- Department of Biology and Health Science, New England College, Henniker, New Hampshire 03242
| | - M. SABRINA PANKEY
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - ADRIANO SENATORE
- Department of Biology, University of Massachusetts, Amherst, Massachusetts 01003
- Present address: Department of Biology, University of Toronto, Mississauga, Ontario L5L 1C6, Canada
| | - PAUL S. KATZ
- Department of Biology, University of Massachusetts, Amherst, Massachusetts 01003
| | - WINSOR H. WATSON
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire 03824
| | - JAMES M. NEWCOMB
- Department of Biology and Health Science, New England College, Henniker, New Hampshire 03242
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De novo assembly, annotation, and characterization of the whole brain transcriptome of male and female Syrian hamsters. Sci Rep 2017; 7:40472. [PMID: 28071753 PMCID: PMC5223125 DOI: 10.1038/srep40472] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 12/06/2016] [Indexed: 01/11/2023] Open
Abstract
Hamsters are an ideal animal model for a variety of biomedical research areas such as cancer, virology, circadian rhythms, and behavioural neuroscience. The use of hamsters has declined, however, most likely due to the dearth of genetic tools available for these animals. Our laboratory uses hamsters to study acute social stress, and we are beginning to investigate the genetic mechanisms subserving defeat-induced behavioural change. We have been limited, however, by the lack of genetic resources available for hamsters. In this study, we sequenced the brain transcriptome of male and female Syrian hamsters to generate the necessary resources to continue our research. We completed a de novo assembly and after assembly optimization, there were 113,329 transcripts representing 14,530 unique genes. This study is the first to characterize transcript expression in both female and male hamster brains and offers invaluable information to promote understanding of a host of important biomedical research questions for which hamsters are an excellent model.
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De Oliveira AL, Wollesen T, Kristof A, Scherholz M, Redl E, Todt C, Bleidorn C, Wanninger A. Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks. BMC Genomics 2016; 17:905. [PMID: 27832738 PMCID: PMC5103448 DOI: 10.1186/s12864-016-3080-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 09/08/2016] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Mollusks display a striking morphological disparity, including, among others, worm-like animals (the aplacophorans), snails and slugs, bivalves, and cephalopods. This phenotypic diversity renders them ideal for studies into animal evolution. Despite being one of the most species-rich phyla, molecular and in silico studies concerning specific key developmental gene families are still scarce, thus hampering deeper insights into the molecular machinery that governs the development and evolution of the various molluscan class-level taxa. RESULTS Next-generation sequencing was used to retrieve transcriptomes of representatives of seven out of the eight recent class-level taxa of mollusks. Similarity searches, phylogenetic inferences, and a detailed manual curation were used to identify and confirm the orthology of numerous molluscan Hox and ParaHox genes, which resulted in a comprehensive catalog that highlights the evolution of these genes in Mollusca and other metazoans. The identification of a specific molluscan motif in the Hox paralog group 5 and a lophotrochozoan ParaHox motif in the Gsx gene is described. Functional analyses using KEGG and GO tools enabled a detailed description of key developmental genes expressed in important pathways such as Hedgehog, Wnt, and Notch during development of the respective species. The KEGG analysis revealed Wnt8, Wnt11, and Wnt16 as Wnt genes hitherto not reported for mollusks, thereby enlarging the known Wnt complement of the phylum. In addition, novel Hedgehog (Hh)-related genes were identified in the gastropod Lottia cf. kogamogai, demonstrating a more complex gene content in this species than in other mollusks. CONCLUSIONS The use of de novo transcriptome assembly and well-designed in silico protocols proved to be a robust approach for surveying and mining large sequence data in a wide range of non-model mollusks. The data presented herein constitute only a small fraction of the information retrieved from the analysed molluscan transcriptomes, which can be promptly employed in the identification of novel genes and gene families, phylogenetic inferences, and other studies using molecular tools. As such, our study provides an important framework for understanding some of the underlying molecular mechanisms involved in molluscan body plan diversification and hints towards functions of key developmental genes in molluscan morphogenesis.
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Affiliation(s)
- A. L. De Oliveira
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - T. Wollesen
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - A. Kristof
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - M. Scherholz
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - E. Redl
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - C. Todt
- University of Bergen, University Museum, The Natural History Collections, Allégaten 41, 5007 Bergen, Norway
| | - C. Bleidorn
- Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), José Gutiérrez Abascal 2, Madrid, 28006 Spain
- Institute of Biology, University of Leipzig, Leipzig, 04103 Germany
| | - A. Wanninger
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
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Northcutt AJ, Lett KM, Garcia VB, Diester CM, Lane BJ, Marder E, Schulz DJ. Deep sequencing of transcriptomes from the nervous systems of two decapod crustaceans to characterize genes important for neural circuit function and modulation. BMC Genomics 2016; 17:868. [PMID: 27809760 PMCID: PMC5096308 DOI: 10.1186/s12864-016-3215-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 10/26/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Crustaceans have been studied extensively as model systems for nervous system function from single neuron properties to behavior. However, lack of molecular sequence information and tools have slowed the adoption of these physiological systems as molecular model systems. In this study, we sequenced and performed de novo assembly for the nervous system transcriptomes of two decapod crustaceans: the Jonah crab (Cancer borealis) and the American lobster (Homarus americanus). RESULTS Forty-two thousand, seven hundred sixty-six and sixty thousand, two hundred seventy-three contigs were assembled from C. borealis and H. americanus respectively, representing 9,489 and 11,061 unique coding sequences. From these transcripts, genes associated with neural function were identified and manually curated to produce a characterization of multiple gene families important for nervous system function. This included genes for 34 distinct ion channel types, 17 biogenic amine and 5 GABA receptors, 28 major transmitter receptor subtypes including glutamate and acetylcholine receptors, and 6 gap junction proteins - the Innexins. CONCLUSION With this resource, crustacean model systems are better poised for incorporation of modern genomic and molecular biology technologies to further enhance the interrogation of fundamentals of nervous system function.
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Affiliation(s)
- Adam J. Northcutt
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO USA
| | - Kawasi M. Lett
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO USA
| | - Virginia B. Garcia
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO USA
| | - Clare M. Diester
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO USA
| | - Brian J. Lane
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO USA
| | - Eve Marder
- Volen Center and Biology Department, Brandeis University, Waltham, MA USA
| | - David J. Schulz
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO USA
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15
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Ip JCH, Leung PTY, Ho KKY, Qiu JW, Leung KMY. De novo transcriptome assembly of the marine gastropod Reishia clavigera for supporting toxic mechanism studies. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 178:39-48. [PMID: 27450239 DOI: 10.1016/j.aquatox.2016.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 07/06/2016] [Accepted: 07/14/2016] [Indexed: 06/06/2023]
Abstract
The intertidal whelk Reishia clavigera is commonly used as a biomonitor of chemical contamination in the marine environment along Western Pacific region, and as a model for mechanistic studies of organotin-mediated imposex development. However, limited genomic resources of R. clavigera have restricted its role for the investigation of molecular mechanisms of such endocrine disruptions. This study, therefore, aimed to establish tissue-specific transcriptomes of the digestive gland, gonad, head ganglia, penis and the remaining body part of the male and female R. clavigera. By combining the results, a global transcriptome was obtained. A total of 578,134,720 high-quality filtered reads were obtained using Illumina sequencing. The R. clavigera transcriptome comprised of 38,466 transcripts and 32,798 unigenes with predicted open reading frames. The average length of transcripts was 1,709bp with N50 of 2,236bp. Based on sequence similarity searches against public databases, 28,657 transcripts and 24,403 unigenes had at least one BLAST hit. There were 17,530 transcripts and 14,897 unigenes annotated with at least one Gene Ontology (GO) term. Moreover, 5,776 transcripts and 5,137 unigenes were associated with 333 Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways. The numbers of unigenes were similar among the five target tissues and between sexes, but tissue-specific expression profiles were revealed by multivariate analyses. Based on the functional annotation, putative steroid hormone-associated unigenes were identified. In particular, we highlighted the presence of steroid hormone receptor homologues that could be the targets for mechanistic studies of the organotin-mediated imposex development in marine gastropods. This newly generated transcriptome assembly of R. clavigera provides a valuable molecular resource for ecotoxicological and environmental genomic studies.
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Affiliation(s)
- Jack C H Ip
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Priscilla T Y Leung
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Kevin K Y Ho
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - J W Qiu
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China; Department of Biology, Hong Kong Baptist University, Waterloo Road, Kowloon, Hong Kong, China
| | - Kenneth M Y Leung
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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16
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Harney E, Dubief B, Boudry P, Basuyaux O, Schilhabel MB, Huchette S, Paillard C, Nunes FLD. De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome. Mar Genomics 2016; 28:11-16. [PMID: 26971316 DOI: 10.1016/j.margen.2016.03.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/03/2016] [Indexed: 02/08/2023]
Abstract
The European abalone Haliotis tuberculata is a delicacy and consequently a commercially valuable gastropod species. Aquaculture production and wild populations are subjected to multiple climate-associated stressors and anthropogenic pressures, including rising sea-surface temperatures, ocean acidification and an emerging pathogenic Vibrio infection. Transcript expression data provides a valuable resource for understanding abalone responses to variation in the biotic and abiotic environment. To generate an extensive transcriptome, we performed next-generation sequencing of RNA on larvae exposed to temperature and pH variation and on haemolymph of adults from two wild populations after experimental infection with Vibrio harveyi. We obtained more than 1.5 billion raw paired-end reads, which were assembled into 328,519 contigs. Filtration and clustering produced a transcriptome of 41,099 transcripts, of which 10,626 (25.85%) were annotated with Blast hits, and 7380 of these were annotated with Gene Ontology (GO) terms in Blast2Go. A differential expression analysis comparing all samples from the two life stages identified 5690 and 10,759 transcripts with significantly higher expression in larvae and adult haemolymph respectively. This is the greatest sequencing effort yet in the Haliotis genus, and provides the first high-throughput transcriptomic resource for H. tuberculata.
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Affiliation(s)
- Ewan Harney
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR6539 CNRS/UBO/IRD/Ifremer, Institut Universitaire Européen de la Mer, University of Brest (UBO), Université Européenne de Bretagne (UEB), Place Nicolas Copernic, 29280, Plouzané, France.
| | - Bruno Dubief
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR6539 CNRS/UBO/IRD/Ifremer, Institut Universitaire Européen de la Mer, University of Brest (UBO), Université Européenne de Bretagne (UEB), Place Nicolas Copernic, 29280, Plouzané, France
| | - Pierre Boudry
- Ifremer, Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR 6539 CNRS/UBO/IRD/Ifremer, Centre Bretagne Z.I. Pointe du Diable, 29280 Plouzané, France
| | - Olivier Basuyaux
- SMEL (Synergie Mer Et Littoral), Centre Expérimental, 50560 Blainville-sur-Mer, France
| | - Markus B Schilhabel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | | | - Christine Paillard
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR6539 CNRS/UBO/IRD/Ifremer, Institut Universitaire Européen de la Mer, University of Brest (UBO), Université Européenne de Bretagne (UEB), Place Nicolas Copernic, 29280, Plouzané, France
| | - Flavia L D Nunes
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), UMR6539 CNRS/UBO/IRD/Ifremer, Institut Universitaire Européen de la Mer, University of Brest (UBO), Université Européenne de Bretagne (UEB), Place Nicolas Copernic, 29280, Plouzané, France
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17
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Kang SW, Patnaik BB, Hwang HJ, Park SY, Wang TH, Park EB, Chung JM, Song DK, Patnaik HH, Lee JB, Kim C, Kim S, Park HS, Lee JS, Han YS, Lee YS. De novo Transcriptome Generation and Annotation for Two Korean Endemic Land Snails, Aegista chejuensis and Aegista quelpartensis, Using Illumina Paired-End Sequencing Technology. Int J Mol Sci 2016; 17:379. [PMID: 26999110 PMCID: PMC4813237 DOI: 10.3390/ijms17030379] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/05/2016] [Accepted: 03/09/2016] [Indexed: 12/24/2022] Open
Abstract
Aegista chejuensis and Aegista quelpartensis (Family-Bradybaenidae) are endemic to Korea, and are considered vulnerable due to declines in their population. The limited genetic resources for these species restricts the ability to prioritize conservation efforts. We sequenced the transcriptomes of these species using Illumina paired-end technology. Approximately 257 and 240 million reads were obtained and assembled into 198,531 and 230,497 unigenes for A. chejuensis and A. quelpartensis, respectively. The average and N50 unigene lengths were 735.4 and 1073 bp, respectively, for A. chejuensis, and 705.6 and 1001 bp, respectively, for A. quelpartensis. In total, 68,484 (34.5%) and 77,745 (33.73%) unigenes for A. chejuensis and A. quelpartensis, respectively, were annotated to databases. Gene Ontology terms were assigned to 23,778 (11.98%) and 26,396 (11.45) unigenes, for A. chejuensis and A. quelpartensis, respectively, while 5050 and 5838 unigenes were mapped to 117 and 124 pathways in the Kyoto Encyclopedia of Genes and Genomes database. In addition, we identified and annotated 9542 and 10,395 putative simple sequence repeats (SSRs) in unigenes from A. chejuensis and A. quelpartensis, respectively. We designed a list of PCR primers flanking the putative SSR regions. These microsatellites may be utilized for future phylogenetics and conservation initiatives.
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Affiliation(s)
- Se Won Kang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Bharat Bhusan Patnaik
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Chandaka Industrial Estate, Chandrasekharpur, Bhubaneswar, Odisha 751024, India.
| | - Hee-Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - So Young Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Tae Hun Wang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Eun Bi Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Jong Min Chung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Dae Kwon Song
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Hongray Howrelia Patnaik
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
| | - Jae Bong Lee
- Korea Zoonosis Research Institute (KOZRI), Chonbuk National University, 820-120 Hana-ro, Iksan, Jeollabuk-do 54528, Korea.
| | - Changmu Kim
- National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Korea.
| | - Soonok Kim
- National Institute of Biological Resources, 42, Hwangyeong-ro, Seo-gu, Incheon 22689, Korea.
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD. 621-6 Banseok-dong, Yuseong-gu, Daejeon 34069, Korea.
| | - Jun Sang Lee
- Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do 243341, Korea.
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Korea.
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungcheongnam-do 31538, Korea.
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18
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Patnaik BB, Wang TH, Kang SW, Hwang HJ, Park SY, Park EB, Chung JM, Song DK, Kim C, Kim S, Lee JS, Han YS, Park HS, Lee YS. Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery. PLoS One 2016; 11:e0148622. [PMID: 26872384 PMCID: PMC4752248 DOI: 10.1371/journal.pone.0148622] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/20/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The freshwater mussel Cristaria plicata (Bivalvia: Eulamellibranchia: Unionidae), is an economically important species in molluscan aquaculture due to its use in pearl farming. The species have been listed as endangered in South Korea due to the loss of natural habitats caused by anthropogenic activities. The decreasing population and a lack of genomic information on the species is concerning for environmentalists and conservationists. In this study, we conducted a de novo transcriptome sequencing and annotation analysis of C. plicata using Illumina HiSeq 2500 next-generation sequencing (NGS) technology, the Trinity assembler, and bioinformatics databases to prepare a sustainable resource for the identification of candidate genes involved in immunity, defense, and reproduction. RESULTS The C. plicata transcriptome analysis included a total of 286,152,584 raw reads and 281,322,837 clean reads. The de novo assembly identified a total of 453,931 contigs and 374,794 non-redundant unigenes with average lengths of 731.2 and 737.1 bp, respectively. Furthermore, 100% coverage of C. plicata mitochondrial genes within two unigenes supported the quality of the assembler. In total, 84,274 unigenes showed homology to entries in at least one database, and 23,246 unigenes were allocated to one or more Gene Ontology (GO) terms. The most prominent GO biological process, cellular component, and molecular function categories (level 2) were cellular process, membrane, and binding, respectively. A total of 4,776 unigenes were mapped to 123 biological pathways in the KEGG database. Based on the GO terms and KEGG annotation, the unigenes were suggested to be involved in immunity, stress responses, sex-determination, and reproduction. A total of 17,251 cDNA simple sequence repeats (cSSRs) were identified from 61,141 unigenes (size of >1 kb) with the most abundant being dinucleotide repeats. CONCLUSIONS This dataset represents the first transcriptome analysis of the endangered mollusc, C. plicata. The transcriptome provides a comprehensive sequence resource for the conservation of genetic information in this species and enrichment of the genetic database. The development of molecular markers will assist in the genetic improvement of C. plicata.
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Affiliation(s)
- Bharat Bhusan Patnaik
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Bhubaneswar- 751024, Odisha, India
| | - Tae Hun Wang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Se Won Kang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Hee-Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - So Young Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Eun Bi Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Jong Min Chung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Dae Kwon Song
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Changmu Kim
- National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Soonok Kim
- National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Jun Sang Lee
- Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 200-701, Republic of Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 300 Yongbong-Dong, Buk-gu, Gwangju, 500-757, Republic of Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 305-150, Republic of Korea
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
- * E-mail:
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Tamvacakis AN, Senatore A, Katz PS. Identification of genes related to learning and memory in the brain transcriptome of the mollusc, Hermissenda crassicornis. Learn Mem 2015; 22:617-21. [PMID: 26572652 PMCID: PMC4749734 DOI: 10.1101/lm.038158.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 09/28/2015] [Indexed: 11/25/2022]
Abstract
The sea slug Hermissenda crassicornis (Mollusca, Gastropoda, Nudibranchia) has been studied extensively in associative learning paradigms. However, lack of genetic information previously hindered molecular-level investigations. Here, the Hermissenda brain transcriptome was sequenced and assembled de novo, producing 165,743 total transcripts. Orthologs of 95 genes implicated in learning were identified. These included genes for a serotonin receptor and a GABA-B receptor subunit that had not been previously described in molluscs, as well as an adenylyl cyclase gene not previously described in gastropods. This study illustrates the Hermissenda transcriptome's potential as an important genetic tool in future learning and memory research.
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Affiliation(s)
- Arianna N Tamvacakis
- Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-4010, USA
| | - Adriano Senatore
- Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-4010, USA
| | - Paul S Katz
- Neuroscience Institute, Georgia State University, Atlanta, Georgia 30302-4010, USA
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Correction: Deep mRNA sequencing of the Tritonia diomedea brain transcriptome provides access to gene homologues for neuronal excitability, synaptic transmission and peptidergic signalling. PLoS One 2015; 10:e0123514. [PMID: 25822976 PMCID: PMC4378960 DOI: 10.1371/journal.pone.0123514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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