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      G protein-coupled receptors as candidates for modulation and activation of the chemical senses in decapod crustaceans

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          Abstract

          Many studies have characterized class A GPCRs in crustaceans; however, their expression in crustacean chemosensory organs has yet to be detailed. Class A GPCRs comprise several subclasses mediating diverse functions. In this study, using sequence homology, we classified all putative class A GPCRs in two chemosensory organs (antennular lateral flagellum [LF] and walking leg dactyls) and brain of four species of decapod crustaceans (Caribbean spiny lobster Panulirus argus, American lobster Homarus americanus, red-swamp crayfish Procambarus clarkii, and blue crab Callinectes sapidus). We identified 333 putative class A GPCRs– 83 from P. argus, 81 from H. americanus, 102 from P. clarkii, and 67 from C. sapidus–which belong to five distinct subclasses. The numbers of sequences for each subclass in the four decapod species are (in parentheses): opsins (19), small-molecule receptors including biogenic amine receptors (83), neuropeptide receptors (90), leucine-rich repeat-containing GPCRs (LGRs) (24), orphan receptors (117). Most class A GPCRs are predominately expressed in the brain; however, we identified multiple transcripts enriched in the LF and several in the dactyl. In total, we found 55 sequences with higher expression in the chemosensory organs relative to the brain across three decapod species. We also identified novel transcripts enriched in the LF including a metabotropic histamine receptor and numerous orphan receptors. Our work establishes expression patterns for class A GPCRs in the chemosensory organs of crustaceans, providing insight into molecular mechanisms mediating neurotransmission, neuromodulation, and possibly chemoreception.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            Trimmomatic: a flexible trimmer for Illumina sequence data

            Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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              MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

              We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SupervisionRole: VisualizationRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: Visualization
                Role: ConceptualizationRole: InvestigationRole: Project administrationRole: ResourcesRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                4 June 2021
                2021
                : 16
                : 6
                : e0252066
                Affiliations
                [1 ] Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
                [2 ] Yale Center for Genomic Analysis, Yale University, New Haven, Connecticut, United States of America
                Wake Forest University, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                [¤]

                Current address: Department of Biology, Colorado State University, Ft. Collins, Colorado, United States of America

                Author information
                https://orcid.org/0000-0002-4474-4138
                https://orcid.org/0000-0002-6157-2462
                https://orcid.org/0000-0002-5599-4976
                Article
                PONE-D-20-38358
                10.1371/journal.pone.0252066
                8177520
                34086685
                834440e1-695f-4f24-ad97-0426c1b9c49f
                © 2021 Rump et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 6 December 2020
                : 7 May 2021
                Page count
                Figures: 4, Tables: 4, Pages: 27
                Funding
                Funded by: Brains & Behavior seed grant
                Award Recipient :
                Funded by: Brains & Behavior Program, Center for Neuromics
                Award Recipient :
                Funded by: Neuroscience Institute of Georgia State University
                Award Recipient :
                Support was provided by a Brains & Behavior seed grant to CDD and student research fellowships from the Brains & Behavior Program, Center for Neuromics, and Neuroscience Institute of Georgia State University to MTR and MTK. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Biochemistry
                Proteins
                Transmembrane Receptors
                G Protein Coupled Receptors
                Biology and Life Sciences
                Cell Biology
                Signal Transduction
                Transmembrane Receptors
                G Protein Coupled Receptors
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Invertebrates
                Arthropoda
                Crustaceans
                Biology and Life Sciences
                Zoology
                Animals
                Invertebrates
                Arthropoda
                Crustaceans
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Transcriptome Analysis
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Transcriptome Analysis
                Biology and Life Sciences
                Biochemistry
                Neurochemistry
                Neurochemicals
                Neuropeptides
                Biology and Life Sciences
                Neuroscience
                Neurochemistry
                Neurochemicals
                Neuropeptides
                Biology and Life Sciences
                Biochemistry
                Hormones
                Peptide Hormones
                Neuropeptides
                Biology and Life Sciences
                Anatomy
                Brain
                Medicine and Health Sciences
                Anatomy
                Brain
                Biology and Life Sciences
                Neuroscience
                Cognitive Science
                Cognitive Psychology
                Perception
                Sensory Perception
                Biology and Life Sciences
                Psychology
                Cognitive Psychology
                Perception
                Sensory Perception
                Social Sciences
                Psychology
                Cognitive Psychology
                Perception
                Sensory Perception
                Biology and Life Sciences
                Neuroscience
                Sensory Perception
                Biology and Life Sciences
                Cell Biology
                Cellular Types
                Animal Cells
                Neurons
                Afferent Neurons
                Olfactory Receptor Neurons
                Biology and Life Sciences
                Neuroscience
                Cellular Neuroscience
                Neurons
                Afferent Neurons
                Olfactory Receptor Neurons
                Research and Analysis Methods
                Animal Studies
                Experimental Organism Systems
                Model Organisms
                Drosophila Melanogaster
                Research and Analysis Methods
                Model Organisms
                Drosophila Melanogaster
                Research and Analysis Methods
                Animal Studies
                Experimental Organism Systems
                Animal Models
                Drosophila Melanogaster
                Biology and Life Sciences
                Zoology
                Entomology
                Insects
                Drosophila
                Drosophila Melanogaster
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Invertebrates
                Arthropoda
                Insects
                Drosophila
                Drosophila Melanogaster
                Biology and Life Sciences
                Zoology
                Animals
                Invertebrates
                Arthropoda
                Insects
                Drosophila
                Drosophila Melanogaster
                Custom metadata
                All data are freely available in open access data repositories. Raw reads are available under BioProject accession PRJNA596786 on NCBI ( https://www.ncbi.nlm.nih.gov/bioproject/prjna596786). DESeq2 data and custom ‘R’ code used to generate MA plots are available under accession S-BSST653 on EBI Biostudies ( https://www.ebi.ac.uk/biostudies/studies/S-BSST653). As an additional resource to crustacean researchers, de novo assembled transcriptomes of the four decapod crustaceans in this study are available with unrestricted access as BLAST databases on CrustyBase ( https://crustybase.org/browser/). All other relevant data are available in the Methods and Supporting Information sections of this manuscript.

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