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Amaral DT, Bonatelli IAS. Opsin diversity and evolution in the Elateroidea superfamily: Insights from transcriptome data. INSECT MOLECULAR BIOLOGY 2024; 33:112-123. [PMID: 37837289 DOI: 10.1111/imb.12881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
Vision plays a vital biological role in organisms, which depends on the visual pigment molecules (opsin plus chromophore). The expansion or reduction of spectral channels in the organisms is determined by distinct opsin classes and copy numbers resulting from duplication or loss. Within Coleoptera, the superfamily Elateroidea exhibits a great diversity of morphological and physiological characteristics, such as bioluminescence, making this group an important model for opsin studies. While molecular and physiological studies have been conducted in Lampyridae and Elateridae, other families remain unexplored. Here, we reused transcriptome datasets from Elateroidea species, including members of Elateridae, Lampyridae, Phengodidae, Rhagophthalmidae, Cantharidae, and Lycidae, to detect the diversity of putative opsin genes in this superfamily. In addition, we tested the signature of sites under positive selection in both ultraviolet (UV)- and long-wavelength (LW)-opsin classes. Although the visual system in Elateroidea is considered simple, we observed events of duplication in LW- and UV-opsin, as well as the absence of UV-opsin in distinct families, such as larval Phengodidae individuals. We detected different copies of LW-opsins that were highly expressed in the eyes of distinct tribes of fireflies, indicating the possible selection of each copy during the evolution of the sexual mating to avoid spectrum overlapping. In Elateridae, we found that the bioluminescent species had a distinct LW-opsin copy compared with the non-bioluminescent species, suggesting events of duplication and loss. The signature of positive selection showed only one residue associated with the chromophore binding site in the Elateroidea, which may produce a bathochromic shift in the wavelength absorption spectra in this family. Overall, this study brings important content and fills gaps regarding opsin evolution in Elateroidea.
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Affiliation(s)
- Danilo T Amaral
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Paulo, Brazil
- Programa de Pós Graduação em Biotecnociências, Universidade Federal do ABC (UFABC), São Paulo, Brazil
| | - Isabel A S Bonatelli
- Departamento de Ecologia e Biologia Evolutiva, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Instituto de Ciências Ambientais, Diadema, Brazil
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Yilmaz A, Hempel de Ibarra N, Kelber A. High diversity of arthropod colour vision: from genes to ecology. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210273. [PMID: 36058249 PMCID: PMC9441235 DOI: 10.1098/rstb.2021.0273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Colour vision allows animals to use the information contained in the spectrum of light to control important behavioural decisions such as selection of habitats, food or mates. Among arthropods, the largest animal phylum, we find completely colour-blind species as well as species with up to 40 different opsin genes or more than 10 spectral types of photoreceptors, we find a large diversity of optical methods shaping spectral sensitivity, we find eyes with different colour vision systems looking into the dorsal and ventral hemisphere, and species in which males and females see the world in different colours. The behavioural use of colour vision shows an equally astonishing diversity. Only the neural mechanisms underlying this sensory ability seems surprisingly conserved—not only within the phylum, but even between arthropods and the other well-studied phylum, chordates. The papers in this special issue allow a glimpse into the colourful world of arthropod colour vision, and besides giving an overview this introduction highlights how much more research is needed to fill in the many missing pieces of this large puzzle. This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.
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Affiliation(s)
- Ayse Yilmaz
- Department of Biology - Functional Zoology, Lund University, Lund 22362, Sweden
| | | | - Almut Kelber
- Department of Biology - Functional Zoology, Lund University, Lund 22362, Sweden
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A thorough annotation of the krill transcriptome offers new insights for the study of physiological processes. Sci Rep 2022; 12:11415. [PMID: 35794144 PMCID: PMC9259678 DOI: 10.1038/s41598-022-15320-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractThe krill species Euphausia superba plays a critical role in the food chain of the Antarctic ecosystem. Significant changes in climate conditions observed in the Antarctic Peninsula region in the last decades have already altered the distribution of krill and its reproductive dynamics. A deeper understanding of the adaptation capabilities of this species is urgently needed. The availability of a large body of RNA-seq assays allowed us to extend the current knowledge of the krill transcriptome. Our study covered the entire developmental process providing information of central relevance for ecological studies. Here we identified a series of genes involved in different steps of the krill moulting cycle, in the reproductive process and in sexual maturation in accordance with what was already described in previous works. Furthermore, the new transcriptome highlighted the presence of differentially expressed genes previously unknown, playing important roles in cuticle development as well as in energy storage during the krill life cycle. The discovery of new opsin sequences, specifically rhabdomeric opsins, one onychopsin, and one non-visual arthropsin, expands our knowledge of the krill opsin repertoire. We have collected all these results into the KrillDB2 database, a resource combining the latest annotation of the krill transcriptome with a series of analyses targeting genes relevant to krill physiology. KrillDB2 provides in a single resource a comprehensive catalog of krill genes; an atlas of their expression profiles over all RNA-seq datasets publicly available; a study of differential expression across multiple conditions. Finally, it provides initial indications about the expression of microRNA precursors, whose contribution to krill physiology has never been reported before.
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Guignard Q, Allison JD, Slippers B. The evolution of insect visual opsin genes with specific consideration of the influence of ocelli and life history traits. BMC Ecol Evol 2022; 22:2. [PMID: 34996358 PMCID: PMC8739693 DOI: 10.1186/s12862-022-01960-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/04/2022] [Indexed: 11/30/2022] Open
Abstract
Background Visual opsins are expressed in the compound eyes and ocelli of insects and enable light detection. Three distinct phylogenetic groups of visual opsins are found in insects, named long (LW), short (SW) and ultraviolet (UV) wavelength sensitive opsins. Recently, the LW group was found to be duplicated into the LW2b and the LW2a opsins. The expression of LW2b opsins is ocelli specific in some insects (e.g., bees, cricket, scorpion flies), but the gene was not found in other orders possessing three or less ocelli (e.g., dragonflies, beetles, moths, bugs). In flies, two LW2b homologs have been characterised, with one expressed in the ocelli and the other in the compound eyes. To date, it remains unclear which evolutionary forces have driven gains and losses of LW opsins in insects. Here we take advantage of the recent rapid increase in available sequence data (i.e., from insect genomes, targeted PCR amplification, RNAseq) to characterize the phylogenetic relationships of 1000 opsin sequences in 18 orders of Insects. The resulting phylogeny discriminates between four main groups of opsins, and onto this phylogeny we mapped relevant morphological and life history traits. Results Our results demonstrate a conserved LW2b opsin only present in insects with three ocelli. Only two groups (Brachycera and Odonata) possess more than one LW2b opsin, likely linked to their life history. In flies, we hypothesize that the duplication of the LW2b opsin occurred after the transition from aquatic to terrestrial larvae. During this transition, higher flies (Brachycera) lost a copy of the LW2a opsin, still expressed and duplicated in the compound eyes of lower flies (Nematocera). In higher flies, the LW2b opsin has been duplicated and expressed in the compound eyes while the ocelli and the LW2b opsin were lost in lower flies. In dragonflies, specialisation of flight capabilities likely drove the diversification of the LW2b visual opsins. Conclusion The presence of the LW2b opsin in insects possessing three ocelli suggests a role in specific flight capabilities (e.g., stationary flight). This study provides the most complete view of the evolution of visual opsin genes in insects yet, and provides new insight into the influence of ocelli and life history traits on opsin evolution in insects. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01960-8.
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Affiliation(s)
- Quentin Guignard
- Department of Zoology and Entomology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa.
| | - Jeremy D Allison
- Department of Zoology and Entomology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa.,Natural Resources Canada, Canadian Forest Service, Great Lakes Forestry Centre, 1219 Queen Street E, Sault Ste. Marie, ON, P6A 2E5, Canada
| | - Bernard Slippers
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa
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Rump MT, Kozma MT, Pawar SD, Derby CD. G protein-coupled receptors as candidates for modulation and activation of the chemical senses in decapod crustaceans. PLoS One 2021; 16:e0252066. [PMID: 34086685 PMCID: PMC8177520 DOI: 10.1371/journal.pone.0252066] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 05/07/2021] [Indexed: 12/16/2022] Open
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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Affiliation(s)
- Matthew T. Rump
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
| | - Mihika T. Kozma
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
| | - Shrikant D. Pawar
- Yale Center for Genomic Analysis, Yale University, New Haven, Connecticut, United States of America
| | - Charles D. Derby
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
- * E-mail:
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Rotenberg D, Baumann AA, Ben-Mahmoud S, Christiaens O, Dermauw W, Ioannidis P, Jacobs CGC, Vargas Jentzsch IM, Oliver JE, Poelchau MF, Rajarapu SP, Schneweis DJ, Snoeck S, Taning CNT, Wei D, Widana Gamage SMK, Hughes DST, Murali SC, Bailey ST, Bejerman NE, Holmes CJ, Jennings EC, Rosendale AJ, Rosselot A, Hervey K, Schneweis BA, Cheng S, Childers C, Simão FA, Dietzgen RG, Chao H, Dinh H, Doddapaneni HV, Dugan S, Han Y, Lee SL, Muzny DM, Qu J, Worley KC, Benoit JB, Friedrich M, Jones JW, Panfilio KA, Park Y, Robertson HM, Smagghe G, Ullman DE, van der Zee M, Van Leeuwen T, Veenstra JA, Waterhouse RM, Weirauch MT, Werren JH, Whitfield AE, Zdobnov EM, Gibbs RA, Richards S. Genome-enabled insights into the biology of thrips as crop pests. BMC Biol 2020; 18:142. [PMID: 33070780 PMCID: PMC7570057 DOI: 10.1186/s12915-020-00862-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. RESULTS We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. CONCLUSIONS Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.
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Affiliation(s)
- Dorith Rotenberg
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Aaron A Baumann
- Virology Section, College of Veterinary Medicine, University of Tennessee, A239 VTH, 2407 River Drive, Knoxville, TN, 37996, USA
| | - Sulley Ben-Mahmoud
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | - Olivier Christiaens
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Panagiotis Ioannidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Vassilika Vouton, 70013, Heraklion, Greece
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany
| | - Jonathan E Oliver
- Department of Plant Pathology, University of Georgia - Tifton Campus, Tifton, GA, 31793-5737, USA
| | | | - Swapna Priya Rajarapu
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Derek J Schneweis
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Simon Snoeck
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Department of Biology, University of Washington, Seattle, WA, 98105, USA
| | - Clauvis N T Taning
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Dong Wei
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China and Ghent University, Ghent, Belgium
| | | | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Samuel T Bailey
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | | | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
- Department of Biology, Mount St. Joseph University, Cincinnati, OH, 45233, USA
| | - Andrew Rosselot
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Kaylee Hervey
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Brandi A Schneweis
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Sammy Cheng
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | | | - Felipe A Simão
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China and Ghent University, Ghent, Belgium
| | - Diane E Ullman
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | | | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Jan A Veenstra
- INCIA UMR 5287 CNRS, University of Bordeaux, Pessac, France
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Swiss Institute of Bioinformatics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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Kozma MT, Ngo-Vu H, Rump MT, Bobkov YV, Ache BW, Derby CD. Single cell transcriptomes reveal expression patterns of chemoreceptor genes in olfactory sensory neurons of the Caribbean spiny lobster, Panulirus argus. BMC Genomics 2020; 21:649. [PMID: 32962631 PMCID: PMC7510291 DOI: 10.1186/s12864-020-07034-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Crustaceans express several classes of receptor genes in their antennules, which house olfactory sensory neurons (OSNs) and non-olfactory chemosensory neurons. Transcriptomics studies reveal that candidate chemoreceptor proteins include variant Ionotropic Receptors (IRs) including both co-receptor IRs and tuning IRs, Transient Receptor Potential (TRP) channels, Gustatory Receptors, epithelial sodium channels, and class A G-protein coupled receptors (GPCRs). The Caribbean spiny lobster, Panulirus argus, expresses in its antennules nearly 600 IRs, 17 TRP channels, 1 Gustatory Receptor, 7 epithelial sodium channels, 81 GPCRs, 6 G proteins, and dozens of enzymes in signaling pathways. However, the specific combinatorial expression patterns of these proteins in single sensory neurons are not known for any crustacean, limiting our understanding of how their chemosensory systems encode chemical quality. RESULTS The goal of this study was to use transcriptomics to describe expression patterns of chemoreceptor genes in OSNs of P. argus. We generated and analyzed transcriptomes from 7 single OSNs, some of which were shown to respond to a food odor, as well as an additional 7 multicell transcriptomes from preparations containing few (2-4), several (ca. 15), or many (ca. 400) OSNs. We found that each OSN expressed the same 2 co-receptor IRs (IR25a, IR93a) but not the other 2 antennular coIRs (IR8a, IR76b), 9-53 tuning IRs but only one to a few in high abundance, the same 5 TRP channels plus up to 5 additional TRPs, 12-17 GPCRs including the same 5 expressed in every single cell transcriptome, the same 3 G proteins plus others, many enzymes in the signaling pathways, but no Gustatory Receptors or epithelial sodium channels. The greatest difference in receptor expression among the OSNs was the identity of the tuning IRs. CONCLUSIONS Our results provide an initial view of the combinatorial expression patterns of receptor molecules in single OSNs in one species of decapod crustacean, including receptors directly involved in olfactory transduction and others likely involved in modulation. Our results also suggest differences in receptor expression in OSNs vs. other chemosensory neurons.
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Affiliation(s)
- Mihika T Kozma
- Neuroscience Institute, Georgia State University, Atlanta, GA, 30303, USA
| | - Hanh Ngo-Vu
- Neuroscience Institute, Georgia State University, Atlanta, GA, 30303, USA
| | - Matthew T Rump
- Neuroscience Institute, Georgia State University, Atlanta, GA, 30303, USA
| | - Yuriy V Bobkov
- Whitney Laboratory, University of Florida, St. Augustine, Florida, 32084, USA
| | - Barry W Ache
- Whitney Laboratory, University of Florida, St. Augustine, Florida, 32084, USA
| | - Charles D Derby
- Neuroscience Institute, Georgia State University, Atlanta, GA, 30303, USA.
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8
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Vizueta J, Escuer P, Frías-López C, Guirao-Rico S, Hering L, Mayer G, Rozas J, Sánchez-Gracia A. Evolutionary History of Major Chemosensory Gene Families across Panarthropoda. Mol Biol Evol 2020; 37:3601-3615. [DOI: 10.1093/molbev/msaa197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
Chemosensory perception is a fundamental biological process of particular relevance in basic and applied arthropod research. However, apart from insects, there is little knowledge of specific molecules involved in this system, which is restricted to a few taxa with uneven phylogenetic sampling across lineages. From an evolutionary perspective, onychophorans (velvet worms) and tardigrades (water bears) are of special interest since they represent the closest living relatives of arthropods, altogether comprising the Panarthropoda. To get insights into the evolutionary origin and diversification of the chemosensory gene repertoire in panarthropods, we sequenced the antenna- and head-specific transcriptomes of the velvet worm Euperipatoides rowelli and analyzed members of all major chemosensory families in representative genomes of onychophorans, tardigrades, and arthropods. Our results suggest that the NPC2 gene family was the only family encoding soluble proteins in the panarthropod ancestor and that onychophorans might have lost many arthropod-like chemoreceptors, including the highly conserved IR25a receptor of protostomes. On the other hand, the eutardigrade genomes lack genes encoding the DEG-ENaC and CD36-sensory neuron membrane proteins, the chemosensory members of which have been retained in arthropods; these losses might be related to lineage-specific adaptive strategies of tardigrades to survive extreme environmental conditions. Although the results of this study need to be further substantiated by an increased taxon sampling, our findings shed light on the diversification of chemosensory gene families in Panarthropoda and contribute to a better understanding of the evolution of animal chemical senses.
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Affiliation(s)
- Joel Vizueta
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Paula Escuer
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristina Frías-López
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | | | - Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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9
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Manni M, Simao FA, Robertson HM, Gabaglio MA, Waterhouse RM, Misof B, Niehuis O, Szucsich NU, Zdobnov EM. The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations. Genome Biol Evol 2020; 12:3534-3549. [PMID: 31778187 PMCID: PMC6938034 DOI: 10.1093/gbe/evz260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/13/2022] Open
Abstract
The dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gb draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens, we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion that might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behavior, and duplicated apoptotic genes might underlie its high regenerative potential. The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.
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Affiliation(s)
- Mosè Manni
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
| | - Felipe A Simao
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign
| | - Marco A Gabaglio
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Swiss Institute of Bioinformatics, University of Lausanne, Switzerland
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Albert Ludwig University, Institute of Biology I (Zoology), Freiburg, Germany
| | | | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
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10
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Martin C, Hering L, Metzendorf N, Hormann S, Kasten S, Fuhrmann S, Werckenthin A, Herberg FW, Stengl M, Mayer G. Analysis of Pigment-Dispersing Factor Neuropeptides and Their Receptor in a Velvet Worm. Front Endocrinol (Lausanne) 2020; 11:273. [PMID: 32477266 PMCID: PMC7235175 DOI: 10.3389/fendo.2020.00273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/14/2020] [Indexed: 11/13/2022] Open
Abstract
Pigment-dispersing factor neuropeptides (PDFs) occur in a wide range of protostomes including ecdysozoans (= molting animals) and lophotrochozoans (mollusks, annelids, flatworms, and allies). Studies in insects revealed that PDFs play a role as coupling factors of circadian pacemaker cells, thereby controlling rest-activity rhythms. While the last common ancestor of protostomes most likely possessed only one pdf gene, two pdf homologs, pdf-I and pdf-II, might have been present in the last common ancestors of Ecdysozoa and Panarthropoda (Onychophora + Tardigrada + Arthropoda). One of these homologs, however, was subsequently lost in the tardigrade and arthropod lineages followed by independent duplications of pdf-I in tardigrades and decapod crustaceans. Due to the ancestral set of two pdf genes, the study of PDFs and their receptor (PDFR) in Onychophora might reveal the ancient organization and function of the PDF/PDFR system in panarthropods. Therefore, we deorphanized the PDF receptor and generated specific antibodies to localize the two PDF peptides and their receptor in the onychophoran Euperipatoides rowelli. We further conducted bioluminescence resonance energy transfer (BRET) experiments on cultured human cells (HEK293T) using an Epac-based sensor (Epac-L) to examine cAMP responses in transfected cells and to reveal potential differences in the interaction of PDF-I and PDF-II with PDFR from E. rowelli. These data show that PDF-II has a tenfold higher potency than PDF-I as an activating ligand. Double immunolabeling revealed that both peptides are co-expressed in E. rowelli but their respective levels of expression differ between specific cells: some neurons express the same amount of both peptides, while others exhibit higher levels of either PDF-I or PDF-II. The detection of the onychophoran PDF receptor in cells that additionally express the two PDF peptides suggests autoreception, whereas spatial separation of PDFR- and PDF-expressing cells supports hormonal release of PDF into the hemolymph. This suggests a dual role of PDF peptides-as hormones and as neurotransmitters/neuromodulators-in Onychophora.
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Affiliation(s)
- Christine Martin
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Niklas Metzendorf
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Sarah Hormann
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Sonja Kasten
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Sonja Fuhrmann
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Achim Werckenthin
- Department of Animal Physiology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Friedrich W. Herberg
- Department of Biochemistry, Institute of Biology, University of Kassel, Kassel, Germany
| | - Monika Stengl
- Department of Animal Physiology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
- *Correspondence: Georg Mayer
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11
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Treffkorn S, Mayer G. Expression of NK genes that are not part of the NK cluster in the onychophoran Euperipatoides rowelli (Peripatopsidae). BMC DEVELOPMENTAL BIOLOGY 2019; 19:7. [PMID: 30987579 PMCID: PMC6466738 DOI: 10.1186/s12861-019-0185-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 03/12/2019] [Indexed: 12/25/2022]
Abstract
Background NK genes are a group of homeobox transcription factors that are involved in various molecular pathways across bilaterians. They are typically divided into two subgroups, the NK cluster (NKC) and NK-linked genes (NKL). While the NKC genes have been studied in various bilaterians, corresponding data of many NKL genes are missing to date. To further investigate the ancestral roles of NK family genes, we analyzed the expression patterns of NKL genes in the onychophoran Euperipatoides rowelli. Results The NKL gene complement of E. rowelli comprises eight genes, including BarH, Bari, Emx, Hhex, Nedx, NK2.1, vax and NK2.2, of which only NK2.2 was studied previously. Our data for the remaining seven NKL genes revealed expression in different structures associated with the developing nervous system in embryos of E. rowelli. While NK2.1 and vax are expressed in distinct medial regions of the developing protocerebrum early in development, BarH, Bari, Emx, Hhex and Nedx are expressed in late developmental stages, after all major structures of the nervous system have been established. Furthermore, BarH and Nedx are expressed in distinct mesodermal domains in the developing limbs. Conclusions Comparison of our expression data to those of other bilaterians revealed similar patterns of NK2.1, vax, BarH and Emx in various aspects of neural development, such as the formation of anterior neurosecretory cells mediated by a conserved molecular mechanism including NK2.1 and vax, and the development of the central and peripheral nervous system involving BarH and Emx. A conserved role in neural development has also been reported from NK2.2, suggesting that the NKL genes might have been primarily involved in neural development in the last common ancestor of bilaterians or at least nephrozoans (all bilaterians excluding xenacoelomorphs). The lack of comparative data for many of the remaining NKL genes, including Bari, Hhex and Nedx currently hampers further evolutionary conclusions. Hence, future studies should focus on the expression of these genes in other bilaterians, which would provide a basis for comparative studies and might help to better understand the role of NK genes in the diversification of bilaterians. Electronic supplementary material The online version of this article (10.1186/s12861-019-0185-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sandra Treffkorn
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany.
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
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12
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Fleming JF, Kristensen RM, Sørensen MV, Park TYS, Arakawa K, Blaxter M, Rebecchi L, Guidetti R, Williams TA, Roberts NW, Vinther J, Pisani D. Molecular palaeontology illuminates the evolution of ecdysozoan vision. Proc Biol Sci 2018; 285:20182180. [PMID: 30518575 PMCID: PMC6283943 DOI: 10.1098/rspb.2018.2180] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/13/2018] [Indexed: 12/25/2022] Open
Abstract
Colour vision is known to have arisen only twice-once in Vertebrata and once within the Ecdysozoa, in Arthropoda. However, the evolutionary history of ecdysozoan vision is unclear. At the molecular level, visual pigments, composed of a chromophore and a protein belonging to the opsin family, have different spectral sensitivities and these mediate colour vision. At the morphological level, ecdysozoan vision is conveyed by eyes of variable levels of complexity; from the simple ocelli observed in the velvet worms (phylum Onychophora) to the marvellously complex eyes of insects, spiders, and crustaceans. Here, we explore the evolution of ecdysozoan vision at both the molecular and morphological level; combining analysis of a large-scale opsin dataset that includes previously unknown ecdysozoan opsins with morphological analyses of key Cambrian fossils with preserved eye structures. We found that while several non-arthropod ecdysozoan lineages have multiple opsins, arthropod multi-opsin vision evolved through a series of gene duplications that were fixed in a period of 35-71 million years (Ma) along the stem arthropod lineage. Our integrative study of the fossil and molecular record of vision indicates that fossils with more complex eyes were likely to have possessed a larger complement of opsin genes.
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Affiliation(s)
- James F Fleming
- School of Earth Sciences, University of Bristol, Queen's Road, Bristol, UK
| | | | | | - Tae-Yoon S Park
- Division of Polar Earth-System Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Mark Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Lorena Rebecchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 213/D, Modena, Italy
| | - Roberto Guidetti
- Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi 213/D, Modena, Italy
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Tyndall Avenue, Bristol, UK
| | - Nicholas W Roberts
- School of Biological Sciences, University of Bristol, Tyndall Avenue, Bristol, UK
| | - Jakob Vinther
- School of Earth Sciences, University of Bristol, Queen's Road, Bristol, UK
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Queen's Road, Bristol, UK
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13
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Schumann I, Kenny N, Hui J, Hering L, Mayer G. Halloween genes in panarthropods and the evolution of the early moulting pathway in Ecdysozoa. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180888. [PMID: 30839709 PMCID: PMC6170570 DOI: 10.1098/rsos.180888] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/17/2018] [Indexed: 05/15/2023]
Abstract
Moulting is a characteristic feature of Ecdysozoa-the clade of moulting animals that includes the hyperdiverse arthropods and less speciose groups, such as onychophorans, tardigrades and nematodes. Moulting has been best analysed in arthropods, specifically in insects and crustaceans, in which a complex neuroendocrine system acts at the genomic level and initiates the transcription of genes responsible for moulting. The key moulting hormones, ecdysone and 20-hydroxyecdysone, are subsequently synthesized from cholesterol ingested with food. Their biosynthesis is regulated by the Rieske-domain protein Neverland and cytochrome P450 enzymes encoded by the so-called 'Halloween' genes. Ecdysone is then released into the haemolymph and modified into 20-hydroxyecdysone, which binds to the nuclear receptor EcR/USP and initiates transcription of the Early genes. As little is known about the moulting pathway of other ecdysozoans, we examined the occurrence of genes involved in ecdysteroid biosynthesis and the early moulting cascade across ecdysozoan subgroups. Genomic and transcriptomic searches revealed no Halloween genes in cycloneuralians, whereas only shadow (CYP315A1) is present in onychophorans and tardigrades, suggesting that the Halloween genes evolved stepwise in panarthropods. These findings imply that the genes which were responsible for the ecdysteroid biosynthesis in the last common ancestor of Ecdysozoa are currently unknown.
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Affiliation(s)
- Isabell Schumann
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Nathan Kenny
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Center of Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, People's Republic of China
| | - Jerome Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Center of Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, People's Republic of China
| | - Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
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14
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Treffkorn S, Kahnke L, Hering L, Mayer G. Expression of NK cluster genes in the onychophoran Euperipatoides rowelli: implications for the evolution of NK family genes in nephrozoans. EvoDevo 2018; 9:17. [PMID: 30026904 PMCID: PMC6050708 DOI: 10.1186/s13227-018-0105-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/06/2018] [Indexed: 02/05/2023] Open
Abstract
Background Understanding the evolution and development of morphological traits of the last common bilaterian ancestor is a major goal of the evo-devo discipline. The reconstruction of this "urbilaterian" is mainly based on comparative studies of common molecular patterning mechanisms in recent model organisms. The NK homeobox genes are key players in many of these molecular pathways, including processes regulating mesoderm, heart and neural development. Shared features seen in the expression patterns of NK genes have been used to determine the ancestral bilaterian characters. However, the commonly used model organisms provide only a limited view on the evolution of these molecular pathways. To further investigate the ancestral roles of NK cluster genes, we analyzed their expression patterns in the onychophoran Euperipatoides rowelli. Results We identified nine transcripts of NK cluster genes in E. rowelli, including single copies of NK1, NK3, NK4, NK5, Msx, Lbx and Tlx, and two copies of NK6. All of these genes except for NK6.1 and NK6.2 are expressed in different mesodermal organs and tissues in embryos of E. rowelli, including the anlagen of somatic musculature and the heart. Furthermore, we found distinct expression patterns of NK3, NK5, NK6, Lbx and Msx in the developing nervous system. The same holds true for the NKL gene NK2.2, which does not belong to the NK cluster but is a related gene playing a role in neural patterning. Surprisingly, NK1, Msx and Lbx are additionally expressed in a segment polarity-like pattern early in development-a feature that has been otherwise reported only from annelids. Conclusion Our results indicate that the NK cluster genes were involved in mesoderm and neural development in the last common ancestor of bilaterians or at least nephrozoans (i.e., bilaterians to the exclusion of xenacoelomorphs). By comparing our data from an onychophoran to those from other bilaterians, we critically review the hypothesis of a complex "urbilaterian" with a segmented body, a pulsatile organ or heart, and a condensed mediolaterally patterned nerve cord.
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Affiliation(s)
- Sandra Treffkorn
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Laura Kahnke
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
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15
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Kirwan JD, Graf J, Smolka J, Mayer G, Henze MJ, Nilsson DE. Low--resolution vision in a velvet worm (Onychophora). ACTA ACUST UNITED AC 2018; 221:jeb.175802. [PMID: 29626113 DOI: 10.1242/jeb.175802] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/15/2018] [Indexed: 01/21/2023]
Abstract
Onychophorans, also known as velvet worms, possess a pair of simple lateral eyes, and are a key lineage with regard to the evolution of vision. They resemble ancient Cambrian forms, and are closely related to arthropods, which boast an unrivalled diversity of eye designs. Nonetheless, the visual capabilities of onychophorans have not been well explored. Here, we assessed the spatial resolution of the onychophoran Euperipatoides rowelli using behavioural experiments, three-dimensional reconstruction, anatomical and optical examinations, and modelling. Exploiting their spontaneous attraction towards dark objects, we found that E. rowelli can resolve stimuli that have the same average luminance as the background. Depending on the assumed contrast sensitivity of the animals, we estimate the spatial resolution to be in the range 15-40 deg. This results from an arrangement where the cornea and lens project the image largely behind the retina. The peculiar ellipsoid shape of the eye in combination with the asymmetric position and tilted orientation of the lens may improve spatial resolution in the forward direction. Nonetheless, the unordered network of interdigitating photoreceptors, which fills the whole eye chamber, precludes high-acuity vision. Our findings suggest that adult specimens of E. rowelli cannot spot or visually identify prey or conspecifics beyond a few centimetres from the eye, but the coarse spatial resolution that the animals exhibited in our experiments is likely to be sufficient to find shelter and suitable microhabitats from further away. To our knowledge, this is the first evidence of resolving vision in an onychophoran.
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Affiliation(s)
- John D Kirwan
- Lund Vision Group, Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Josefine Graf
- Lund Vision Group, Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Jochen Smolka
- Lund Vision Group, Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Georg Mayer
- Department of Zoology, University of Kassel, 34132 Kassel, Germany
| | - Miriam J Henze
- Lund Vision Group, Department of Biology, Lund University, 223 62 Lund, Sweden .,Queensland Brain Institute, University of Queensland, St Lucia 4072, QLD, Australia
| | - Dan-Eric Nilsson
- Lund Vision Group, Department of Biology, Lund University, 223 62 Lund, Sweden
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16
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Ramirez MD, Pairett AN, Pankey MS, Serb JM, Speiser DI, Swafford AJ, Oakley TH. The Last Common Ancestor of Most Bilaterian Animals Possessed at Least Nine Opsins. Genome Biol Evol 2018; 8:3640-3652. [PMID: 28172965 PMCID: PMC5521729 DOI: 10.1093/gbe/evw248] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2016] [Indexed: 12/17/2022] Open
Abstract
The opsin gene family encodes key proteins animals use to sense light and has expanded dramatically as it originated early in animal evolution. Understanding the origins of opsin diversity can offer clues to how separate lineages of animals have repurposed different opsin paralogs for different light-detecting functions. However, the more we look for opsins outside of eyes and from additional animal phyla, the more opsins we uncover, suggesting we still do not know the true extent of opsin diversity, nor the ancestry of opsin diversity in animals. To estimate the number of opsin paralogs present in both the last common ancestor of the Nephrozoa (bilaterians excluding Xenoacoelomorpha), and the ancestor of Cnidaria + Bilateria, we reconstructed a reconciled opsin phylogeny using sequences from 14 animal phyla, especially the traditionally poorly-sampled echinoderms and molluscs. Our analysis strongly supports a repertoire of at least nine opsin paralogs in the bilaterian ancestor and at least four opsin paralogs in the last common ancestor of Cnidaria + Bilateria. Thus, the kernels of extant opsin diversity arose much earlier in animal history than previously known. Further, opsins likely duplicated and were lost many times, with different lineages of animals maintaining different repertoires of opsin paralogs. This phylogenetic information can inform hypotheses about the functions of different opsin paralogs and can be used to understand how and when opsins were incorporated into complex traits like eyes and extraocular sensors.
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Affiliation(s)
- M Desmond Ramirez
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA
| | - Autum N Pairett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA
| | - M Sabrina Pankey
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH
| | - Jeanne M Serb
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA
| | - Daniel I Speiser
- Department of Biological Sciences, University of South Carolina, Columbia, SC
| | - Andrew J Swafford
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA
| | - Todd H Oakley
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA
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17
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Perry M, Konstantinides N, Pinto-Teixeira F, Desplan C. Generation and Evolution of Neural Cell Types and Circuits: Insights from the Drosophila Visual System. Annu Rev Genet 2017; 51:501-527. [PMID: 28961025 DOI: 10.1146/annurev-genet-120215-035312] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The Drosophila visual system has become a premier model for probing how neural diversity is generated during development. Recent work has provided deeper insight into the elaborate mechanisms that control the range of types and numbers of neurons produced, which neurons survive, and how they interact. These processes drive visual function and influence behavioral preferences. Other studies are beginning to provide insight into how neuronal diversity evolved in insects by adding new cell types and modifying neural circuits. Some of the most powerful comparisons have been those made to the Drosophila visual system, where a deeper understanding of molecular mechanisms allows for the generation of hypotheses about the evolution of neural anatomy and function. The evolution of new neural types contributes additional complexity to the brain and poses intriguing questions about how new neurons interact with existing circuitry. We explore how such individual changes in a variety of species might play a role over evolutionary timescales. Lessons learned from the fly visual system apply to other neural systems, including the fly central brain, where decisions are made and memories are stored.
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Affiliation(s)
- Michael Perry
- Department of Biology, New York University, New York, NY 10003, USA;
| | | | - Filipe Pinto-Teixeira
- Department of Biology, New York University, New York, NY 10003, USA; .,Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA; .,Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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18
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Martin C, Gross V, Hering L, Tepper B, Jahn H, de Sena Oliveira I, Stevenson PA, Mayer G. The nervous and visual systems of onychophorans and tardigrades: learning about arthropod evolution from their closest relatives. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2017; 203:565-590. [DOI: 10.1007/s00359-017-1186-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/02/2017] [Accepted: 05/29/2017] [Indexed: 12/19/2022]
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19
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Nelson DR. Cytochrome P450 diversity in the tree of life. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:141-154. [PMID: 28502748 DOI: 10.1016/j.bbapap.2017.05.003] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 04/27/2017] [Accepted: 05/06/2017] [Indexed: 12/26/2022]
Abstract
Sequencing in all areas of the tree of life has produced >300,000 cytochrome P450 (CYP) sequences that have been mined and collected. Nomenclature has been assigned to >41,000 CYP sequences and the majority of the remainder has been sorted by BLAST searches into clans, families and subfamilies in preparation for naming. The P450 sequence space is being systematically explored and filled in. Well-studied groups like vertebrates are covered in greater depth while new insights are being added into uncharted territories like horseshoe crab (Limulus polyphemus), tardigrades (Hypsibius dujardini), velvet worm (Euperipatoides_rowelli), and basal land plants like hornworts, liverworts and mosses. CYPs from the fungi, one of the most diverse groups, are being explored and organized as nearly 800 fungal species are now sequenced. The CYP clan structure in fungi is emerging with 805 CYP families sorting into 32 CYP clans. >3000 bacterial sequences are named, mostly from terrestrial or freshwater sources. Of 18,379 bacterial sequences downloaded from the CYPED database, all are >43% identical to named CYPs. Therefore, they fit in the 602 named P450 prokaryotic families. Diversity in this group is becoming saturated, however 25% of 3305 seawater bacterial P450s did not match known P450 families, indicating marine bacterial CYPs are not as well sampled as land/freshwater based bacterial CYPs. Future sequencing plans of the Genome 10K project, i5k and GIGA (Global Invertebrate Genomics Alliance) are expected to produce more than one million cytochrome P450 sequences by 2020. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- David R Nelson
- University of Tennessee Health Science Center, Dept. of Microbiology, Immunology and Biochemistry, 858 Madison Ave. Suite G01, Memphis, TN 38163, USA.
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Sharkey CR, Fujimoto MS, Lord NP, Shin S, McKenna DD, Suvorov A, Martin GJ, Bybee SM. Overcoming the loss of blue sensitivity through opsin duplication in the largest animal group, beetles. Sci Rep 2017; 7:8. [PMID: 28127058 PMCID: PMC5428366 DOI: 10.1038/s41598-017-00061-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/16/2016] [Indexed: 11/09/2022] Open
Abstract
Opsin proteins are fundamental components of animal vision whose structure largely determines the sensitivity of visual pigments to different wavelengths of light. Surprisingly little is known about opsin evolution in beetles, even though they are the most species rich animal group on Earth and exhibit considerable variation in visual system sensitivities. We reveal the patterns of opsin evolution across 62 beetle species and relatives. Our results show that the major insect opsin class (SW) that typically confers sensitivity to "blue" wavelengths was lost ~300 million years ago, before the origin of modern beetles. We propose that UV and LW opsin gene duplications have restored the potential for trichromacy (three separate channels for colour vision) in beetles up to 12 times and more specifically, duplications within the UV opsin class have likely led to the restoration of "blue" sensitivity up to 10 times. This finding reveals unexpected plasticity within the insect visual system and highlights its remarkable ability to evolve and adapt to the available light and visual cues present in the environment.
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Affiliation(s)
- Camilla R Sharkey
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT, 84602, USA.
| | - M Stanley Fujimoto
- Computer Science Department, Brigham Young University, Provo, Utah, 84602, USA
| | - Nathan P Lord
- Department of Biological and Environmental Sciences, Georgia College & State University, Campus Box 081, Milledgeville, GA, 31061, USA
| | - Seunggwan Shin
- Department of Biological Sciences, University of Memphis, 3700 Walker Avenue, Memphis, TN, 38152, USA
| | - Duane D McKenna
- Department of Biological Sciences, University of Memphis, 3700 Walker Avenue, Memphis, TN, 38152, USA
| | - Anton Suvorov
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT, 84602, USA
| | - Gavin J Martin
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT, 84602, USA
| | - Seth M Bybee
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT, 84602, USA
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Suvorov A, Jensen NO, Sharkey CR, Fujimoto MS, Bodily P, Wightman HMC, Ogden TH, Clement MJ, Bybee SM. Opsins have evolved under the permanent heterozygote model: insights from phylotranscriptomics of Odonata. Mol Ecol 2016; 26:1306-1322. [DOI: 10.1111/mec.13884] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 09/24/2016] [Accepted: 10/04/2016] [Indexed: 02/04/2023]
Affiliation(s)
- Anton Suvorov
- Department of Biology; Brigham Young University; Provo UT 84602 USA
| | | | | | | | - Paul Bodily
- Computer Science Department; Brigham Young University; Provo UT 84602 USA
| | | | - T. Heath Ogden
- Department of Biology; Utah Valley University; Orem UT 84058 USA
| | - Mark J. Clement
- Computer Science Department; Brigham Young University; Provo UT 84602 USA
| | - Seth M. Bybee
- Department of Biology; Brigham Young University; Provo UT 84602 USA
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22
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Pauli T, Vedder L, Dowling D, Petersen M, Meusemann K, Donath A, Peters RS, Podsiadlowski L, Mayer C, Liu S, Zhou X, Heger P, Wiehe T, Hering L, Mayer G, Misof B, Niehuis O. Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects : Insect insulator proteins. BMC Genomics 2016; 17:861. [PMID: 27809783 PMCID: PMC5094011 DOI: 10.1186/s12864-016-3205-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 10/25/2016] [Indexed: 01/19/2023] Open
Abstract
Background Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the origin of IBPs in insects and other arthropods. Results Our study shows that the last common ancestor of insects (Hexapoda) already possessed a substantial number of IBPs. Specifically, of the known twelve insect IBPs, at least three (i.e., CP190, Su(Hw), and CTCF) already existed prior to the evolution of insects. Furthermore we found GAF orthologs in early branching insect orders, including Zygentoma (silverfish and firebrats) and Diplura (two-pronged bristletails). Mod(mdg4) is most likely a derived feature of Neoptera, while Pita is likely an evolutionary novelty of holometabolous insects. Zw5 appears to be restricted to schizophoran flies, whereas BEAF-32, ZIPIC and the Elba complex, are probably unique to the genus Drosophila. Selection models indicate that insect IBPs evolved under neutral or purifying selection. Conclusions Our results suggest that a substantial number of IBPs either pre-date the evolution of insects or evolved early during insect evolution. This suggests an evolutionary history of insulator binding proteins in insects different to that previously thought. Moreover, our study demonstrates the versatility of the 1KITE transcriptomic data for comparative analyses in insects and other arthropods. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3205-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Pauli
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany.
| | - Lucia Vedder
- University of Tübingen, Geschwister-Scholl-Platz, 72074, Tübingen, Germany
| | - Daniel Dowling
- Johannes Gutenberg University Mainz, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Malte Petersen
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany
| | - Karen Meusemann
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany.,Department for Evolutionary Biology and Ecology (Institut for Biology I, Zoology), University of Freiburg, Hauptstr. 1, 79104, Freiburg, Germany.,Australian National Insect Collection, CSIRO National Research Collections Australia, Clunies Ross Street, Acton, ACT, 2601, Australia
| | - Alexander Donath
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany
| | - Ralph S Peters
- Zoological Research Museum Alexander Koenig, Arthropod Department, Adenauerallee 160, 53113, Bonn, Germany
| | - Lars Podsiadlowski
- University of Bonn, Institute of Evolutionary Biology and Ecology, An der Immenburg 1, 53121, Bonn, Germany
| | - Christoph Mayer
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany
| | - Shanlin Liu
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, Guangdong Province, 518083, China.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100193, China.,College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Peter Heger
- University of Cologne, Cologne Biocenter, Institute for Genetics, Zülpicher Straße 47a, 50674, Köln, Germany
| | - Thomas Wiehe
- University of Cologne, Cologne Biocenter, Institute for Genetics, Zülpicher Straße 47a, 50674, Köln, Germany
| | - Lars Hering
- Department of Zoology, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany
| | - Georg Mayer
- Department of Zoology, University of Kassel, Heinrich-Plett-Str. 40, 34132, Kassel, Germany
| | - Bernhard Misof
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany
| | - Oliver Niehuis
- Center of Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 51113, Bonn, Germany.
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23
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Schumann I, Hering L, Mayer G. Immunolocalization of Arthropsin in the Onychophoran Euperipatoides rowelli (Peripatopsidae). Front Neuroanat 2016; 10:80. [PMID: 27540356 PMCID: PMC4972820 DOI: 10.3389/fnana.2016.00080] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/14/2016] [Indexed: 01/09/2023] Open
Abstract
Opsins are light-sensitive proteins that play a key role in animal vision and are related to the ancient photoreceptive molecule rhodopsin found in unicellular organisms. In general, opsins involved in vision comprise two major groups: the rhabdomeric (r-opsins) and the ciliary opsins (c-opsins). The functionality of opsins, which is dependent on their protein structure, may have changed during evolution. In arthropods, typically r-opsins are responsible for vision, whereas in vertebrates c-opsins are components of visual photoreceptors. Recently, an enigmatic r-opsin-like protein called arthropsin has been identified in various bilaterian taxa, including arthropods, lophotrochozoans, and chordates, by performing transcriptomic and genomic analyses. Since the role of arthropsin and its distribution within the body are unknown, we immunolocalized this protein in a representative of Onychophora – Euperipatoides rowelli – an ecdysozoan taxon which is regarded as one of the closest relatives of Arthropoda. Our data show that arthropsin is expressed in the central nervous system of E. rowelli, including the brain and the ventral nerve cords, but not in the eyes. These findings are consistent with previous results based on reverse transcription PCR in a closely related onychophoran species and suggest that arthropsin is a non-visual protein. Based on its distribution in the central brain region and the mushroom bodies, we speculate that the onychophoran arthropsin might be either a photosensitive molecule playing a role in the circadian clock, or a non-photosensitive protein involved in olfactory pathways, or both.
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Affiliation(s)
- Isabell Schumann
- Department of Zoology, Institute of Biology, University of Kassel, KasselGermany; Molecular Evolution and Animal Systematics, University of Leipzig, LeipzigGermany
| | - Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel, Kassel Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Kassel Germany
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24
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Hering L, Bouameur JE, Reichelt J, Magin TM, Mayer G. Novel origin of lamin-derived cytoplasmic intermediate filaments in tardigrades. eLife 2016; 5:e11117. [PMID: 26840051 PMCID: PMC4829535 DOI: 10.7554/elife.11117] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 02/02/2016] [Indexed: 12/24/2022] Open
Abstract
Intermediate filament (IF) proteins, including nuclear lamins and cytoplasmic IF proteins, are essential cytoskeletal components of bilaterian cells. Despite their important role in protecting tissues against mechanical force, no cytoplasmic IF proteins have been convincingly identified in arthropods. Here we show that the ancestral cytoplasmic IF protein gene was lost in the entire panarthropod (onychophoran + tardigrade + arthropod) rather than arthropod lineage and that nuclear, lamin-derived proteins instead acquired new cytoplasmic roles at least three times independently in collembolans, copepods, and tardigrades. Transcriptomic and genomic data revealed three IF protein genes in the tardigrade Hypsibius dujardini, one of which (cytotardin) occurs exclusively in the cytoplasm of epidermal and foregut epithelia, where it forms belt-like filaments around each epithelial cell. These results suggest that a lamin derivative has been co-opted to enhance tissue stability in tardigrades, a function otherwise served by cytoplasmic IF proteins in all other bilaterians. DOI:http://dx.doi.org/10.7554/eLife.11117.001 Different proteins exist to support the stability of animal cells. The intermediate filament proteins are an important example. One type – called lamins – stabilizes the nucleus (the structure within an animal cell that stores most of its DNA), while another forms scaffold-like structures in the rest of cell. The second type, referred to as “cytoplasmic” intermediate filaments, are not found in many hard-bodied creatures including insects and their closest relatives. This is probably because these animals, which are collectively known as arthropods, are instead supported by their tough external skeleton. The soft-bodied animals called tardigrades (also known as water bears or moss piglets) are closely related to the arthropods. These microscopic animals can endure extreme environmental conditions such as freezing. The tardigrade’s endurance is likely to require some way to stabilize the animal’s cells. This might involve cytoplasmic intermediate filaments, but nothing was known about these proteins in tardigrades. Now, Hering, Bouameur, Reichelt et al. have investigated if, and where, intermediate filaments are found in the cells of tardigrades. First, the complete set of active genes was analyzed for a species of tardigrade called Hypsibius dujardini; this revealed that three genes for intermediate filament proteins were active. Staining tissue slices or whole tardigrades with a marker that binds to intermediate filament proteins revealed that two of the three proteins were lamins and located within the nucleus. The third protein, which has been named "cytotardin", was found outside of the nucleus. However, unlike well-known cytoplasmic intermediate filaments, this protein did not form scaffold-like structures throughout the cell. Instead, cytotardin formed belt-like filaments that encircled each cell in the skin of the tardigrades. Hering, Bouameur, Reichelt et al. then discovered that cytotardin seems to be more closely related to lamins than it is to cytoplasmic intermediate filaments. This suggests that cytotardin actually evolved from a tardigrade lamin and then acquired a new role in building filaments outside of the nucleus. The fact that cytotardin is only found in the skin of the tardigrade and in those tissues that experience mechanical stress (for example, the mouth and legs) hints that it might help stabilize these cells. This could mean that the protein also helps these animals to resist extreme conditions. Further studies should focus on clarifying cytotardin’s role in stabilizing cells, in particular if it is required for the tardigrades' tolerance to environmental stress. DOI:http://dx.doi.org/10.7554/eLife.11117.002
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Affiliation(s)
- Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany.,Animal Evolution and Development, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Jamal-Eddine Bouameur
- Institute of Biology and Translational Center for Regenerative Medicine, University of Leipzig, Leipzig, Germany
| | - Julian Reichelt
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Thomas M Magin
- Institute of Biology and Translational Center for Regenerative Medicine, University of Leipzig, Leipzig, Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Kassel, Germany.,Animal Evolution and Development, Institute of Biology, University of Leipzig, Leipzig, Germany
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25
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Henze MJ, Oakley TH. The Dynamic Evolutionary History of Pancrustacean Eyes and Opsins. Integr Comp Biol 2015; 55:830-42. [DOI: 10.1093/icb/icv100] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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26
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Expression study of the hunchback ortholog in embryos of the onychophoran Euperipatoides rowelli. Dev Genes Evol 2015; 225:207-19. [DOI: 10.1007/s00427-015-0505-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/02/2015] [Indexed: 10/23/2022]
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27
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Franke FA, Schumann I, Hering L, Mayer G. Phylogenetic analysis and expression patterns of Pax genes in the onychophoran Euperipatoides rowelli reveal a novel bilaterian Pax subfamily. Evol Dev 2015; 17:3-20. [PMID: 25627710 DOI: 10.1111/ede.12110] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Pax family genes encode a class of transcription factors that regulate various developmental processes. To shed light on the evolutionary history of these genes in Panarthropoda (Onychophora + Tardigrada + Arthropoda), we analyzed the Pax repertoire in the embryonic and adult transcriptomes of the onychophoran Euperipatoides rowelli. Our data revealed homologs of all five major bilaterian Pax subfamilies in this species, including Pax2/5/8, Pax4/6, Pox-neuro, Pax1/9/Pox-meso, and Pax3/7. In addition, we identified a new Pax member, pax-α, which does not fall into any other known Pax subfamily but instead clusters in the heterogenic Pax-α/β clade containing deuterostome, ecdysozoan, and lophotrochozoan gene sequences. These findings suggest that the last common bilaterian ancestor possessed six rather than five Pax genes, which have been retained in the panarthropod lineage. The expression data of Pax orthologs in the onychophoran embryo revealed distinctive patterns, some of which might be related to their ancestral roles in the last common panarthropod ancestor, whereas others might be specific to the onychophoran lineage. The derived roles include, for example, an involvement of pax2/5/8, pox-neuro, and pax3/7 in onychophoran nephridiogenesis, and an additional function of pax2/5/8 in the formation of the ventral and preventral organs. Furthermore, our transcriptomic analyses suggest that at least some Pax genes, including pax6 and pax-α, are expressed in the adult onychophoran head, although the corresponding functions remain to be clarified. The remarkable diversity of the Pax expression patterns highlights the functional and evolutionary plasticity of these genes in panarthropods.
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Affiliation(s)
- Franziska Anni Franke
- Animal Evolution & Development, , Institute of Biology, University of Leipzig, Talstraße 33, D-04103, Leipzig, Germany
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28
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Mayer G, Hering L, Stosch JM, Stevenson PA, Dircksen H. Evolution of pigment-dispersing factor neuropeptides in panarthropoda: Insights from onychophora (velvet worms) and tardigrada (water bears). J Comp Neurol 2015; 523:1865-85. [DOI: 10.1002/cne.23767] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Georg Mayer
- Animal Evolution and Development; Institute of Biology, University of Leipzig; D-04103 Leipzig Germany
- Department of Zoology; Institute of Biology, University of Kassel; D-34132 Kassel Germany
| | - Lars Hering
- Animal Evolution and Development; Institute of Biology, University of Leipzig; D-04103 Leipzig Germany
| | - Juliane M. Stosch
- Animal Evolution and Development; Institute of Biology, University of Leipzig; D-04103 Leipzig Germany
| | - Paul A. Stevenson
- Physiology of Animals and Behavior; Institute of Biology, University of Leipzig; D-04103 Leipzig Germany
| | - Heinrich Dircksen
- Department of Zoology; Stockholm University; S-10691 Stockholm Sweden
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29
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Beckmann H, Hering L, Henze MJ, Kelber A, Stevenson PA, Mayer G. Spectral sensitivity in Onychophora (velvet worms) revealed by electroretinograms, phototactic behaviour and opsin gene expression. J Exp Biol 2015; 218:915-22. [DOI: 10.1242/jeb.116780] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
ABSTRACT
Onychophorans typically possess a pair of simple eyes, inherited from the last common ancestor of Panarthropoda (Onychophora+Tardigrada+Arthropoda). These visual organs are thought to be homologous to the arthropod median ocelli, whereas the compound eyes probably evolved in the arthropod lineage. To gain insights into the ancestral function and evolution of the visual system in panarthropods, we investigated phototactic behaviour, opsin gene expression and the spectral sensitivity of the eyes in two representative species of Onychophora: Euperipatoides rowelli (Peripatopsidae) and Principapillatus hitoyensis (Peripatidae). Our behavioural analyses, in conjunction with previous data, demonstrate that both species exhibit photonegative responses to wavelengths ranging from ultraviolet to green light (370–530 nm), and electroretinograms reveal that the onychophoran eye is maximally sensitive to blue light (peak sensitivity ∼480 nm). Template fits to these sensitivities suggest that the onychophoran eye is monochromatic. To clarify which type of opsin the single visual pigment is based on, we localised the corresponding mRNA in the onychophoran eye and brain using in situ hybridization. Our data show that the r-opsin gene (onychopsin) is expressed exclusively in the photoreceptor cells of the eye, whereas c-opsin mRNA is confined to the optic ganglion cells and the brain. Together, our findings suggest that the onychopsin is involved in vision, whereas c-opsin might have a photoreceptive, non-visual function in onychophorans.
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Affiliation(s)
- Holger Beckmann
- Department of Animal Evolution and Development, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig D-04103, Germany
- Rudolf-Boehm-Institute of Pharmacology and Toxicology, University of Leipzig, Haertelstrasse 16–18, Leipzig D-04107, Germany
| | - Lars Hering
- Department of Animal Evolution and Development, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig D-04103, Germany
| | - Miriam J. Henze
- Department of Biology, Lund University, Sölvegatan 35, Lund 22362, Sweden
| | - Almut Kelber
- Department of Biology, Lund University, Sölvegatan 35, Lund 22362, Sweden
| | - Paul A. Stevenson
- Department of Animal Physiology, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig D-04103, Germany
| | - Georg Mayer
- Department of Animal Evolution and Development, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig D-04103, Germany
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany
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30
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Franke FA, Mayer G. Controversies surrounding segments and parasegments in onychophora: insights from the expression patterns of four "segment polarity genes" in the peripatopsid Euperipatoides rowelli. PLoS One 2014; 9:e114383. [PMID: 25470738 PMCID: PMC4255022 DOI: 10.1371/journal.pone.0114383] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 11/10/2014] [Indexed: 12/20/2022] Open
Abstract
Arthropods typically show two types of segmentation: the embryonic parasegments and the adult segments that lie out of register with each other. Such a dual nature of body segmentation has not been described from Onychophora, one of the closest arthropod relatives. Hence, it is unclear whether onychophorans have segments, parasegments, or both, and which of these features was present in the last common ancestor of Onychophora and Arthropoda. To address this issue, we analysed the expression patterns of the "segment polarity genes" engrailed, cubitus interruptus, wingless and hedgehog in embryos of the onychophoran Euperipatoides rowelli. Our data revealed that these genes are expressed in repeated sets with a specific anterior-to-posterior order along the body in embryos of E. rowelli. In contrast to arthropods, the expression occurs after the segmental boundaries have formed. Moreover, the initial segmental furrow retains its position within the engrailed domain throughout development, whereas no new furrow is formed posterior to this domain. This suggests that no re-segmentation of the embryo occurs in E. rowelli. Irrespective of whether or not there is a morphological or genetic manifestation of parasegments in Onychophora, our data clearly show that parasegments, even if present, cannot be regarded as the initial metameric units of the onychophoran embryo, because the expression of key genes that define the parasegmental boundaries in arthropods occurs after the segmental boundaries have formed. This is in contrast to arthropods, in which parasegments rather than segments are the initial metameric units of the embryo. Our data further revealed that the expression patterns of "segment polarity genes" correspond to organogenesis rather than segment formation. This is in line with the concept of segmentation as a result of concerted evolution of individual periodic structures rather than with the interpretation of 'segments' as holistic units.
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Affiliation(s)
- Franziska Anni Franke
- Animal Evolution & Development, Institute of Biology, University of Leipzig, Talstraße 33, D-04103 Leipzig, Germany
| | - Georg Mayer
- Animal Evolution & Development, Institute of Biology, University of Leipzig, Talstraße 33, D-04103 Leipzig, Germany
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31
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Hering L, Mayer G. Analysis of the opsin repertoire in the tardigrade Hypsibius dujardini provides insights into the evolution of opsin genes in panarthropoda. Genome Biol Evol 2014; 6:2380-91. [PMID: 25193307 PMCID: PMC4202329 DOI: 10.1093/gbe/evu193] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2014] [Indexed: 01/17/2023] Open
Abstract
Screening of a deeply sequenced transcriptome using Illumina sequencing as well as the genome of the tardigrade Hypsibius dujardini revealed a set of five opsin genes. To clarify the phylogenetic position of these genes and to elucidate the evolutionary history of opsins in Panarthropoda (Onychophora + Tardigrada + Arthropoda), we reconstructed the phylogeny of broadly sampled metazoan opsin genes using maximum likelihood and Bayesian inference methods in conjunction with carefully selected substitution models. According to our findings, the opsin repertoire of H. dujardini comprises representatives of all three major bilaterian opsin clades, including one r-opsin, three c-opsins, and a Group 4 opsin (neuropsin/opsin-5). The identification of the tardigrade ortholog of neuropsin/opsin-5 is the first record of this opsin type in a protostome, but our screening of available metazoan genomes revealed that it is also present in other protostomes. Our opsin phylogeny further suggests that two r-opsins, including an "arthropsin," were present in the last common ancestor of Panarthropoda. Although both r-opsin lineages were retained in Onychophora and Arthropoda, the arthropsin was lost in Tardigrada. The single (most likely visual) r-opsin found in H. dujardini supports the hypothesis of monochromatic vision in the panarthropod ancestor, whereas two duplications of the ancestral panarthropod c-opsin have led to three c-opsins in tardigrades. Although the early-branching nodes are unstable within the metazoans, our findings suggest that the last common ancestor of Bilateria possessed six opsins: Two r-opsins, one c-opsin, and three Group 4 opsins, one of which (Go opsin) was lost in the ecdysozoan lineage.
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Affiliation(s)
- Lars Hering
- Animal Evolution and Development, Institute of Biology, University of Leipzig, Germany
| | - Georg Mayer
- Animal Evolution and Development, Institute of Biology, University of Leipzig, Germany
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32
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Struck TH, Wey-Fabrizius AR, Golombek A, Hering L, Weigert A, Bleidorn C, Klebow S, Iakovenko N, Hausdorf B, Petersen M, Kück P, Herlyn H, Hankeln T. Platyzoan paraphyly based on phylogenomic data supports a noncoelomate ancestry of spiralia. Mol Biol Evol 2014; 31:1833-49. [PMID: 24748651 DOI: 10.1093/molbev/msu143] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Based on molecular data three major clades have been recognized within Bilateria: Deuterostomia, Ecdysozoa, and Spiralia. Within Spiralia, small-sized and simply organized animals such as flatworms, gastrotrichs, and gnathostomulids have recently been grouped together as Platyzoa. However, the representation of putative platyzoans was low in the respective molecular phylogenetic studies, in terms of both, taxon number and sequence data. Furthermore, increased substitution rates in platyzoan taxa raised the possibility that monophyletic Platyzoa represents an artifact due to long-branch attraction. In order to overcome such problems, we employed a phylogenomic approach, thereby substantially increasing 1) the number of sampled species within Platyzoa and 2) species-specific sequence coverage in data sets of up to 82,162 amino acid positions. Using established and new measures (long-branch score), we disentangled phylogenetic signal from misleading effects such as long-branch attraction. In doing so, our phylogenomic analyses did not recover a monophyletic origin of platyzoan taxa that, instead, appeared paraphyletic with respect to the other spiralians. Platyhelminthes and Gastrotricha formed a monophylum, which we name Rouphozoa. To the exclusion of Gnathifera, Rouphozoa and all other spiralians represent a monophyletic group, which we name Platytrochozoa. Platyzoan paraphyly suggests that the last common ancestor of Spiralia was a simple-bodied organism lacking coelomic cavities, segmentation, and complex brain structures, and that more complex animals such as annelids evolved from such a simply organized ancestor. This conclusion contradicts alternative evolutionary scenarios proposing an annelid-like ancestor of Bilateria and Spiralia and several independent events of secondary reduction.
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Affiliation(s)
- Torsten H Struck
- Zoological Research Museum Alexander Koenig, Bonn, GermanyUniversity of Osnabrück, FB05 Biology/Chemistry, AG Zoology, Osnabrück, Germany
| | - Alexandra R Wey-Fabrizius
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, Mainz, Germany
| | - Anja Golombek
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Lars Hering
- Animal Evolution and Development, Institute of Biology II, University of Leipzig, Leipzig, Germany
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Christoph Bleidorn
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Sabrina Klebow
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, Mainz, Germany
| | - Nataliia Iakovenko
- Department of Biology and Ecology, Ostravian University in Ostrava, Ostrava, Czech RepublicDepartment of Invertebrate Fauna and Systematics, Schmalhausen Institute of Zoology NAS of Ukraine, Kyiv, Ukraine
| | | | - Malte Petersen
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Patrick Kück
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Holger Herlyn
- Institute of Anthropology, Johannes Gutenberg University, Mainz, Germany
| | - Thomas Hankeln
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, Mainz, Germany
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Janssen R, Eriksson BJ, Tait NN, Budd GE. Onychophoran Hox genes and the evolution of arthropod Hox gene expression. Front Zool 2014; 11:22. [PMID: 24594097 PMCID: PMC4015684 DOI: 10.1186/1742-9994-11-22] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/21/2014] [Indexed: 11/24/2022] Open
Abstract
Introduction Onychophora is a relatively small phylum within Ecdysozoa, and is considered to be the sister group to Arthropoda. Compared to the arthropods, that have radiated into countless divergent forms, the onychophoran body plan is overall comparably simple and does not display much in-phylum variation. An important component of arthropod morphological diversity consists of variation of tagmosis, i.e. the grouping of segments into functional units (tagmata), and this in turn is correlated with differences in expression patterns of the Hox genes. How these genes are expressed in the simpler onychophorans, the subject of this paper, would therefore be of interest in understanding their subsequent evolution in the arthropods, especially if an argument can be made for the onychophoran system broadly reflecting the ancestral state in the arthropods. Results The sequences and embryonic expression patterns of the complete set of ten Hox genes of an onychophoran (Euperipatoides kanangrensis) are described for the first time. We find that they are all expressed in characteristic patterns that suggest a function as classical Hox genes. The onychophoran Hox genes obey spatial colinearity, and with the exception of Ultrabithorax (Ubx), they all have different and distinct anterior expression borders. Notably, Ubx transcripts form a posterior to anterior gradient in the onychophoran trunk. Expression of all onychophoran Hox genes extends continuously from their anterior border to the rear end of the embryo. Conclusions The spatial expression pattern of the onychophoran Hox genes may contribute to a combinatorial Hox code that is involved in giving each segment its identity. This patterning of segments in the uniform trunk, however, apparently predates the evolution of distinct segmental differences in external morphology seen in arthropods. The gradient-like expression of Ubx may give posterior segments their specific identity, even though they otherwise express the same set of Hox genes. We suggest that the confined domains of Hox gene expression seen in arthropods evolved from an ancestral onychophoran-like Hox gene pattern. Reconstruction of the ancestral arthropod Hox pattern and comparison with the patterns in the different arthropod classes reveals phylogenetic support for Mandibulata and Tetraconata, but not Myriochelata and Atelocerata.
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Affiliation(s)
- Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236 Uppsala, Sweden.
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Bull JK, Sands CJ, Garrick RC, Gardner MG, Tait NN, Briscoe DA, Rowell DM, Sunnucks P. Environmental complexity and biodiversity: the multi-layered evolutionary history of a log-dwelling velvet worm in Montane Temperate Australia. PLoS One 2013; 8:e84559. [PMID: 24358365 PMCID: PMC3866147 DOI: 10.1371/journal.pone.0084559] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 11/15/2013] [Indexed: 11/19/2022] Open
Abstract
Phylogeographic studies provide a framework for understanding the importance of intrinsic versus extrinsic factors in shaping patterns of biodiversity through identifying past and present microevolutionary processes that contributed to lineage divergence. Here we investigate population structure and diversity of the Onychophoran (velvet worm) Euperipatoides rowelli in southeastern Australian montane forests that were not subject to Pleistocene glaciations, and thus likely retained more forest cover than systems under glaciation. Over a ~100 km transect of structurally-connected forest, we found marked nuclear and mitochondrial (mt) DNA genetic structuring, with spatially-localised groups. Patterns from mtDNA and nuclear data broadly corresponded with previously defined geographic regions, consistent with repeated isolation in refuges during Pleistocene climatic cycling. Nevertheless, some E. rowelli genetic contact zones were displaced relative to hypothesized influential landscape structures, implying more recent processes overlying impacts of past environmental history. Major impacts at different timescales were seen in the phylogenetic relationships among mtDNA sequences, which matched geographic relationships and nuclear data only at recent timescales, indicating historical gene flow and/or incomplete lineage sorting. Five major E. rowelli phylogeographic groups were identified, showing substantial but incomplete reproductive isolation despite continuous habitat. Regional distinctiveness, in the face of lineages abutting within forest habitat, could indicate pre- and/or postzygotic gene flow limitation. A potentially functional phenotypic character, colour pattern variation, reflected the geographic patterns in the molecular data. Spatial-genetic patterns broadly match those in previously-studied, co-occurring low-mobility organisms, despite a variety of life histories. We suggest that for E. rowelli, the complex topography and history of the region has led to interplay among limited dispersal ability, historical responses to environmental change, local adaptation, and some resistance to free admixture at geographic secondary contact, leading to strong genetic structuring at fine spatial scale.
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Affiliation(s)
- James K. Bull
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
- * E-mail:
| | - Chester J. Sands
- Natural Environment Research Council, British Antarctic Survey, Cambridge, United Kingdom
| | - Ryan C. Garrick
- Department of Biology, University of Mississippi, Oxford, Mississippi, United States of America
| | - Michael G. Gardner
- School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - Noel N. Tait
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - David A. Briscoe
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - David M. Rowell
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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de Sena Oliveira I, Tait NN, Strübing I, Mayer G. The role of ventral and preventral organs as attachment sites for segmental limb muscles in Onychophora. Front Zool 2013; 10:73. [PMID: 24308783 PMCID: PMC3866996 DOI: 10.1186/1742-9994-10-73] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 11/27/2013] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The so-called ventral organs are amongst the most enigmatic structures in Onychophora (velvet worms). They were described as segmental, ectodermal thickenings in the onychophoran embryo, but the same term has also been applied to mid-ventral, cuticular structures in adults, although the relationship between the embryonic and adult ventral organs is controversial. In the embryo, these structures have been regarded as anlagen of segmental ganglia, but recent studies suggest that they are not associated with neural development. Hence, their function remains obscure. Moreover, their relationship to the anteriorly located preventral organs, described from several onychophoran species, is also unclear. To clarify these issues, we studied the anatomy and development of the ventral and preventral organs in several species of Onychophora. RESULTS Our anatomical data, based on histology, and light, confocal and scanning electron microscopy in five species of Peripatidae and three species of Peripatopsidae, revealed that the ventral and preventral organs are present in all species studied. These structures are covered externally with cuticle that forms an internal, longitudinal, apodeme-like ridge. Moreover, phalloidin-rhodamine labelling for f-actin revealed that the anterior and posterior limb depressor muscles in each trunk and the slime papilla segment attach to the preventral and ventral organs, respectively. During embryonic development, the ventral and preventral organs arise as large segmental, paired ectodermal thickenings that decrease in size and are subdivided into the smaller, anterior anlagen of the preventral organs and the larger, posterior anlagen of the ventral organs, both of which persist as paired, medially-fused structures in adults. Our expression data of the genes Delta and Notch from embryos of Euperipatoides rowelli revealed that these genes are expressed in two, paired domains in each body segment, corresponding in number, position and size with the anlagen of the ventral and preventral organs. CONCLUSIONS Our findings suggest that the ventral and preventral organs are a common feature of onychophorans that serve as attachment sites for segmental limb depressor muscles. The origin of these structures can be traced back in the embryo as latero-ventral segmental, ectodermal thickenings, previously suggested to be associated with the development of the nervous system.
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Affiliation(s)
- Ivo de Sena Oliveira
- Animal Evolution and Development, Institute of Biology, University of Leipzig, Talstraße 33, D-04103, Leipzig, Germany.
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Expression of the decapentaplegic ortholog in embryos of the onychophoran Euperipatoides rowelli. Gene Expr Patterns 2013; 13:384-94. [DOI: 10.1016/j.gep.2013.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/07/2013] [Accepted: 07/10/2013] [Indexed: 12/21/2022]
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Lagman D, Ocampo Daza D, Widmark J, Abalo XM, Sundström G, Larhammar D. The vertebrate ancestral repertoire of visual opsins, transducin alpha subunits and oxytocin/vasopressin receptors was established by duplication of their shared genomic region in the two rounds of early vertebrate genome duplications. BMC Evol Biol 2013; 13:238. [PMID: 24180662 PMCID: PMC3826523 DOI: 10.1186/1471-2148-13-238] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 10/29/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vertebrate color vision is dependent on four major color opsin subtypes: RH2 (green opsin), SWS1 (ultraviolet opsin), SWS2 (blue opsin), and LWS (red opsin). Together with the dim-light receptor rhodopsin (RH1), these form the family of vertebrate visual opsins. Vertebrate genomes contain many multi-membered gene families that can largely be explained by the two rounds of whole genome duplication (WGD) in the vertebrate ancestor (2R) followed by a third round in the teleost ancestor (3R). Related chromosome regions resulting from WGD or block duplications are said to form a paralogon. We describe here a paralogon containing the genes for visual opsins, the G-protein alpha subunit families for transducin (GNAT) and adenylyl cyclase inhibition (GNAI), the oxytocin and vasopressin receptors (OT/VP-R), and the L-type voltage-gated calcium channels (CACNA1-L). RESULTS Sequence-based phylogenies and analyses of conserved synteny show that the above-mentioned gene families, and many neighboring gene families, expanded in the early vertebrate WGDs. This allows us to deduce the following evolutionary scenario: The vertebrate ancestor had a chromosome containing the genes for two visual opsins, one GNAT, one GNAI, two OT/VP-Rs and one CACNA1-L gene. This chromosome was quadrupled in 2R. Subsequent gene losses resulted in a set of five visual opsin genes, three GNAT and GNAI genes, six OT/VP-R genes and four CACNA1-L genes. These regions were duplicated again in 3R resulting in additional teleost genes for some of the families. Major chromosomal rearrangements have taken place in the teleost genomes. By comparison with the corresponding chromosomal regions in the spotted gar, which diverged prior to 3R, we could time these rearrangements to post-3R. CONCLUSIONS We present an extensive analysis of the paralogon housing the visual opsin, GNAT and GNAI, OT/VP-R, and CACNA1-L gene families. The combined data imply that the early vertebrate WGD events contributed to the evolution of vision and the other neuronal and neuroendocrine functions exerted by the proteins encoded by these gene families. In pouched lamprey all five visual opsin genes have previously been identified, suggesting that lampreys diverged from the jawed vertebrates after 2R.
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Affiliation(s)
- David Lagman
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
| | - Daniel Ocampo Daza
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
| | - Jenny Widmark
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
| | - Xesús M Abalo
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
| | - Görel Sundström
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
- Present address: Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Box 582, SE-75123 Uppsala, Sweden
| | - Dan Larhammar
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
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A degenerative retinal process in HIV-associated non-infectious retinopathy. PLoS One 2013; 8:e74712. [PMID: 24069333 PMCID: PMC3775801 DOI: 10.1371/journal.pone.0074712] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 08/04/2013] [Indexed: 01/04/2023] Open
Abstract
HIV retinopathy is the most common non-infectious complication in the eyes of HIV-positive individuals. Oncotic lesions in the retinal nerve fiber layer, referred to as cotton wool spots (CWS), and intraretinal (IR) hemorrhages are frequently observed but are not unique to this pathology. HIV-positive patients have impaired color vision and contrast sensitivity, which worsens with age. Evidence of inner-retinal lesions and damage have been documented ophthalmoscopically, however their long term structural effect has not been investigated. It has been hypothesized that they may be partially responsible for loss of visual function and visual field. In this study we utilized clinical data, retinal imaging and transcriptomics approaches to comprehensively interrogate non-infectious HIV retinopathy. The methods employed encompassed clinical examinations, fundus photography, indirect ophthalmoscopy, Farmsworth-Munsell 100 hue discrimination testing and Illumina BeadChip analyses. Here we show that changes in the outer retina, specifically in the retinal pigment epithelium (RPE) and photoreceptor outer segments (POS) contribute to vision changes in non-infectious HIV retinopathy. We find that in HIV-positive retinae there is an induction of rhodopsin and other transcripts (including PDE6A, PDE6B, PDE6G, CNGA1, CNGB1, CRX, NRL) involved in visual transduction, as well as structural components of the rod photoreceptors (ABCA4 and ROM1). This is consistent with an increased rate of renewal of rod outer segments induced via increased phagocytosis by HIV-infected RPE previously reported in culture. Cone-specific transcripts (OPN1SW, OPN1LW, PDE6C, PDE6H and GRK7) are uniformly downregulated in HIV positive retina, likely due to a partial loss of cone photoreceptors. Active cotton wool spots and intraretinal hemorrhages (IRH) may not affect photoreceptors directly and the interaction of photoreceptors with the aging RPE may be the key to the progressive vision changes in HIV-positive patients.
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Eriksson BJ, Fredman D, Steiner G, Schmid A. Characterisation and localisation of the opsin protein repertoire in the brain and retinas of a spider and an onychophoran. BMC Evol Biol 2013; 13:186. [PMID: 24010579 PMCID: PMC3851285 DOI: 10.1186/1471-2148-13-186] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 09/03/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Opsins have been found in the majority of animals and their most apparent functions are related to vision and light-guided behaviour. As an increasing number of sequences have become available it has become clear that many opsin-like transcripts are expressed in tissues other than the eyes. Opsins can be divided into three main groups: rhabdomeric opsins (r-opsins), ciliary opsins (c-opsins) and group 4 opsins. In arthropods, the main focus has been on the r-opsins involved in vision. However, with increased sequencing it is becoming clear that arthropods also possess opsins of the c-type, group 4 opsins and the newly discovered arthropsins but the functions of these opsins are unknown in arthropods and data on their localisation is limited or absent. RESULTS We identified opsins from the spider Cupiennius salei and the onychophoran Euperipatoides kanangrensis and characterised the phylogeny and localisation of these transcripts. We recovered all known visual opsins in C. salei, and in addition found a peropsin, a c-opsin and an opsin resembling Daphnia pulex arthropsin. The peropsin was expressed in all eye types except the anterior median eyes. The arthropsin and the c-opsin were expressed in the central nervous system but not the eyes. In E. kanangrensis we found: a c-opsin; an opsin resembling D. pulex arthropsins; and an r-opsin with high sequence similarity to previously published onychophoran onychopsins. The E. kanangrensis c-opsin and onychopsin were expressed in both the eyes and the brain but the arthropsin only in the brain. CONCLUSION Our novel finding that opsins of both the ciliary and rhabdomeric type are present in the onychophoran and a spider suggests that these two types of opsins were present in the last common ancestor of the Onychophora and Euarthropoda. The expression of the c-opsin in the eye of an onychophoran indicates that c-opsins may originally have been involved in vision in the arthropod clade. The lack of c-opsin expression in the spider retina suggests that the role for c-opsin in vision was lost in the euarthropods. Our discovery of arthropsin in onychophorans and spiders dates the emergence of arthropsin to the common ancestor of Onychophora and Euarthropoda and their expression in the brain suggests a non-visual function.
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Affiliation(s)
- Bo Joakim Eriksson
- Department of Neurobiology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
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Ou Q, Shu D, Mayer G. Cambrian lobopodians and extant onychophorans provide new insights into early cephalization in Panarthropoda. Nat Commun 2013; 3:1261. [PMID: 23232391 PMCID: PMC3535342 DOI: 10.1038/ncomms2272] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 11/08/2012] [Indexed: 01/11/2023] Open
Abstract
Cambrian lobopodians are important for understanding the evolution of arthropods, but despite their soft-bodied preservation, the organization of the cephalic region remains obscure. Here we describe new material of the early Cambrian lobopodian Onychodictyon ferox from southern China, which reveals hitherto unknown head structures. These include a proboscis with a terminal mouth, an anterior arcuate sclerite, a pair of ocellus-like eyes and branched, antenniform appendages associated with this ocular segment. These findings, combined with a comparison with other lobopodians, suggest that the head of the last common ancestor of fossil lobopodians and extant panarthropods comprized a single ocular segment with a proboscis and terminal mouth. The lack of specialized mouthparts in O. ferox and the involvement of non-homologous mouthparts in onychophorans, tardigrades and arthropods argue against a common origin of definitive mouth openings among panarthropods, whereas the embryonic stomodaeum might well be homologous at least in Onychophora and Arthropoda. Lobopodians include stem-group arthropods and panarthropods, and date back to the early Cambrian. Ou et al. describe specimens of the early Cambrian lobopodian Onychodictyon ferox, revealing new head structures such as modified appendages, eyes, a terminal mouth and a sucking pharynx.
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Affiliation(s)
- Qiang Ou
- Early Life Evolution Laboratory, School of Earth Sciences and Resources, China University of Geosciences, Beijing 100083, China.
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Oliveira IDS, Franke FA, Hering L, Schaffer S, Rowell DM, Weck-Heimann A, Monge-Nájera J, Morera-Brenes B, Mayer G. Unexplored character diversity in onychophora (velvet worms): A comparative study of three peripatid species. PLoS One 2012; 7:e51220. [PMID: 23284667 PMCID: PMC3524137 DOI: 10.1371/journal.pone.0051220] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 10/30/2012] [Indexed: 01/23/2023] Open
Abstract
Low character variation among onychophoran species has been an obstacle for taxonomic and phylogenetic studies in the past, however we have identified a number of new and informative characters using morphological, molecular, and chromosomal techniques. Our analyses involved a detailed examination of Epiperipatus biolleyi from Costa Rica, Eoperipatus sp. from Thailand, and a new onychophoran species and genus from Costa Rica, Principapillatus hitoyensisgen. et sp. nov.. Scanning electron microscopy on embryos and specimens of varying age revealed novel morphological characters and character states, including the distribution of different receptor types along the antennae, the arrangement and form of papillae on the head, body and legs, the presence and shape of interpedal structures and fields of modified scales on the ventral body surface, the arrangement of lips around the mouth, the number, position and structure of crural tubercles and anal gland openings, and the presence and shape of embryonic foot projections. Karyotypic analyses revealed differences in the number and size of chromosomes among the species studied. The results of our phylogenetic analyses using mitochondrial COI and 12S rRNA gene sequences are in line with morphological and karyotype data. However, our data show a large number of unexplored, albeit informative, characters in the Peripatidae. We suggest that analysing these characters in additional species would help unravel species diversity and phylogeny in the Onychophora, and that inconsistencies among most diagnostic features used for the peripatid genera in the literature could be addressed by identifying a suite of characters common to all peripatids.
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Affiliation(s)
- Ivo de Sena Oliveira
- Animal Evolution and Development, Institute of Biology, University of Leipzig, Leipzig, Germany.
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