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Farfán-Beltrán ME, Chávez-Pesqueira M, Hernández-Cumplido J, Cano-Santana Z. A quick evaluation of ecological restoration based on arthropod communities and trophic guilds in an urban ecological preserve in Mexico City. REVISTA CHILENA DE HISTORIA NATURAL 2022. [DOI: 10.1186/s40693-022-00108-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Restoration practices usually emphasize on the structural part of the biodiversity; also, most studies have focused on plants and very few have been conducted on arthropods and its function after restoration. The Pedregal de San Angel Ecological Reserve (PSAER) is a protected area immersed in Mexico City and it has been drastically affected by different anthropogenic disturbances. The aim of this study was to compare the relative diversity, richness, and abundance of species level identification, but also the composition through an analysis of ordination of taxonomic (species, family, and order level) and functional (trophic guild) traits of arthropods in three sites subjected to ecological restoration within the PSAER. Restored sites were also compared to conserved and disturbed sites, to evaluate whether restoration efforts are effective at the reserve.
Methods
Arthropods were sampled using pan traps during September 2013 in 11 sites (three restored, four conserved and four disturbed) inside the PSAER. All sampled species were taxonomically identified at species of morphospecies (inside a family) and assigned to a trophic guild. Differences in diversity, richness and abundance were evaluated through effective number of species, comparisons of Chao’s1 estimated richness and a non-parametric Kruskal–Wallis test, respectively. Both taxonomic and trophic guild composition were evaluated using a multivariate analysis and a post hoc test.
Results
We found some differences in richness, abundance, and diversity between sites, but not a clear pattern of differentiation between restored to disturbed sites. The NMDS showed differences at species and order level, and with trophic guilds, among site types. Families were not useful to differentiate types of sites. Regarding guilds, predators were more abundant in conserved sites, while phytophagous insects were more abundant in disturbed sites.
Conclusions
Species and order level were useful to identify differences in communities of arthropods in sites with different management. The trophic guild approach provides information about the functional state of the restored sites. Nevertheless, our quick evaluation shows that restoration efforts at PSAER have not been successful in differentiate restored to disturbed sites yet.
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2
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Tihelka E, Howard RJ, Cai C, Lozano-Fernandez J. Was There a Cambrian Explosion on Land? The Case of Arthropod Terrestrialization. BIOLOGY 2022; 11:biology11101516. [PMID: 36290419 PMCID: PMC9598930 DOI: 10.3390/biology11101516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 01/24/2023]
Abstract
Arthropods, the most diverse form of macroscopic life in the history of the Earth, originated in the sea. Since the early Cambrian, at least ~518 million years ago, these animals have dominated the oceans of the world. By the Silurian-Devonian, the fossil record attests to arthropods becoming the first animals to colonize land, However, a growing body of molecular dating and palaeontological evidence suggests that the three major terrestrial arthropod groups (myriapods, hexapods, and arachnids), as well as vascular plants, may have invaded land as early as the Cambrian-Ordovician. These dates precede the oldest fossil evidence of those groups and suggest an unrecorded continental "Cambrian explosion" a hundred million years prior to the formation of early complex terrestrial ecosystems in the Silurian-Devonian. We review the palaeontological, phylogenomic, and molecular clock evidence pertaining to the proposed Cambrian terrestrialization of the arthropods. We argue that despite the challenges posed by incomplete preservation and the scarcity of early Palaeozoic terrestrial deposits, the discrepancy between molecular clock estimates and the fossil record is narrower than is often claimed. We discuss strategies for closing the gap between molecular clock estimates and fossil data in the evolution of early ecosystems on land.
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Affiliation(s)
- Erik Tihelka
- School of Earth and Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Richard J. Howard
- Department of Earth Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Chenyang Cai
- School of Earth and Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jesus Lozano-Fernandez
- School of Earth and Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- Department of Genetics, Microbiology and Statistics & Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Spain
- Correspondence:
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3
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Gonzalez CJ, Hildebrandt TR, O'Donnell B. Characterizing Hox genes in mayflies (Ephemeroptera), with Hexagenia limbata as a new mayfly model. EvoDevo 2022; 13:15. [PMID: 35897030 PMCID: PMC9331126 DOI: 10.1186/s13227-022-00200-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 06/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hox genes are key regulators of appendage development in the insect body plan. The body plan of mayfly (Ephemeroptera) nymphs differs due to the presence of abdominal appendages called gills. Despite mayflies' phylogenetic position in Paleoptera and novel morphology amongst insects, little is known of their developmental genetics, such as the appendage-regulating Hox genes. To address this issue we present an annotated, early instar transcriptome and embryonic expression profiles for Antennapedia, Ultrabithorax, and Abdominal A proteins in the mayfly Hexagenia limbata, identify putative Hox protein sequences in the mayflies H. limbata, Cloeon dipterum, and Ephemera danica, and describe the genomic organization of the Hox gene cluster in E. danica. RESULTS Transcriptomic sequencing of early instar H. limbata nymphs yielded a high-quality assembly of 83,795 contigs, of which 22,975 were annotated against Folsomia candida, Nilaparvata lugens, Zootermopsis nevadensis and UniRef90 protein databases. Homeodomain protein phylogeny and peptide annotations identified coding sequences for eight of the ten canonical Hox genes (excluding zerknüllt/Hox3 and fushi tarazu) in H. limbata and C. dipterum, and all ten in E. danica. Mayfly Hox protein sequences and embryonic expression patterns of Antp, Ubx, and Abd-A appear highly conserved with those seen in other non-holometabolan insects. Similarly, the genomic organization of the Hox cluster in E. danica resembles that seen in most insects. CONCLUSIONS We present evidence that mayfly Hox peptide sequences and the embryonic expression patterns for Antp, Ubx, and Abd-A are extensively conserved with other insects, as is organization of the mayfly Hox gene cluster. The protein data suggest mayfly Antp, Ubx, and Abd-A play appendage promoting and repressing roles during embryogenesis in the thorax and abdomen, respectively, as in other insects. The identified expression of eight Hox genes, including Ubx and abd-A, in early instar nymphs further indicates a post-embryonic role, possibly in gill development. These data provide a basis for H. limbata as a complementary Ephemeridae model to the growing repertoire of mayfly model species and molecular techniques.
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Affiliation(s)
| | - Tobias R Hildebrandt
- Computational and Applied Mathematic Science, Plymouth State University, Plymouth, NH, USA
| | - Brigid O'Donnell
- Biological Sciences, Plymouth State University, Plymouth, NH, USA
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4
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Krehenwinkel H, Weber S, Künzel S, Kennedy SR. The bug in a teacup-monitoring arthropod-plant associations with environmental DNA from dried plant material. Biol Lett 2022; 18:20220091. [PMID: 35702982 PMCID: PMC9198770 DOI: 10.1098/rsbl.2022.0091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Environmental DNA analysis (eDNA) has revolutionized the field of biomonitoring in the past years. Various sources have been shown to contain eDNA of diverse organisms, for example, water, soil, gut content and plant surfaces. Here we show that dried plant material is a highly promising source for arthropod community eDNA. We designed a metabarcoding assay to enrich diverse arthropod communities while preventing amplification of plant DNA. Using this assay, we analysed various commercially produced teas and herbs. These samples recovered ecologically and taxonomically diverse arthropod communities, a total of over a thousand species in more than 20 orders, many of them specific to their host plant and its geographical origin. Atypically for eDNA, arthropod DNA in dried plants shows very high temporal stability, opening up plant archives as a source for historical arthropod eDNA. Considering these results, dried plant material appears excellently suited as a novel tool to monitor arthropods and arthropod–plant interactions, detect agricultural pests and identify the geographical origin of imported plant material. The simplicity of our approach and the ability to detect highly diverse arthropod communities from all over the world in tea bags also highlights its utility for outreach purposes and to raise awareness about biodiversity.
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Affiliation(s)
| | | | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Ploen, Germany
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5
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Massey JH, Newton ILG. Diversity and function of arthropod endosymbiont toxins. Trends Microbiol 2022; 30:185-198. [PMID: 34253453 PMCID: PMC8742837 DOI: 10.1016/j.tim.2021.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 02/03/2023]
Abstract
Bacterial endosymbionts induce dramatic phenotypes in their arthropod hosts, including cytoplasmic incompatibility, feminization, parthenogenesis, male killing, parasitoid defense, and pathogen blocking. The molecular mechanisms underlying these effects remain largely unknown but recent evidence suggests that protein toxins secreted by the endosymbionts play a role. Here, we describe the diversity and function of endosymbiont proteins with homology to known bacterial toxins. We focus on maternally transmitted endosymbionts belonging to the Wolbachia, Rickettsia, Arsenophonus, Hamiltonella, Spiroplasma, and Cardinium genera because of their ability to induce the above phenotypes. We identify at least 16 distinct toxin families with diverse enzymatic activities, including AMPylases, nucleases, proteases, and glycosyltransferases. Notably, several annotated toxins contain domains with homology to eukaryotic proteins, suggesting that arthropod endosymbionts mimic host biochemistry to manipulate host physiology, similar to bacterial pathogens.
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Affiliation(s)
| | - Irene L. G. Newton
- Department of Biology, Indiana University, Bloomington, Indiana, USA,Corresponding author,
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6
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Lim JY, Patiño J, Noriyuki S, Cayetano L, Gillespie RG, Krehenwinkel H. Semi-quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island. Mol Ecol 2021; 31:1416-1429. [PMID: 34882855 DOI: 10.1111/mec.16323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 11/28/2022]
Abstract
Spatial variation in climatic conditions along elevation gradients provides an important backdrop by which communities assemble and diversify. Lowland habitats tend to be connected through time, whereas highlands can be continuously or periodically isolated, conditions that have been hypothesized to promote high levels of species endemism. This tendency is expected to be accentuated among taxa that show niche conservatism within a given climatic envelope. While species distribution modeling approaches have allowed extensive exploration of niche conservatism among target taxa, a broad understanding of the phenomenon requires sampling of entire communities. Species-rich groups such as arthropods are ideal case studies for understanding ecological and biodiversity dynamics along elevational gradients given their important functional role in many ecosystems, but community-level studies have been limited due to their tremendous diversity. Here, we develop a novel semi-quantitative metabarcoding approach that combines specimen counts and size-sorting to characterize arthropod community-level diversity patterns along elevational transects on two different volcanoes of the island of Hawai'i. We found that arthropod communities between the two transects became increasingly distinct compositionally at higher elevations. Resistance surface approaches suggest that climatic differences between sampling localities are an important driver in shaping beta-diversity patterns, though the relative importance of climate varies across taxonomic groups. Nevertheless, the climatic niche position of OTUs between transects was highly correlated, suggesting that climatic filters shape the colonization between adjacent volcanoes. Taken together, our results highlight climatic niche conservatism as an important factor shaping ecological assembly along elevational gradients and suggest topographic complexity as an important driver of diversification.
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Affiliation(s)
- Jun Ying Lim
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Jairo Patiño
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Spain.,Department of Botany, Ecology and Plant Physiology, University of La Laguna, La Laguna, Spain
| | - Suzuki Noriyuki
- Faculty of Agriculture and Marine Science, Kochi University, Kochi, Japan
| | - Luis Cayetano
- Biology Department, Merced College, Merced, California, USA
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | - Henrik Krehenwinkel
- Department of Biogeography, Faculty of Regional and Environmental Sciences, Trier University, Trier, Germany
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7
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Tihelka E, Cai C, Giacomelli M, Lozano-Fernandez J, Rota-Stabelli O, Huang D, Engel MS, Donoghue PCJ, Pisani D. The evolution of insect biodiversity. Curr Biol 2021; 31:R1299-R1311. [PMID: 34637741 DOI: 10.1016/j.cub.2021.08.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Insects comprise over half of all described animal species. Together with the Protura (coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form the Hexapoda, a terrestrial arthropod lineage characterised by possessing six legs. Exponential growth of genome-scale data for the hexapods has substantially altered our understanding of the origin and evolution of insect biodiversity. Phylogenomics has provided a new framework for reconstructing insect evolutionary history, resolving their position among the arthropods and some long-standing internal controversies such as the placement of the termites, twisted-winged insects, lice and fleas. However, despite the greatly increased size of phylogenomic datasets, contentious relationships among key insect clades remain unresolved. Further advances in insect phylogeny cannot rely on increased depth and breadth of genome and taxon sequencing. Improved modelling of the substitution process is fundamental to countering tree-reconstruction artefacts, while gene content, modelling of duplications and deletions, and comparative morphology all provide complementary lines of evidence to test hypotheses emerging from the analysis of sequence data. Finally, the integration of molecular and morphological data is key to the incorporation of fossil species within insect phylogeny. The emerging integrated framework of insect evolution will help explain the origins of insect megadiversity in terms of the evolution of their body plan, species diversity and ecology. Future studies of insect phylogeny should build upon an experimental, hypothesis-driven approach where the robustness of hypotheses generated is tested against increasingly realistic evolutionary models as well as complementary sources of phylogenetic evidence.
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Affiliation(s)
- Erik Tihelka
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | - Chenyang Cai
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | | | - Jesus Lozano-Fernandez
- School of Biological Sciences, University of Bristol, Bristol, UK; Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all Adige, Italy; Center Agriculture Food Environment, University of Trento, 38010 San Michele all Adige, Italy
| | - Diying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
| | - Michael S Engel
- Division of Entomology, Natural History Museum, University of Kansas, Lawrence, KS, USA; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | | | - Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol, UK; School of Biological Sciences, University of Bristol, Bristol, UK.
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8
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Lima LF, Torres AQ, Jardim R, Mesquita RD, Schama R. Evolution of Toll, Spatzle and MyD88 in insects: the problem of the Diptera bias. BMC Genomics 2021; 22:562. [PMID: 34289811 PMCID: PMC8296651 DOI: 10.1186/s12864-021-07886-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/13/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Arthropoda, the most numerous and diverse metazoan phylum, has species in many habitats where they encounter various microorganisms and, as a result, mechanisms for pathogen recognition and elimination have evolved. The Toll pathway, involved in the innate immune system, was first described as part of the developmental pathway for dorsal-ventral differentiation in Drosophila. Its later discovery in vertebrates suggested that this system was extremely conserved. However, there is variation in presence/absence, copy number and sequence divergence in various genes along the pathway. As most studies have only focused on Diptera, for a comprehensive and accurate homology-based approach it is important to understand gene function in a number of different species and, in a group as diverse as insects, the use of species belonging to different taxonomic groups is essential. RESULTS We evaluated the diversity of Toll pathway gene families in 39 Arthropod genomes, encompassing 13 different Insect Orders. Through computational methods, we shed some light into the evolution and functional annotation of protein families involved in the Toll pathway innate immune response. Our data indicates that: 1) intracellular proteins of the Toll pathway show mostly species-specific expansions; 2) the different Toll subfamilies seem to have distinct evolutionary backgrounds; 3) patterns of gene expansion observed in the Toll phylogenetic tree indicate that homology based methods of functional inference might not be accurate for some subfamilies; 4) Spatzle subfamilies are highly divergent and also pose a problem for homology based inference; 5) Spatzle subfamilies should not be analyzed together in the same phylogenetic framework; 6) network analyses seem to be a good first step in inferring functional groups in these cases. We specifically show that understanding Drosophila's Toll functions might not indicate the same function in other species. CONCLUSIONS Our results show the importance of using species representing the different orders to better understand insect gene content, origin and evolution. More specifically, in intracellular Toll pathway gene families the presence of orthologues has important implications for homology based functional inference. Also, the different evolutionary backgrounds of Toll gene subfamilies should be taken into consideration when functional studies are performed, especially for TOLL9, TOLL, TOLL2_7, and the new TOLL10 clade. The presence of Diptera specific clades or the ones lacking Diptera species show the importance of overcoming the Diptera bias when performing functional characterization of Toll pathways.
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Affiliation(s)
- Letícia Ferreira Lima
- Laboratório de Biologia Computacional e Sistemas, Oswaldo Cruz Foundation, Fiocruz, Rio de Janeiro, Brazil
| | - André Quintanilha Torres
- Laboratório de Biologia Computacional e Sistemas, Oswaldo Cruz Foundation, Fiocruz, Rio de Janeiro, Brazil
| | - Rodrigo Jardim
- Laboratório de Biologia Computacional e Sistemas, Oswaldo Cruz Foundation, Fiocruz, Rio de Janeiro, Brazil
| | - Rafael Dias Mesquita
- Laboratório de Bioinformática, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular-INCT-EM, Rio de Janeiro, Brazil
| | - Renata Schama
- Laboratório de Biologia Computacional e Sistemas, Oswaldo Cruz Foundation, Fiocruz, Rio de Janeiro, Brazil.
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular-INCT-EM, Rio de Janeiro, Brazil.
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9
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Ballarin L, Karahan A, Salvetti A, Rossi L, Manni L, Rinkevich B, Rosner A, Voskoboynik A, Rosental B, Canesi L, Anselmi C, Pinsino A, Tohumcu BE, Jemec Kokalj A, Dolar A, Novak S, Sugni M, Corsi I, Drobne D. Stem Cells and Innate Immunity in Aquatic Invertebrates: Bridging Two Seemingly Disparate Disciplines for New Discoveries in Biology. Front Immunol 2021; 12:688106. [PMID: 34276677 PMCID: PMC8278520 DOI: 10.3389/fimmu.2021.688106] [Citation(s) in RCA: 12] [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: 03/30/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022] Open
Abstract
The scopes related to the interplay between stem cells and the immune system are broad and range from the basic understanding of organism's physiology and ecology to translational studies, further contributing to (eco)toxicology, biotechnology, and medicine as well as regulatory and ethical aspects. Stem cells originate immune cells through hematopoiesis, and the interplay between the two cell types is required in processes like regeneration. In addition, stem and immune cell anomalies directly affect the organism's functions, its ability to cope with environmental changes and, indirectly, its role in ecosystem services. However, stem cells and immune cells continue to be considered parts of two branches of biological research with few interconnections between them. This review aims to bridge these two seemingly disparate disciplines towards much more integrative and transformative approaches with examples deriving mainly from aquatic invertebrates. We discuss the current understanding of cross-disciplinary collaborative and emerging issues, raising novel hypotheses and comments. We also discuss the problems and perspectives of the two disciplines and how to integrate their conceptual frameworks to address basic equations in biology in a new, innovative way.
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Affiliation(s)
| | - Arzu Karahan
- Middle East Technical University, Institute of Marine Sciences, Erdemli, Mersin, Turkey
| | - Alessandra Salvetti
- Department of Clinical and Experimental Medicine, Unit of Experimental Biology and Genetics, University of Pisa, Pisa, Italy
| | - Leonardo Rossi
- Department of Clinical and Experimental Medicine, Unit of Experimental Biology and Genetics, University of Pisa, Pisa, Italy
| | - Lucia Manni
- Department of Biology, University of Padua, Padua, Italy
| | - Baruch Rinkevich
- Department of Biology, Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Amalia Rosner
- Department of Biology, Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa, Israel
| | - Ayelet Voskoboynik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, United States
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, United States
- Department of Biology, Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Regenerative Medicine and Stem Cells, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Laura Canesi
- Department of Earth Environment and Life Sciences (DISTAV), University of Genoa, Genoa, Italy
| | - Chiara Anselmi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, United States
- Department of Biology, Stanford University, Hopkins Marine Station, Pacific Grove, CA, United States
| | - Annalisa Pinsino
- Institute for Biomedical Research and Innovation, National Research Council, Palermo, Italy
| | - Begüm Ece Tohumcu
- Middle East Technical University, Institute of Marine Sciences, Erdemli, Mersin, Turkey
| | - Anita Jemec Kokalj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Andraž Dolar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sara Novak
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, Siena, Italy
| | - Damjana Drobne
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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10
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Li F, Zheng Z, Li H, Fu R, Xu L, Yang F. Crayfish hemocytes develop along the granular cell lineage. Sci Rep 2021; 11:13099. [PMID: 34162929 PMCID: PMC8222279 DOI: 10.1038/s41598-021-92473-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/09/2021] [Indexed: 01/21/2023] Open
Abstract
Despite the central role of hemocytes in crustacean immunity, the process of hemocyte differentiation and maturation remains unclear. In some decapods, it has been proposed that the two main types of hemocytes, granular cells (GCs) and semigranular cells (SGCs), differentiate along separate lineages. However, our current findings challenge this model. By tracking newly produced hemocytes and transplanted cells, we demonstrate that almost all the circulating hemocytes of crayfish belong to the GC lineage. SGCs and GCs may represent hemocytes of different developmental stages rather than two types of fully differentiated cells. Hemocyte precursors produced by progenitor cells differentiate in the hematopoietic tissue (HPT) for 3 ~ 4 days. Immature hemocytes are released from HPT in the form of SGCs and take 1 ~ 3 months to mature in the circulation. GCs represent the terminal stage of development. They can survive for as long as 2 months. The changes in the expression pattern of marker genes during GC differentiation support our conclusions. Further analysis of hemocyte phagocytosis indicates the existence of functionally different subpopulations. These findings may reshape our understanding of crustacean hematopoiesis and may lead to reconsideration of the roles and relationship of circulating hemocytes.
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Affiliation(s)
- Fang Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184# Daxue Road, Xiamen, 361005, China. .,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China.
| | - Zaichao Zheng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184# Daxue Road, Xiamen, 361005, China
| | - Hongyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184# Daxue Road, Xiamen, 361005, China
| | - Rongrong Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184# Daxue Road, Xiamen, 361005, China
| | - Limei Xu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184# Daxue Road, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Feng Yang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, 184# Daxue Road, Xiamen, 361005, China. .,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China.
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11
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Cuesta EB, Coulibaly B, Bukhari T, Eiglmeier K, Kone R, Coulibaly MB, Zongo S, Barry M, Gneme A, Guelbeogo WM, Beavogui AH, Traore SF, Sagnon N, Vernick KD, Riehle MM. Comprehensive Ecological and Geographic Characterization of Eukaryotic and Prokaryotic Microbiomes in African Anopheles. Front Microbiol 2021; 12:635772. [PMID: 34054746 PMCID: PMC8153677 DOI: 10.3389/fmicb.2021.635772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/12/2021] [Indexed: 12/14/2022] Open
Abstract
Exposure of mosquitoes to numerous eukaryotic and prokaryotic microbes in their associated microbiomes has probably helped drive the evolution of the innate immune system. To our knowledge, a metagenomic catalog of the eukaryotic microbiome has not been reported from any insect. Here we employ a novel approach to preferentially deplete host 18S ribosomal RNA gene amplicons to reveal the composition of the eukaryotic microbial communities of Anopheles larvae sampled in Kenya, Burkina Faso and Republic of Guinea (Conakry). We identified 453 eukaryotic operational taxonomic units (OTUs) associated with Anopheles larvae in nature, but an average of 45% of the 18S rRNA sequences clustered into OTUs that lacked a taxonomic assignment in the Silva database. Thus, the Anopheles microbiome contains a striking proportion of novel eukaryotic taxa. Using sequence similarity matching and de novo phylogenetic placement, the fraction of unassigned sequences was reduced to an average of 4%, and many unclassified OTUs were assigned as relatives of known taxa. A novel taxon of the genus Ophryocystis in the phylum Apicomplexa (which also includes Plasmodium) is widespread in Anopheles larvae from East and West Africa. Notably, Ophryocystis is present at fluctuating abundance among larval breeding sites, consistent with the expected pattern of an epidemic pathogen. Species richness of the eukaryotic microbiome was not significantly different across sites from East to West Africa, while species richness of the prokaryotic microbiome was significantly lower in West Africa. Laboratory colonies of Anopheles coluzzii harbor 26 eukaryotic OTUs, of which 38% (n = 10) are shared with wild populations, while 16 OTUs are unique to the laboratory colonies. Genetically distinct An. coluzzii colonies co-housed in the same facility maintain different prokaryotic microbiome profiles, suggesting a persistent host genetic influence on microbiome composition. These results provide a foundation to understand the role of the Anopheles eukaryotic microbiome in vector immunity and pathogen transmission. We hypothesize that prevalent apicomplexans such as Ophryocystis associated with Anopheles could induce interference or competition against Plasmodium within the vector. This and other members of the eukaryotic microbiome may offer candidates for new vector control tools.
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Affiliation(s)
- Eugeni Belda Cuesta
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- CNRS Unit of Evolutionary Genomics, Modeling, and Health (UMR2000), Institut Pasteur, Paris, France
| | - Boubacar Coulibaly
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - Tullu Bukhari
- International Centre of Insect Physiology and Ecology, Department of Human Health. Nairobi,Kenya
| | - Karin Eiglmeier
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- CNRS Unit of Evolutionary Genomics, Modeling, and Health (UMR2000), Institut Pasteur, Paris, France
| | - Raymond Kone
- Centre de Formation et de Recherche en Santé Rurale de Mafèrinyah, Conakry, Guinea
| | - Mamadou B. Coulibaly
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - Soumanaba Zongo
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Mamadou Barry
- Centre de Formation et de Recherche en Santé Rurale de Mafèrinyah, Conakry, Guinea
| | - Awa Gneme
- Département de Biologie et Physiologie Animales, Université Joseph Ki-Zerbo, Ouagadougou, Burkina Faso
| | - Wamdaogo M. Guelbeogo
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Abdoul H. Beavogui
- Centre de Formation et de Recherche en Santé Rurale de Mafèrinyah, Conakry, Guinea
| | - Sekou F. Traore
- Malaria Research and Training Centre, Faculty of Medicine and Dentistry, University of Mali, Bamako, Mali
| | - N’Fale Sagnon
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Kenneth D. Vernick
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- CNRS Unit of Evolutionary Genomics, Modeling, and Health (UMR2000), Institut Pasteur, Paris, France
| | - Michelle M. Riehle
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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12
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Budd GE. The origin and evolution of the euarthropod labrum. ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 62:101048. [PMID: 33862532 DOI: 10.1016/j.asd.2021.101048] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 05/16/2023]
Abstract
A widely (although not universally) accepted model of arthropod head evolution postulates that the labrum, a structure seen in almost all living euarthropods, evolved from an anterior pair of appendages homologous to the frontal appendages of onychophorans. However, the implications of this model for the interpretation of fossil arthropods have not been fully integrated into reconstructions of the euarthropod stem group, which remains in a state of some disorder. Here I review the evidence for the nature and evolution of the labrum from living taxa, and reconsider how fossils should be interpreted in the light of this. Identification of the segmental identity of head appendage in fossil arthropods remains problematic, and often rests ultimately on unproven assertions. New evidence from the Cambrian stem-group euarthropod Parapeytoia is presented to suggest that an originally protocerebral appendage persisted well up into the upper stem-group of the euarthropods, which prompts a re-evaluation of widely-accepted segmental homologies and the interpretation of fossil central nervous systems. Only a protocerebral brain was implicitly present in a large part of the euarthropod stem group, and the deutocerebrum must have been a relatively late addition.
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Affiliation(s)
- Graham E Budd
- Department of Earth Sciences, Palaeobiology Programme, Uppsala University, Villavägen 16, Uppsala, SE 752 36, Sweden.
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13
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Zhu J, Iannucci A, Dani FR, Knoll W, Pelosi P. Lipocalins in Arthropod Chemical Communication. Genome Biol Evol 2021; 13:6261314. [PMID: 33930146 PMCID: PMC8214410 DOI: 10.1093/gbe/evab091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2021] [Indexed: 12/17/2022] Open
Abstract
Lipocalins represent one of the most successful superfamilies of proteins. Most of them are extracellular carriers for hydrophobic ligands across aqueous media, but other functions have been reported. They are present in most living organisms including bacteria. In animals they have been identified in mammals, molluscs, and arthropods; sequences have also been reported for plants. A subgroup of lipocalins, referred to as odorant-binding proteins (OBPs), mediate chemical communication in mammals by ferrying specific pheromones to the vomeronasal organ. So far, these proteins have not been reported as carriers of semiochemicals in other living organisms; instead chemical communication in arthropods is mediated by other protein families structurally unrelated to lipocalins. A search in the databases has revealed extensive duplication and differentiation of lipocalin genes in some species of insects, crustaceans, and chelicerates. Their large numbers, ranging from a handful to few dozens in the same species, their wide divergence, both within and between species, and their expression in chemosensory organs suggest that such expansion may have occurred under environmental pressure, thus supporting the hypothesis that lipocalins may be involved in chemical communication in arthropods.
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Affiliation(s)
- Jiao Zhu
- Austrian Institute of Technology GmbH, Biosensor Technologies, Tulln, Austria.,Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Alessio Iannucci
- Departement of Biology, University of Firenze, Sesto Fiorentino, Italy
| | | | - Wolfgang Knoll
- Austrian Institute of Technology GmbH, Biosensor Technologies, Tulln, Austria
| | - Paolo Pelosi
- Austrian Institute of Technology GmbH, Biosensor Technologies, Tulln, Austria
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14
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Zhu S, Gao B, Peigneur S, Tytgat J. How a Scorpion Toxin Selectively Captures a Prey Sodium Channel: The Molecular and Evolutionary Basis Uncovered. Mol Biol Evol 2021; 37:3149-3164. [PMID: 32556211 DOI: 10.1093/molbev/msaa152] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The growing resistance of insects to chemical pesticides is reducing the effectiveness of conventional methods for pest control and thus, the development of novel insecticidal agents is imperative. Scorpion toxins specific for insect voltage-gated sodium channels (Navs) have been considered as one of the most promising insecticide alternatives due to their host specificity, rapidly evoked toxicity, biodegradability, and the lack of resistance. However, they have not been developed for uses in agriculture and public health, mainly because of a limited understanding of their molecular and evolutionary basis controlling their phylogenetic selectivity. Here, we show that the traditionally defined insect-selective scorpion toxin LqhIT2 specifically captures a prey Nav through a conserved trapping apparatus comprising a three-residue-formed cavity and a structurally adjacent leucine. The former serves as a detector to recognize and bind a highly exposed channel residue conserved in insects and spiders, two major prey items for scorpions; and the latter subsequently seizes the "moving" voltage sensor via hydrophobic interactions to reduce activation energy for channel opening, demonstrating its action in an enzyme-like manner. Based on the established toxin-channel interaction model in combination with toxicity assay, we enlarged the toxic spectrum of LqhIT2 to spiders and certain other arthropods. Furthermore, we found that genetic background-dependent cavity shapes determine the species selectivity of LqhIT2-related toxins. We expect that the discovery of the trapping apparatus will improve our understanding of the evolution and design principle of Nav-targeted toxins from a diversity of arthropod predators and accelerate their uses in pest control.
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Affiliation(s)
- Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects & Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Steve Peigneur
- Department of Toxicology and Pharmacology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Jan Tytgat
- Department of Toxicology and Pharmacology, University of Leuven (KU Leuven), Leuven, Belgium
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15
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Uozumi T, Ishiwata K, Grygier MJ, Sanoamuang LO, Su ZH. Three nuclear protein-coding genes corroborate a recent phylogenomic model of the Branchiopoda (Crustacea) and provide estimates of the divergence times of the major branchiopodan taxa. Genes Genet Syst 2021; 96:13-24. [PMID: 33716233 DOI: 10.1266/ggs.20-00046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The class Branchiopoda (Crustacea) shows great diversity in morphology and lifestyle among its constituent higher-level taxa: Anostraca, Notostraca, Laevicaudata, Spinicaudata, Cyclestherida and Cladocera. The phylogenetic relationships among these taxa have long been controversial. We sequenced three orthologous nuclear genes that encode the catalytic subunit of DNA polymerase delta and the largest and second-largest subunits of RNA polymerase II in the expectation that the amino acid sequences encoded by these genes might be effective in clarifying branchiopod phylogeny and estimating the times of divergence of the major branchiopodan taxa. The results of phylogenetic analyses based on these amino acid sequences support the monophyly of Branchiopoda and provide strong molecular evidence in support of the following phylogenetic relationships: (Anostraca, (Notostraca, (Laevicaudata, (Spinicaudata, (Cyclestherida, Cladocera))))). Within Cladocera, comparison of the nucleotide sequences of these same genes shows Ctenopoda to be the sister group of Haplopoda + Anomopoda. Three statistical tests based on the present amino acid sequence data-the approximately unbiased test, Kishino-Hasegawa test and weighted Shimodaira-Hasegawa test-tend to refute most of the previous molecular phylogenetic studies on Branchiopoda, which have placed Notostraca differently than here; however, our results corroborate those of one recent phylogenomic study, thus confirming the effectiveness of these three genes to investigate relationships among branchiopod higher taxa. Divergence time estimates calibrated on the basis of fossil evidence suggest that the first divergence of extant branchiopods occurred about 534 Ma during the early Cambrian period and that diversification within the extant branchiopod lineages started in or after the late Permian.
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Affiliation(s)
- Taro Uozumi
- Department of Biological Sciences, Graduate School of Science, Osaka University.,JT Biohistory Research Hall, Takatsuki
| | - Keisuke Ishiwata
- Department of Biological Sciences, Graduate School of Science, Osaka University.,JT Biohistory Research Hall, Takatsuki
| | - Mark J Grygier
- Lake Biwa Museum.,Center of Excellence for the Oceans, National Taiwan Ocean University
| | - La-Orsri Sanoamuang
- Applied Taxonomic Research Center and International College, Khon Kaen University
| | - Zhi-Hui Su
- Department of Biological Sciences, Graduate School of Science, Osaka University.,JT Biohistory Research Hall, Takatsuki
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16
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Impact of transposable elements on genome size variation between two closely related crustacean species. Anal Biochem 2020; 600:113770. [DOI: 10.1016/j.ab.2020.113770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/13/2020] [Accepted: 05/05/2020] [Indexed: 12/19/2022]
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17
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Riciluca KCT, Borges AC, Mello JFR, de Oliveira UC, Serdan DC, Florez-Ariza A, Chaparro E, Nishiyama MY, Cassago A, Junqueira-de-Azevedo ILM, van Heel M, Silva PI, Portugal RV. Myriapod haemocyanin: the first three-dimensional reconstruction of Scolopendra subspinipes and preliminary structural analysis of S. viridicornis. Open Biol 2020; 10:190258. [PMID: 32228398 PMCID: PMC7241075 DOI: 10.1098/rsob.190258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Haemocyanins (Hcs) are copper-containing, respiratory proteins that occur in the haemolymph of many arthropod species. Here, we report the presence of Hcs in the chilopode Myriapoda, demonstrating that these proteins are more widespread among the Arthropoda than previously thought. The analysis of transcriptome of S. subspinipes subpinipes reveals the presence of two distinct subunits of Hc, where the signal peptide is present, and six of prophenoloxidase (PPO), where the signal peptide is absent, in the 75 kDa range. Size exclusion chromatography profiles indicate different quaternary organization for Hc of both species, which was corroborated by TEM analysis: S. viridicornis Hc is a 6 × 6-mer and S. subspinipes Hc is a 3 × 6-mer, which resembles the half-structure of the 6 × 6-mer but also includes the presence of phenoloxidases, since the 1 × 6-mer quaternary organization is commonly associated with hexamers of PPO. Studies with Chelicerata showed that PPO activity are exclusively associated with the Hcs. This study indicates that Scolopendra may have different proteins playing oxygen transport (Hc) and PO function, both following the hexameric oligomerization observed in Hcs.
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Affiliation(s)
- K C T Riciluca
- Laboratório Nacional de Nanotecnologia (LNNano), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, Brazil.,Laboratório de Toxinologia Aplicada (LETA), Centro de Toxinas, Imuno-Resposta e Sinalização Celular (CeTICS/CEPID) - Instituto Butantan, São Paulo, Brazil
| | - A C Borges
- Laboratório Nacional de Nanotecnologia (LNNano), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, Brazil
| | - J F R Mello
- Laboratório Nacional de Nanotecnologia (LNNano), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, Brazil
| | - U C de Oliveira
- Laboratório de Toxinologia Aplicada (LETA), Centro de Toxinas, Imuno-Resposta e Sinalização Celular (CeTICS/CEPID) - Instituto Butantan, São Paulo, Brazil
| | - D C Serdan
- Laboratório Nacional de Nanotecnologia (LNNano), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, Brazil
| | - A Florez-Ariza
- Laboratório Nacional de Nanotecnologia (LNNano), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, Brazil
| | - E Chaparro
- Laboratório de Toxinologia Aplicada (LETA), Centro de Toxinas, Imuno-Resposta e Sinalização Celular (CeTICS/CEPID) - Instituto Butantan, São Paulo, Brazil.,Interunidades em Biotecnologia, Universidade de São Paulo, São Paulo, Brazil
| | - M Y Nishiyama
- Laboratório de Toxinologia Aplicada (LETA), Centro de Toxinas, Imuno-Resposta e Sinalização Celular (CeTICS/CEPID) - Instituto Butantan, São Paulo, Brazil
| | - A Cassago
- Laboratório Nacional de Nanotecnologia (LNNano), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, Brazil
| | - I L M Junqueira-de-Azevedo
- Laboratório de Toxinologia Aplicada (LETA), Centro de Toxinas, Imuno-Resposta e Sinalização Celular (CeTICS/CEPID) - Instituto Butantan, São Paulo, Brazil
| | - M van Heel
- Laboratório Nacional de Nanotecnologia (LNNano), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, Brazil
| | - P I Silva
- Laboratório de Toxinologia Aplicada (LETA), Centro de Toxinas, Imuno-Resposta e Sinalização Celular (CeTICS/CEPID) - Instituto Butantan, São Paulo, Brazil.,Interunidades em Biotecnologia, Universidade de São Paulo, São Paulo, Brazil
| | - R V Portugal
- Laboratório Nacional de Nanotecnologia (LNNano), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, Brazil
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18
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Kozma MT, Ngo-Vu H, Wong YY, Shukla NS, Pawar SD, Senatore A, Schmidt M, Derby CD. Comparison of transcriptomes from two chemosensory organs in four decapod crustaceans reveals hundreds of candidate chemoreceptor proteins. PLoS One 2020; 15:e0230266. [PMID: 32163507 PMCID: PMC7067487 DOI: 10.1371/journal.pone.0230266] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/25/2020] [Indexed: 12/18/2022] Open
Abstract
Crustaceans express genes for at least three classes of putative chemosensory proteins. These are: Ionotropic Receptors (IRs), derived from the heterotetrameric ionotropic glutamate receptors (iGluRs); Transient Receptor Potential (TRP) channels, a diverse set of sensor-channels that include several families of chemoreceptor channels; and Gustatory Receptor Like receptors (GRLs), ionotropic receptors that are homologues of Gustatory Receptors (GRs) of insects and are expressed sparingly in most crustaceans so far studied. IRs are typically numerically the most dominant of these receptor proteins in crustaceans and include two classes: co-receptor IRs, which are necessary for making a functional receptor-channel; and tuning IRs, whose specific combination in the IR subunits in the heterotetramer confers chemical specificity. Previous work showed that the transcriptomes from two major chemosensory organs-the lateral flagellum of the antennule (LF) and the tips of the legs (dactyls)-of the Caribbean spiny lobster Panulirus argus express four co-receptor IRs and over 100 tuning IRs. In this paper, we examined and compared the transcriptomes from the LF and dactyls of P. argus and three other decapod crustaceans-the clawed lobster Homarus americanus, red swamp crayfish Procambarus clarkii, and the blue crab Callinectes sapidus. Each species has at least ca. 100 to 250 IRs, 1 to 4 GRLs, and ca. 15 TRP channels including those shown to be involved in chemoreception in other species. The IRs show different degrees of phylogenetic conservation: some are arthropod-conserved, others are pancrustacean-conserved, others appear to be crustacean-conserved, and some appear to be species-specific. Many IRs appear to be more highly expressed in the LF than dactyl. Our results show that decapod crustaceans express an abundance of genes for chemoreceptor proteins of different types, phylogenetic conservation, and expression patterns. An understanding of their functional roles awaits determining their expression patterns in individual chemosensory neurons and the central projections of those neurons.
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Affiliation(s)
- Mihika T. Kozma
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
| | - Hanh Ngo-Vu
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
| | - Yuen Yan Wong
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Neal S. Shukla
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
| | - Shrikant D. Pawar
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - Adriano Senatore
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Manfred Schmidt
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
| | - Charles D. Derby
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
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19
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Kennedy SR, Tsau S, Gillespie R, Krehenwinkel H. Are you what you eat? A highly transient and prey-influenced gut microbiome in the grey house spider Badumna longinqua. Mol Ecol 2020; 29:1001-1015. [PMID: 32011756 DOI: 10.1111/mec.15370] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/16/2020] [Accepted: 01/29/2020] [Indexed: 01/01/2023]
Abstract
Stable core microbial communities have been described in numerous animal species and are commonly associated with fitness benefits for their hosts. Recent research, however, highlights examples of species whose microbiota are transient and environmentally derived. Here, we test the effect of diet on gut microbial community assembly in the spider Badumna longinqua. Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we analyzed diversity and abundance of the spider's gut microbes, and simultaneously characterized its prey communities using nuclear rRNA markers. We found a clear correlation between community similarity of the spider's insect prey and gut microbial DNA, suggesting that microbiome assembly is primarily diet-driven. This assumption is supported by a feeding experiment, in which two types of prey-crickets and fruit flies-both substantially altered microbial diversity and community similarity between spiders, but did so in different ways. After cricket consumption, numerous cricket-derived microbes appeared in the spider's gut, resulting in a rapid homogenization of microbial communities among spiders. In contrast, few prey-associated bacteria were detected after consumption of fruit flies; instead, the microbial community was remodelled by environmentally sourced microbes, or abundance shifts of rare taxa in the spider's gut. The reshaping of the microbiota by both prey taxa mimicked a stable core microbiome in the spiders for several weeks post feeding. Our results suggest that the spider's gut microbiome undergoes pronounced temporal fluctuations, that its assembly is dictated by the consumed prey, and that different prey taxa may remodel the microbiota in drastically different ways.
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Affiliation(s)
- Susan R Kennedy
- Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA.,Universität Trier Biogeographie, Trier, Germany.,Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Sophia Tsau
- Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Rosemary Gillespie
- Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Henrik Krehenwinkel
- Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA.,Universität Trier Biogeographie, Trier, Germany
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20
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Shedding Light on the Antimicrobial Peptide Arsenal of Terrestrial Isopods: Focus on Armadillidins, a New Crustacean AMP Family. Genes (Basel) 2020; 11:genes11010093. [PMID: 31947541 PMCID: PMC7017220 DOI: 10.3390/genes11010093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 11/30/2022] Open
Abstract
In crustaceans, antimicrobial peptides (AMPs) are clustered into four major groups according to their amino acid composition and structure: (1) single-domain peptides containing cysteine residues such as anti-lipopolysaccharide-factor (ALF), (2) multi-domain or chimeric AMPs such as crustins, (3) non-conventional AMPs, and (4) linear single-domain AMPs. The majority of AMPs has been described in commercially exploited crustaceans, particularly decapods living in aquatic environments (crab, shrimp, lobster, and crayfish). Here, we aimed at establishing the AMPs repertoire of terrestrial isopods (Oniscidea), an original suborder of crustaceans adapted to life outside of the aquatic environment. Using transcriptomic data from 21 species, we identified 110 ALF and 73 crustin sequences. We also characterized the full-length sequence of armadillidins from 17 species, similar to the AMP previously described in the terrestrial isopod Armadillidium vulgare. Furthermore, we tested the antimicrobial activity of three armadillidin peptides characterized from three distantly related species. This analysis revealed similar activity spectra against pathogens, despite extensive structural variation among the tested peptides. In addition to conventional crustacean AMPs, our work highlights armadillidins as a new and independent family of AMPs specific to the Oniscidea, thus opening new perspectives concerning the study of the immune system of terrestrial isopods.
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21
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Zhang YX, Chen X, Wang JP, Zhang ZQ, Wei H, Yu HY, Zheng HK, Chen Y, Zhang LS, Lin JZ, Sun L, Liu DY, Tang J, Lei Y, Li XM, Liu M. Genomic insights into mite phylogeny, fitness, development, and reproduction. BMC Genomics 2019; 20:954. [PMID: 31818245 PMCID: PMC6902594 DOI: 10.1186/s12864-019-6281-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 11/13/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Predatory mites (Acari: Phytoseiidae) are the most important beneficial arthropods used in augmentative biological pest control of protected crops around the world. However, the genomes of mites are far less well understood than those of insects and the evolutionary relationships among mite and other chelicerate orders are contested, with the enigmatic origin of mites at one of the centres in discussion of the evolution of Arachnida. RESULTS We here report the 173 Mb nuclear genome (from 51.75 Gb pairs of Illumina reads) of the predatory mite, Neoseiulus cucumeris, a biocontrol agent against pests such as mites and thrips worldwide. We identified nearly 20.6 Mb (~ 11.93% of this genome) of repetitive sequences and annotated 18,735 protein-coding genes (a typical gene 2888 bp in size); the total length of protein-coding genes was about 50.55 Mb (29.2% of this assembly). About 37% (6981) of the genes are unique to N. cucumeris based on comparison with other arachnid genomes. Our phylogenomic analysis supported the monophyly of Acari, therefore rejecting the biphyletic origin of mites advocated by other studies based on limited gene fragments or few taxa in recent years. Our transcriptomic analyses of different life stages of N. cucumeris provide new insights into genes involved in its development. Putative genes involved in vitellogenesis, regulation of oviposition, sex determination, development of legs, signal perception, detoxification and stress-resistance, and innate immune systems are identified. CONCLUSIONS Our genomics and developmental transcriptomics analyses of N. cucumeris provide invaluable resources for further research on the development, reproduction, and fitness of this economically important mite in particular and Arachnida in general.
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Affiliation(s)
- Yan-Xuan Zhang
- Research Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 People’s Republic of China
| | - Xia Chen
- Research Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 People’s Republic of China
| | - Jie-Ping Wang
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350013 People’s Republic of China
| | - Zhi-Qiang Zhang
- Landcare Research, Auckland and School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Hui Wei
- Research Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 People’s Republic of China
| | - Hai-Yan Yu
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
| | - Hong-Kun Zheng
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
| | - Yong Chen
- Research Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 People’s Republic of China
| | - Li-Sheng Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Jian-Zhen Lin
- Fujian Yanxuan Bio-preventing and Technology Biocontrol Corporation, Fuzhou, People’s Republic of China
| | - Li Sun
- Research Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 People’s Republic of China
| | - Dong-Yuan Liu
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
| | - Juan Tang
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
| | - Yan Lei
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
| | - Xu-Ming Li
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
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Fernandes CS, Batalha MA, Bichuette ME. Dark diversity in the dark: a new approach to subterranean conservation. SUBTERRANEAN BIOLOGY 2019. [DOI: 10.3897/subtbiol.32.38121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
When trying to predict biodiversity patterns, species absences in a community can be as informative as species presences. The concept of dark diversity considers geographical and ecological filters to set an expected species pool and to compare it with the observed species pool, through an index known as community completeness. Completeness shows no relationship with latitude, allowing the comparison of different communities and regions concerning community saturation. Here we propose the use of these methods to a better understanding of subterranean biodiversity patterns. We applied patterns of co-occurrence among phylogenetically related species to set the theoretical species pool and then compared it with the observed richness, using isopods as model taxon. Except for one cave, dark diversity was equal or higher than observed richness. Even though completeness was low in most cases, those caves with higher completeness represent a valuable sample of regional subterranean species pool and may act as a repository of diversity. Our study showed that the dark diversity approach is adaptable to studies of subterranean communities and may be coupled with other conservation tools towards more effective management decisions.
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Sabiá Júnior EF, Menezes LFS, de Araújo IFS, Schwartz EF. Natural Occurrence in Venomous Arthropods of Antimicrobial Peptides Active against Protozoan Parasites. Toxins (Basel) 2019; 11:E563. [PMID: 31557900 PMCID: PMC6832604 DOI: 10.3390/toxins11100563] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 08/31/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023] Open
Abstract
Arthropoda is a phylum of invertebrates that has undergone remarkable evolutionary radiation, with a wide range of venomous animals. Arthropod venom is a complex mixture of molecules and a source of new compounds, including antimicrobial peptides (AMPs). Most AMPs affect membrane integrity and produce lethal pores in microorganisms, including protozoan pathogens, whereas others act on internal targets or by modulation of the host immune system. Protozoan parasites cause some serious life-threatening diseases among millions of people worldwide, mostly affecting the poorest in developing tropical regions. Humans can be infected with protozoan parasites belonging to the genera Trypanosoma, Leishmania, Plasmodium, and Toxoplasma, responsible for Chagas disease, human African trypanosomiasis, leishmaniasis, malaria, and toxoplasmosis. There is not yet any cure or vaccine for these illnesses, and the current antiprotozoal chemotherapeutic compounds are inefficient and toxic and have been in clinical use for decades, which increases drug resistance. In this review, we will present an overview of AMPs, the diverse modes of action of AMPs on protozoan targets, and the prospection of novel AMPs isolated from venomous arthropods with the potential to become novel clinical agents to treat protozoan-borne diseases.
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Affiliation(s)
- Elias Ferreira Sabiá Júnior
- Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF 70910-900, Brazil.
| | - Luis Felipe Santos Menezes
- Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF 70910-900, Brazil.
| | - Israel Flor Silva de Araújo
- Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF 70910-900, Brazil.
| | - Elisabeth Ferroni Schwartz
- Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF 70910-900, Brazil.
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Skelly J, Pushparajan C, Duncan EJ, Dearden PK. Evolution of the Torso activation cassette, a pathway required for terminal patterning and moulting. INSECT MOLECULAR BIOLOGY 2019; 28:392-408. [PMID: 30548465 DOI: 10.1111/imb.12560] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Embryonic terminal patterning and moulting are critical developmental processes in insects. In Drosophila and Tribolium both of these processes are regulated by the Torso-activation cassette (TAC). The TAC consists of a common receptor, Torso, ligands Trunk and prothoracicotropic hormone (PTTH), and the spatially restricted protein Torso-like, with combinations of these elements acting mechanistically to activate the receptor in different developmental contexts. In order to trace the evolutionary history of the TAC we determined the presence or absence of TAC components in the genomes of arthropods. Our analyses reveal that Torso, Trunk and PTTH are evolutionarily labile components of the TAC with multiple individual or combined losses occurring in the arthropod lineages leading to and within the insects. These losses are often correlated, with both ligands and receptor missing from the genome of the same species. We determine that the PTTH gene evolved in the common ancestor of Hemiptera and Holometabola, and is missing from the genomes of a number of species with experimentally demonstrated PTTH activity, implying another molecule may be involved in ecdysis in these species. In contrast, the torso-like gene is a common component of pancrustacean genomes.
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Affiliation(s)
- J Skelly
- Laboratory for Evolution and Development, Genomics Aotearoa, Biochemistry Department, University of Otago, Dunedin, Aotearoa-New Zealand
| | - C Pushparajan
- Laboratory for Evolution and Development, Genomics Aotearoa, Biochemistry Department, University of Otago, Dunedin, Aotearoa-New Zealand
| | - E J Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - P K Dearden
- Laboratory for Evolution and Development, Genomics Aotearoa, Biochemistry Department, University of Otago, Dunedin, Aotearoa-New Zealand
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26
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Krehenwinkel H, Pomerantz A, Henderson JB, Kennedy SR, Lim JY, Swamy V, Shoobridge JD, Graham N, Patel NH, Gillespie RG, Prost S. Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale. Gigascience 2019; 8:giz006. [PMID: 30824940 PMCID: PMC6503943 DOI: 10.1093/gigascience/giz006] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 10/30/2018] [Accepted: 01/10/2019] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies). FINDINGS Using a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed Nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates. CONCLUSIONS Sequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost-effective, portable, and universal approach for eukaryote DNA barcoding. Although bulk community analyses using long-amplicon approaches may introduce biases, the long rDNA amplicons approach signifies a powerful tool for enabling the accurate recovery of taxonomic and phylogenetic diversity across biological communities.
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Affiliation(s)
- Henrik Krehenwinkel
- Department of Biogeography, Trier University, Faculty of Regional and Environmental Sciences, Trier 54286, Germany
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, 94720, USA
- Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California, 94118, USA
| | - Aaron Pomerantz
- Department of Integrative Biology, University of California, Berkeley, California, 94720, USA
| | - James B Henderson
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California, 94118, USA
- Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California, 94118, USA
| | - Susan R Kennedy
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, 94720, USA
| | - Jun Ying Lim
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, 94720, USA
- Department of Integrative Biology, University of California, Berkeley, California, 94720, USA
| | - Varun Swamy
- San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, California, 92027, USA
| | - Juan Diego Shoobridge
- Applied Botany Laboratory, Research and development Laboratories, Cayetano Heredia University, Av. Honorio Delgado 430, Urb Ingenieria, Lima, Perú
| | - Natalie Graham
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, 94720, USA
| | - Nipam H Patel
- Department of Integrative Biology, University of California, Berkeley, California, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720, USA
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, 94720, USA
| | - Stefan Prost
- Department of Integrative Biology, University of California, Berkeley, California, 94720, USA
- Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, 0184, South Africa
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27
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Ando T, Sekine S, Inagaki S, Misaki K, Badel L, Moriya H, Sami MM, Itakura Y, Chihara T, Kazama H, Yonemura S, Hayashi S. Nanopore Formation in the Cuticle of an Insect Olfactory Sensillum. Curr Biol 2019; 29:1512-1520.e6. [PMID: 31006566 DOI: 10.1016/j.cub.2019.03.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/18/2019] [Accepted: 03/20/2019] [Indexed: 10/27/2022]
Abstract
Nanometer-level patterned surface structures form the basis of biological functions, including superhydrophobicity, structural coloration, and light absorption [1-3]. In insects, the cuticle overlying the olfactory sensilla has multiple small (50- to 200-nm diameter) pores [4-8], which are supposed to function as a filter that admits odorant molecules, while preventing the entry of larger airborne particles and limiting water loss. However, the cellular processes underlying the patterning of extracellular matrices into functional nano-structures remain unknown. Here, we show that cuticular nanopores in Drosophila olfactory sensilla originate from a curved ultrathin film that is formed in the outermost envelope layer of the cuticle and secreted from specialized protrusions in the plasma membrane of the hair forming (trichogen) cell. The envelope curvature coincides with plasma membrane undulations associated with endocytic structures. The gore-tex/Osiris23 gene encodes an endosomal protein that is essential for envelope curvature, nanopore formation, and odor receptivity and is expressed specifically in developing olfactory trichogen cells. The 24-member Osiris gene family is expressed in cuticle-secreting cells and is found only in insect genomes. These results reveal an essential requirement for nanopores for odor reception and identify Osiris genes as a platform for investigating the evolution of surface nano-fabrication in insects.
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Affiliation(s)
- Toshiya Ando
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Sayaka Sekine
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Sachi Inagaki
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Kazuyo Misaki
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Laurent Badel
- RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Moriya
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Mustafa M Sami
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yuki Itakura
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Takahiro Chihara
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Hokto Kazama
- RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shigenobu Yonemura
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Shigeo Hayashi
- RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Biology, Kobe University Graduate School of Science, Kobe, Hyogo 657-8501, Japan.
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28
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Van Dam MH, Trautwein M, Spicer GS, Esposito L. Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny. Mol Ecol Resour 2019; 19:465-475. [PMID: 30411860 DOI: 10.1111/1755-0998.12962] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 10/26/2018] [Accepted: 10/30/2018] [Indexed: 11/30/2022]
Abstract
Mites (Acari) are one of the most diverse groups of life on Earth; yet, their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution, we design targeted ultraconserved genomic elements (UCEs) probes, intended for resolving the complex relationships between mite lineages and closely related arachnids. We then test our Acari UCE baits in-silico by constructing a phylogeny using 13 existing Acari genomes, as well as 6 additional taxa from a variety of genomic sources. Our Acari-specific probe kit improves the recovery of loci within mites over an existing general arachnid UCE probe set. Our initial phylogeny recovers the major mite lineages, yet finds mites to be non-monophyletic overall, with Opiliones (harvestmen) and Ricinuleidae (hooded tickspiders) rendering Parasitiformes paraphyletic.
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Affiliation(s)
- Matthew H Van Dam
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California
| | - Michelle Trautwein
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California
| | - Greg S Spicer
- Department of Biology, San Francisco State University, San Francisco, California
| | - Lauren Esposito
- Entomology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California
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29
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Abstract
The millions of extant arthropod species are testament to their evolutionary success that can at least partially be attributed to venom usage, which evolved independently in at least 19 arthropod lineages. While some arthropods primarily use venom for predation (e.g., spiders and centipedes) or defense (e.g., bees and caterpillars), it can also have more specialised functions (e.g. in parasitoid wasps to paralyse arthropods for their brood to feed on) or even a combination of functions (e.g. the scorpion Parabuthus transvaalicus can deliver a prevenom for predator deterrence and a venom for predation). Most arthropod venoms are complex cocktails of water, salts, small bioactive molecules, peptides, enzymes and larger proteins, with peptides usually comprising the majority of toxins. Some spider venoms have been reported to contain >1000 peptide toxins, which function as combinatorial libraries to provide an evolutionary advantage. The astounding diversity of venomous arthropods multiplied by their enormous toxin arsenals results in an almost infinite resource for novel bioactive molecules. The main challenge for exploiting this resource is the small size of most arthropods, which can be a limitation for current venom extraction techniques. Fortunately, recent decades have seen an incredible improvement in transcriptomic and proteomic techniques that have provided increasing sensitivity while reducing sample requirements. In turn, this has provided a much larger variety of arthropod venom compounds for potential applications such as therapeutics, molecular probes for basic research, bioinsecticides or anti-parasitic drugs. This special issue of Toxicon aims to cover the breadth of arthropod venom research, including toxin evolution, pharmacology, toxin discovery and characterisation, toxin structures, clinical aspects, and potential applications.
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Affiliation(s)
- Volker Herzig
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia.
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30
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Rosario K, Mettel KA, Benner BE, Johnson R, Scott C, Yusseff-Vanegas SZ, Baker CCM, Cassill DL, Storer C, Varsani A, Breitbart M. Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates. PeerJ 2018; 6:e5761. [PMID: 30324030 PMCID: PMC6186406 DOI: 10.7717/peerj.5761] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/16/2018] [Indexed: 11/20/2022] Open
Abstract
Viruses encoding a replication-associated protein (Rep) within a covalently closed, single-stranded (ss)DNA genome are among the smallest viruses known to infect eukaryotic organisms, including economically valuable agricultural crops and livestock. Although circular Rep-encoding ssDNA (CRESS DNA) viruses are a widespread group for which our knowledge is rapidly expanding, biased sampling toward vertebrates and land plants has limited our understanding of their diversity and evolution. Here, we screened terrestrial arthropods for CRESS DNA viruses and report the identification of 44 viral genomes and replicons associated with specimens representing all three major terrestrial arthropod lineages, namely Euchelicerata (spiders), Hexapoda (insects), and Myriapoda (millipedes). We identified virus genomes belonging to three established CRESS DNA viral families (Circoviridae, Genomoviridae, and Smacoviridae); however, over half of the arthropod-associated viral genomes are only distantly related to currently classified CRESS DNA viral sequences. Although members of viral and satellite families known to infect plants (Geminiviridae, Nanoviridae, Alphasatellitidae) were not identified in this study, these plant-infecting CRESS DNA viruses and replicons are transmitted by hemipterans. Therefore, members from six out of the seven established CRESS DNA viral families circulate among arthropods. Furthermore, a phylogenetic analysis of Reps, including endogenous viral sequences, reported to date from a wide array of organisms revealed that most of the known CRESS DNA viral diversity circulates among invertebrates. Our results highlight the vast and unexplored diversity of CRESS DNA viruses among invertebrates and parallel findings from RNA viral discovery efforts in undersampled taxa.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Kaitlin A Mettel
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Bayleigh E Benner
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Ryan Johnson
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
| | - Catherine Scott
- Department of Biological Sciences, University of Toronto, Scarborough, Scarborough, ON, Canada
| | | | - Christopher C M Baker
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Deby L Cassill
- Department of Biological Sciences, University of South Florida Saint Petersburg, Saint Petersburg, FL, USA
| | - Caroline Storer
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, USA
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31
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Structural diversity of arthropod venom toxins. Toxicon 2018; 152:46-56. [DOI: 10.1016/j.toxicon.2018.07.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 06/29/2018] [Accepted: 07/19/2018] [Indexed: 11/19/2022]
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32
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Langeloh H, Wasser H, Richter N, Bicker G, Stern M. Neuromuscular transmitter candidates of a centipede ( Lithobius forficatus, Chilopoda). Front Zool 2018; 15:28. [PMID: 30123311 PMCID: PMC6090918 DOI: 10.1186/s12983-018-0274-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/10/2018] [Indexed: 11/10/2022] Open
Abstract
Background The neuromuscular junction is the chemical synapse where motor neurons communicate with skeletal muscle fibers. Whereas vertebrates and many invertebrates use acetylcholine as transmitter at the neuromuscular junction, in those arthropods examined up to now, glutamate and GABA are used instead. With respect to taxon sampling in a phylogenetic context, there is, however, only a limited amount of data available, focusing mainly on crustaceans and hexapods, and neglecting other, arthropod groups. Here we investigate the neurotransmitter equipment of neuromuscular synapses of a myriapod, Lithobius forficatus, using immunofluorescence and histochemical staining methods. Results Glutamate and GABA could be found colocalised with synapsin in synaptic boutons of body wall and leg muscles of Lithobius forficatus. Acetylcholinesterase activity as a marker for cholinergic synapses was found abundantly in the central nervous system and also in some peripheral nerves, but not at neuromuscular junctions. Furthermore, a large number of leg sensory neurons displayed GABA-immunofluorescence and was also labeled with an antiserum against the GABA-synthesizing enzyme, glutamate decarboxylase. Conclusions Our data indicate that glutamate and GABA are neurotransmitters at Lithobius forficatus neuromuscular junctions, whereas acetylcholine is very unlikely to play a role here. This is in line with the concept of glutamate as excitatory and GABA as the main inhibitory neuromuscular transmitters in euarthropods. Furthermore, we have, to our knowledge for the first time, localized GABA in euarthropod leg sensory neurons, indicating the possibility that neurotransmitter panel in arthropod sensory systems may be far more extensive than hitherto assumed.
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Affiliation(s)
- Hendrik Langeloh
- University of Veterinary Medicine Hannover, Division of Cell Biology, Bischofsholer Damm 15/102, D-30173 Hannover, Germany
| | - Hannah Wasser
- University of Veterinary Medicine Hannover, Division of Cell Biology, Bischofsholer Damm 15/102, D-30173 Hannover, Germany
| | - Nicole Richter
- University of Veterinary Medicine Hannover, Division of Cell Biology, Bischofsholer Damm 15/102, D-30173 Hannover, Germany
| | - Gerd Bicker
- University of Veterinary Medicine Hannover, Division of Cell Biology, Bischofsholer Damm 15/102, D-30173 Hannover, Germany
| | - Michael Stern
- University of Veterinary Medicine Hannover, Division of Cell Biology, Bischofsholer Damm 15/102, D-30173 Hannover, Germany
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33
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Krehenwinkel H, Kennedy SR, Rueda A, Lam A, Gillespie RG. Scaling up
DNA
barcoding – Primer sets for simple and cost efficient arthropod systematics by multiplex
PCR
and Illumina amplicon sequencing. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13064] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Henrik Krehenwinkel
- Environmental Sciences Policy and Management University of California Berkeley Berkeley California
- Center for Comparative Genomics California Academy of Sciences Music Concourse Drive San Francisco California
| | - Susan R. Kennedy
- Environmental Sciences Policy and Management University of California Berkeley Berkeley California
| | - Alexandra Rueda
- Environmental Sciences Policy and Management University of California Berkeley Berkeley California
- Laboratorio de Zoología y Entomología Acuática Departamento de Ciencias Biológicas Universidad de los Andes, Bogotá Colombia
| | - Athena Lam
- Center for Comparative Genomics California Academy of Sciences Music Concourse Drive San Francisco California
| | - Rosemary G. Gillespie
- Environmental Sciences Policy and Management University of California Berkeley Berkeley California
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34
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Gainett G, Sharma PP, Giribet G, Willemart RH. The sensory equipment of a sandokanid: An extreme case of tarsal reduction in harvestmen (Arachnida, Opiliones, Laniatores). J Morphol 2018; 279:1206-1223. [PMID: 29893061 DOI: 10.1002/jmor.20843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/30/2018] [Accepted: 05/05/2018] [Indexed: 12/30/2022]
Abstract
The study of sensory structures has the potential to provide insights into the natural history and evolution of animals. The sensory structures of arachnids are usually concentrated on the pedipalps (the tritocerebral appendages) or on the distal podomere (tarsus) of the anterior walking legs, the latter being the case for armored harvestmen (Opiliones, Laniatores). Therefore, modifications of the tarsus could have direct impacts on the sensory equipment of these animals. Using scanning electron microscopy, we investigated the sensory equipment in an extreme case of reduction in tarsal articles in the harvestman Sandokan truncatus (Sandokanidae), which bears a single tarsomere in all legs, and the potential consequences of this reduction. Additionally, we review the literature on the natural history of the family Sandokanidae. Tarsomeres of all legs are equipped with gustatory sensilla, mechanoreceptors, and a pore organ, but wall-pored olfactory sensilla are restricted to tarsi I and II. Tarsi II present a higher density of olfactory sensilla and also putative campaniform sensilla (strain detectors), which indicates a special sensory function of this pair of legs. Other podomeres are covered with shelled sensilla, a probable chemoreceptor previously unreported in Opiliones. Overall, S. truncatus has types of sensilla largely comparable to harvestmen with longer and subdivided tarsi. However, S. truncatus also exhibits extra-tarsal sensory fields of sensilla basiconica (putative thermo-/hygroreceptors) in previously undescribed sites, and the unique pore organs. Our results establish a basis for further research investigating the natural history, as well as the evolutionary correlations and mechanistic causes of the tarsal reduction in this enigmatic lineage.
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Affiliation(s)
- Guilherme Gainett
- Laboratório de Ecologia Sensorial e Comportamento de Artrópodes, Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, SP, 03828-000, Brazil.,Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, USA
| | - Rodrigo H Willemart
- Laboratório de Ecologia Sensorial e Comportamento de Artrópodes, Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, SP, 03828-000, Brazil.,Programa de Pós-Graduação em Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 08-055-090, Brazil.,Programa de Pós-Graduação em Ecologia e Evolução, Universidade Federal de São Paulo, Diadema, SP, 09972-270, Brazil
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35
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Laroche M, Bérenger JM, Delaunay P, Charrel R, Pradines B, Berger F, Ranque S, Bitam I, Davoust B, Raoult D, Parola P. Medical Entomology: A Reemerging Field of Research to Better Understand Vector-Borne Infectious Diseases. Clin Infect Dis 2018; 65:S30-S38. [PMID: 28859353 DOI: 10.1093/cid/cix463] [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] [Indexed: 12/23/2022] Open
Abstract
In the last decade, the Chikungunya and Zika virus outbreaks have turned public attention to the possibility of the expansion of vector-borne infectious diseases worldwide. Medical entomology is focused on the study of arthropods involved in human health. We review here some of the research approaches taken by the medical entomology team of the University Hospital Institute (UHI) Méditerranée Infection of Marseille, France, with the support of recent or representative studies. We propose our approaches to technical innovations in arthropod identification and the detection of microorganisms in arthropods, the use of arthropods as epidemiological or diagnostic tools, entomological investigations around clinical cases or within specific populations, and how we have developed experimental models to decipher the interactions between arthropods, microorganisms, and humans.
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Affiliation(s)
- Maureen Laroche
- Aix Marseille Université, CNRS 7278, IRD 198 (Dakar, Sénégal), Inserm 1095, Assistance Publique-Hôpitaux de Marseille (AP-HM), Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Marseille
| | - Jean-Michel Bérenger
- Aix Marseille Université, CNRS 7278, IRD 198 (Dakar, Sénégal), Inserm 1095, Assistance Publique-Hôpitaux de Marseille (AP-HM), Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Marseille
| | - Pascal Delaunay
- Service de Parasitologie-Mycologie, Hôpital de l'Archet, Centre Hospitalier Universitaire de Nice, Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, Université de Nice-Sophia Antipolis
| | - Remi Charrel
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille Université, IRD 190, Inserm 1207, EHESP), AP-HM, IHU Méditerranée Infection
| | - Bruno Pradines
- Aix Marseille Université, CNRS 7278, IRD 198 (Dakar, Sénégal), Inserm 1095, Assistance Publique-Hôpitaux de Marseille ( AP-HM), Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Marseille.,Unité Parasitologie et Entomologie, Institut de Recherche Biomédicale des Armées.,Centre National de Référence du Paludisme
| | - Franck Berger
- GSBDD Marseille-Aubagne, Centre d'épidémiologie et de santé publique des armées, Marseille, France
| | - Stéphane Ranque
- Aix Marseille Université, CNRS 7278, IRD 198 (Dakar, Sénégal), Inserm 1095, Assistance Publique-Hôpitaux de Marseille (AP-HM), Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Marseille
| | - Idir Bitam
- Laboratoire Biodiversité et Environnement: Interactions Génomes, Faculté des Sciences Biologiques Université des Sciences et de la Technologie Houari Boumediene, Bab Ezzouar, Algeria
| | - Bernard Davoust
- Aix Marseille Université, CNRS 7278, IRD 198 (Dakar, Sénégal), Inserm 1095, Assistance Publique-Hôpitaux de Marseille (AP-HM), Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Marseille
| | - Didier Raoult
- Aix Marseille Université, CNRS 7278, IRD 198 (Dakar, Sénégal), Inserm 1095, Assistance Publique-Hôpitaux de Marseille (AP-HM), Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Marseille
| | - Philippe Parola
- Aix Marseille Université, CNRS 7278, IRD 198 (Dakar, Sénégal), Inserm 1095, Assistance Publique-Hôpitaux de Marseille (AP-HM), Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), IHU Méditerranée Infection, Marseille
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36
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Hein H, Scholtz G. Larval neurogenesis in the copepod Tigriopus californicus (Tetraconata, Multicrustacea). Dev Genes Evol 2018; 228:119-129. [DOI: 10.1007/s00427-018-0610-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/02/2018] [Indexed: 01/06/2023]
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37
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Lewis SH, Quarles KA, Yang Y, Tanguy M, Frézal L, Smith SA, Sharma PP, Cordaux R, Gilbert C, Giraud I, Collins DH, Zamore PD, Miska EA, Sarkies P, Jiggins FM. Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements. Nat Ecol Evol 2018; 2:174-181. [PMID: 29203920 PMCID: PMC5732027 DOI: 10.1038/s41559-017-0403-4] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/02/2017] [Indexed: 02/02/2023]
Abstract
In animals, small RNA molecules termed PIWI-interacting RNAs (piRNAs) silence transposable elements (TEs), protecting the germline from genomic instability and mutation. piRNAs have been detected in the soma in a few animals, but these are believed to be specific adaptations of individual species. Here, we report that somatic piRNAs were probably present in the ancestral arthropod more than 500 million years ago. Analysis of 20 species across the arthropod phylum suggests that somatic piRNAs targeting TEs and messenger RNAs are common among arthropods. The presence of an RNA-dependent RNA polymerase in chelicerates (horseshoe crabs, spiders and scorpions) suggests that arthropods originally used a plant-like RNA interference mechanism to silence TEs. Our results call into question the view that the ancestral role of the piRNA pathway was to protect the germline and demonstrate that small RNA silencing pathways have been repurposed for both somatic and germline functions throughout arthropod evolution.
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Affiliation(s)
- Samuel H Lewis
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
- Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.
- Institute for Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK.
| | - Kaycee A Quarles
- Howard Hughes Medical Institute, RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Yujing Yang
- Howard Hughes Medical Institute, RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Melanie Tanguy
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, CB2 1QN, UK
| | - Lise Frézal
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, CB2 1QN, UK
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Inserm, Ecole Normale Supérieure, Paris Sciences & Lettres Research University, 75005, Paris, France
| | - Stephen A Smith
- Department of Biomedical Sciences and Pathobiology, Virginia Maryland College of Veterinary Medicine, 205 Duck Pond Drive, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 352 Birge Hall, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Richard Cordaux
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Clément Gilbert
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
- Laboratoire Evolution, Génomes, Comportement, Écologie, Unité Mixte de Recherche 9191 Centre National de la Recherche Scientifique and Unité Mixte de Recherche 247 Institut de Recherche pour le Développement, Université Paris-Sud, 91198, Gif-sur-Yvette, France
| | - Isabelle Giraud
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
| | - David H Collins
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Phillip D Zamore
- Howard Hughes Medical Institute, RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Eric A Miska
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, CB2 1QN, UK
| | - Peter Sarkies
- Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute for Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Francis M Jiggins
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
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Abstract
The discovery of fossilized brains and ventral nerve cords in lower and mid-Cambrian arthropods has led to crucial insights about the evolution of their central nervous system, the segmental identity of head appendages and the early evolution of eyes and their underlying visual systems. Fundamental ground patterns of lower Cambrian arthropod brains and nervous systems correspond to the ground patterns of brains and nervous systems belonging to three of four major extant panarthropod lineages. These findings demonstrate the evolutionary stability of early neural arrangements over an immense time span. Here, we put these fossil discoveries in the context of evidence from cladistics, as well as developmental and comparative neuroanatomy, which together suggest that despite many evolved modifications of neuropil centers within arthropod brains and ganglia, highly conserved arrangements have been retained. Recent phylogenies of the arthropods, based on fossil and molecular evidence, and estimates of divergence dates, suggest that neural ground patterns characterizing onychophorans, chelicerates and mandibulates are likely to have diverged between the terminal Ediacaran and earliest Cambrian, heralding the exuberant diversification of body forms that account for the Cambrian Explosion.
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Affiliation(s)
- Nicholas J Strausfeld
- Department of Neuroscience and Center for Insect Science, University of Arizona, Tucson, AZ 85721, USA.
| | - Xiaoya Ma
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Yunnan Key Laboratory for Palaeobiology, Yunnan University, Kunming 650091, People's Republic of China
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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39
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Weinstein SB, Kuris AM. Independent origins of parasitism in Animalia. Biol Lett 2017; 12:rsbl.2016.0324. [PMID: 27436119 DOI: 10.1098/rsbl.2016.0324] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/24/2016] [Indexed: 11/12/2022] Open
Abstract
Nearly half of all animals may have a parasitic lifestyle, yet the number of transitions to parasitism and their potential for species diversification remain unresolved. Based on a comprehensive survey of the animal kingdom, we find that parasitism has independently evolved at least 223 times in just 15 phyla, with the majority of identified independent parasitic groups occurring in the Arthropoda, at or below the level of Family. Metazoan parasitology is dominated by the study of helminthes; however, only 20% of independently derived parasite taxa belong to those groups, with numerous transitions also seen in Mollusca, Rotifera, Annelida and Cnidaria. Parasitism is almost entirely absent from deuterostomes, and although worm-like morphology and host associations are widespread across Animalia, the dual symbiotic and trophic interactions required for parasitism may constrain its evolution from antecedent consumer strategies such as generalist predators and filter feeders. In general, parasitic groups do not differ from their free-living relatives in their potential for speciation. However, the 10 largest parasitic clades contain 90% of described parasitic species, or perhaps 40% of all animal species. Hence, a substantial fraction of animal diversity on the Earth arose following these few transitions to a parasitic trophic strategy.
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Affiliation(s)
- Sara B Weinstein
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - Armand M Kuris
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
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40
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Labreuche Y, Chenivesse S, Jeudy A, Le Panse S, Boulo V, Ansquer D, Pagès S, Givaudan A, Czjzek M, Le Roux F. Nigritoxin is a bacterial toxin for crustaceans and insects. Nat Commun 2017; 8:1248. [PMID: 29093459 PMCID: PMC5665878 DOI: 10.1038/s41467-017-01445-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 09/14/2017] [Indexed: 11/29/2022] Open
Abstract
The Tetraconata (Pancrustacea) concept proposes that insects are more closely related to aquatic crustaceans than to terrestrial centipedes or millipedes. The question therefore arises whether insects have kept crustacean-specific genetic traits that could be targeted by specific toxins. Here we show that a toxin (nigritoxin), originally identified in a bacterial pathogen of shrimp, is lethal for organisms within the Tetraconata and non-toxic to other animals. X-ray crystallography reveals that nigritoxin possesses a new protein fold of the α/β type. The nigritoxin N-terminal domain is essential for cellular translocation and likely encodes specificity for Tetraconata. Once internalized by eukaryotic cells, nigritoxin induces apoptotic cell death through structural features that are localized in the C-terminal domain of the protein. We propose that nigritoxin will be an effective means to identify a Tetraconata evolutionarily conserved pathway and speculate that nigritoxin holds promise as an insecticidal protein. The Tetraconata concept suggests that insects and crustaceans may share evolutionarily conserved pathways. Here, the authors describe the animal tropism and structure-function relationship of nigritoxin, showing that this protein is lethal for insects and crustaceans but harmless to other animals.
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Affiliation(s)
- Yannick Labreuche
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France.,Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Sabine Chenivesse
- Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Alexandra Jeudy
- Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Sophie Le Panse
- CNRS, FR 2424, Plateforme Merimage, Station Biologique de Roscoff, Place Georges Teissier, CS 90074, F-29688, Roscoff cedex, France
| | - Viviane Boulo
- Département Lagons, Ecosystèmes et Aquaculture Durables en Nouvelle-Calédonie, IFREMER, BP 2059, 98846, Nouméa cedex, New Caledonia
| | - Dominique Ansquer
- Département Lagons, Ecosystèmes et Aquaculture Durables en Nouvelle-Calédonie, IFREMER, BP 2059, 98846, Nouméa cedex, New Caledonia
| | - Sylvie Pagès
- UMR 1333 "Diversité, Génomes & Interactions Microorganismes - Insectes" Université Montpellier 2 - Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Alain Givaudan
- UMR 1333 "Diversité, Génomes & Interactions Microorganismes - Insectes" Université Montpellier 2 - Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Mirjam Czjzek
- Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
| | - Frédérique Le Roux
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France. .,Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France.
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41
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Smith FW, Bartels PJ, Goldstein B. A Hypothesis for the Composition of the Tardigrade Brain and its Implications for Panarthropod Brain Evolution. Integr Comp Biol 2017; 57:546-559. [DOI: 10.1093/icb/icx081] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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42
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Vicente Dos Santos V, Tixier MS. Which molecular markers for assessing which taxonomic level? The case study of the mite family Phytoseiidae (Acari: Mesostigmata). Cladistics 2017; 33:251-267. [PMID: 34715727 DOI: 10.1111/cla.12166] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2016] [Indexed: 11/29/2022] Open
Abstract
The use of molecular markers for resolving systematics issues has improved our knowledge of life history. However, for the taxa studied herein-the predatory mite family Phytoseiidae-molecular phylogeny is impeded by a lack of suitable markers for deeper taxonomic levels. This study aims (i) to establish DNA amplification protocols for molecular markers known to resolve supraspecific nodes in other taxa, (ii) to determine their individual performance in assessing the clustering of species, genera, tribes and subfamilies, and (iii) to characterize the additional information provided when markers are concatenated. A new phylogenetic index is proposed based on ecological concepts, considering trees as a community of nodes. New and efficient protocols for DNA amplification of six molecular markers are provided. The concatenated tree globally provides more robust and reliable information, especially for deeper nodes. However, for assessing species identification and within-genera phylogenies, the combined use of six markers does not seem necessary, underlining the need to resize experiments depending on their taxonomic objectives. Finally, this study lays the methodological foundations with which to test the present Phytoseiidae classification as the first phylogeny obtained shows incongruence with the present morphological classification.
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Affiliation(s)
- Victor Vicente Dos Santos
- Montpellier SupAgro, Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations (INRA/IRD/CIRAD/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, Montferrier-sur-Lez Cedex, 34988, France
| | - Marie-Stephane Tixier
- Montpellier SupAgro, Unité Mixte de Recherche Centre de Biologie pour la Gestion des Populations (INRA/IRD/CIRAD/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, Montferrier-sur-Lez Cedex, 34988, France
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43
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Ortega-Hernández J, Janssen R, Budd GE. Origin and evolution of the panarthropod head - A palaeobiological and developmental perspective. ARTHROPOD STRUCTURE & DEVELOPMENT 2017; 46:354-379. [PMID: 27989966 DOI: 10.1016/j.asd.2016.10.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/15/2016] [Accepted: 10/25/2016] [Indexed: 05/14/2023]
Abstract
The panarthropod head represents a complex body region that has evolved through the integration and functional specialization of the anterior appendage-bearing segments. Advances in the developmental biology of diverse extant organisms have led to a substantial clarity regarding the relationships of segmental homology between Onychophora (velvet worms), Tardigrada (water bears), and Euarthropoda (e.g. arachnids, myriapods, crustaceans, hexapods). The improved understanding of the segmental organization in panarthropods offers a novel perspective for interpreting the ubiquitous Cambrian fossil record of these successful animals. A combined palaeobiological and developmental approach to the study of the panarthropod head through deep time leads us to propose a consensus hypothesis for the intricate evolutionary history of this important tagma. The contribution of exceptionally preserved brains in Cambrian fossils - together with the recognition of segmentally informative morphological characters - illuminate the polarity for major anatomical features. The euarthropod stem-lineage provides a detailed view of the step-wise acquisition of critical characters, including the origin of a multiappendicular head formed by the fusion of several segments, and the transformation of the ancestral protocerebral limb pair into the labrum, following the postero-ventral migration of the mouth opening. Stem-group onychophorans demonstrate an independent ventral migration of the mouth and development of a multisegmented head, as well as the differentiation of the deutocerebral limbs as expressed in extant representatives. The anterior organization of crown-group Tardigrada retains several ancestral features, such as an anterior-facing mouth and one-segmented head. The proposed model aims to clarify contentious issues on the evolution of the panarthropod head, and lays the foundation from which to further address this complex subject in the future.
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Affiliation(s)
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala SE-752 36, Sweden
| | - Graham E Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala SE-752 36, Sweden
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44
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Janssen R. A molecular view of onychophoran segmentation. ARTHROPOD STRUCTURE & DEVELOPMENT 2017; 46:341-353. [PMID: 27725255 DOI: 10.1016/j.asd.2016.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/22/2016] [Accepted: 10/03/2016] [Indexed: 06/06/2023]
Abstract
This paper summarizes our current knowledge on the expression and assumed function of Drosophila and (other) arthropod segmentation gene orthologs in Onychophora, a closely related outgroup to Arthropoda. This includes orthologs of the so-called Drosophila segmentation gene cascade including the Hox genes, as well as other genetic factors and pathways involved in non-drosophilid arthropods. Open questions about and around the topic are addressed, such as the definition of segments in onychophorans, the unclear regulation of conserved expression patterns downstream of non-conserved factors, and the potential role of mesodermal patterning in onychophoran segmentation.
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Affiliation(s)
- Ralf Janssen
- Uppsala University, Department of Earth Sciences, Palaeobiology, Villavägen 16, 75236 Uppsala, Sweden.
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Geoghegan JL, Duchêne S, Holmes EC. Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families. PLoS Pathog 2017; 13:e1006215. [PMID: 28178344 PMCID: PMC5319820 DOI: 10.1371/journal.ppat.1006215] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/21/2017] [Accepted: 02/02/2017] [Indexed: 01/20/2023] Open
Abstract
The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families. Notably, our analysis reveals that cross-species transmission is a near universal feature of the viruses analyzed here, with virus-host co-divergence occurring less frequently and always on a subset of viruses. Despite the overall high topological incongruence among virus and host phylogenies, the Hepadnaviridae, Polyomaviridae, Poxviridae, Papillomaviridae and Adenoviridae, all of which possess double-stranded DNA genomes, exhibited more frequent co-divergence than the other virus families studied here. At the other extreme, the virus and host trees for all the RNA viruses studied here, particularly the Rhabdoviridae and the Picornaviridae, displayed high levels of topological incongruence, indicative of frequent host switching. Overall, we show that cross-species transmission plays a major role in virus evolution, with all the virus families studied here having the potential to jump host species, and that increased sampling will likely reveal more instances of host jumping.
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Affiliation(s)
- Jemma L. Geoghegan
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Sebastián Duchêne
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Centre for Systems Genomics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
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Caron JB, Aria C. Cambrian suspension-feeding lobopodians and the early radiation of panarthropods. BMC Evol Biol 2017; 17:29. [PMID: 28137244 PMCID: PMC5282736 DOI: 10.1186/s12862-016-0858-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 12/17/2016] [Indexed: 11/19/2022] Open
Abstract
Background Arthropoda, Tardigrada and Onychophora evolved from lobopodians, a paraphyletic group of disparate Palaeozoic vermiform animals with soft legs. Although the morphological diversity that this group encompasses likely illustrates the importance of niche diversification in the early radiation of panarthropods, the ecology of lobopodians remains poorly characterized. Results Here we describe a new luolishaniid taxon from the middle Cambrian Burgess Shale (Walcott Quarry) in British Columbia, Canada, whose specialized morphology epitomizes the suspension-feeding ecology of this clade, and is convergent with some modern marine animals, such as caprellid crustaceans. This species possesses two long pairs and four shorter pairs of elongate spinose lobopods at the front, each bearing two slender claws, and three pairs of stout lobopods bearing single, strong, hook-like anterior-facing claws at the back. The trunk is remarkably bare, widening rearwards, and, at the front, extends beyond the first pair of lobopods into a small “head” bearing a pair of visual organs and a short proboscis with numerous teeth. Based on a critical reappraisal of character coding in lobopodians and using Bayesian and parsimony-based tree searches, two alternative scenarios for early panarthropod evolution are retrieved. In both cases, hallucigeniids and luolishaniids are found to be extinct radiative stem group panarthropods, in contrast to previous analyses supporting a position of hallucigeniids as part of total-group Onychophora. Our Bayesian topology finds luolishaniids and hallucigeniids to form two successive clades at the base of Panarthropoda. Disparity analyses suggest that luolishaniids, hallucigeniids and total-group Onychophora each occupy a distinct region of morphospace. Conclusions Hallucigeniids and luolishaniids were comparably diverse and successful, representing two major lobopodian clades in the early Palaeozoic, and both evolved body plans adapted to different forms of suspension feeding. A Bayesian approach to cladistics supports the view that a semi-sessile, suspension-feeding lifestyle characterized the origin and rise of Panarthropoda from cycloneuralian body plans. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0858-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jean-Bernard Caron
- Department of Natural History (Palaeobiology Section), Royal Ontario Museum, Toronto, Ontario, Canada. .,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada. .,Department of Earth Sciences, University of Toronto, Toronto, Ontario, Canada.
| | - Cédric Aria
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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Candido-Ferreira IL, Kronenberger T, Sayegh RSR, Batista IDFC, da Silva Junior PI. Evidence of an Antimicrobial Peptide Signature Encrypted in HECT E3 Ubiquitin Ligases. Front Immunol 2017; 7:664. [PMID: 28119686 PMCID: PMC5220581 DOI: 10.3389/fimmu.2016.00664] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/16/2016] [Indexed: 12/11/2022] Open
Abstract
The ubiquitin-proteasome pathway (UPP) is a hallmark of the eukaryotic cell. In jawed vertebrates, it has been co-opted by the adaptive immune system, where proteasomal degradation produces endogenous peptides for major histocompatibility complex class I antigen presentation. However, proteolytic products are also necessary for the phylogenetically widespread innate immune system, as they often play a role as host defense peptides (HDPs), pivotal effectors against pathogens. Here, we report the identification of the arachnid HDP oligoventin, which shares homology to a core member of the UPP, E3 ubiquitin ligases. Oligoventin has broad antimicrobial activity and shows strong synergy with lysozymes. Using computational and phylogenetic approaches, we show high conservation of the oligoventin signature in HECT E3s. In silico simulation of HECT E3s self-proteolysis provides evidence that HDPs can be generated by fine-tuned 26S proteasomal degradation, and therefore are consistent with the hypothesis that oligoventin is a cryptic peptide released by the proteolytic processing of an Nedd4 E3 precursor protein. Finally, we compare the production of HDPs and endogenous antigens from orthologous HECT E3s by proteasomal degradation as a means of analyzing the UPP coupling to metazoan immunity. Our results highlight the functional plasticity of the UPP in innate and adaptive immune systems as a possibly recurrent mechanism to generate functionally diverse peptides.
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Affiliation(s)
- Ivan Lavander Candido-Ferreira
- Special Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, São Paulo, Brazil; Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Thales Kronenberger
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo , São Paulo, São Paulo , Brazil
| | - Raphael Santa Rosa Sayegh
- Special Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, São Paulo, Brazil; Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Pedro Ismael da Silva Junior
- Special Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Butantan Institute , São Paulo, São Paulo , Brazil
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Wang YH, Engel MS, Rafael JA, Wu HY, Rédei D, Xie Q, Wang G, Liu XG, Bu WJ. Fossil record of stem groups employed in evaluating the chronogram of insects (Arthropoda: Hexapoda). Sci Rep 2016; 6:38939. [PMID: 27958352 PMCID: PMC5154178 DOI: 10.1038/srep38939] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 11/16/2016] [Indexed: 11/08/2022] Open
Abstract
Insecta s. str. (=Ectognatha), comprise the largest and most diversified group of living organisms, accounting for roughly half of the biodiversity on Earth. Understanding insect relationships and the specific time intervals for their episodes of radiation and extinction are critical to any comprehensive perspective on evolutionary events. Although some deeper nodes have been resolved congruently, the complete evolution of insects has remained obscure due to the lack of direct fossil evidence. Besides, various evolutionary phases of insects and the corresponding driving forces of diversification remain to be recognized. In this study, a comprehensive sample of all insect orders was used to reconstruct their phylogenetic relationships and estimate deep divergences. The phylogenetic relationships of insect orders were congruently recovered by Bayesian inference and maximum likelihood analyses. A complete timescale of divergences based on an uncorrelated log-normal relaxed clock model was established among all lineages of winged insects. The inferred timescale for various nodes are congruent with major historical events including the increase of atmospheric oxygen in the Late Silurian and earliest Devonian, the radiation of vascular plants in the Devonian, and with the available fossil record of the stem groups to various insect lineages in the Devonian and Carboniferous.
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Affiliation(s)
- Yan-hui Wang
- College of Computer and Control Engineering, Nankai University, 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin 300350, China
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Michael S. Engel
- Division of Entomology, Natural History Museum, and Department of Ecology & Evolutionary Biology, 1501 Crestline Drive – Suite 140, University of Kansas, Lawrence, Kansas 66045, USA
| | - José A. Rafael
- Instituto Nacional de Pesquisas da Amazônia, INPA, Caixa Postal 478, 69011-970 Manaus, Amazonas, Brazil
| | - Hao-yang Wu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Dávid Rédei
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Qiang Xie
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Gang Wang
- College of Computer and Control Engineering, Nankai University, 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin 300350, China
| | - Xiao-guang Liu
- College of Computer and Control Engineering, Nankai University, 38 Tongyan Road, Haihe Education Park, Jinnan District, Tianjin 300350, China
| | - Wen-jun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, China
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Altenburger A. The neuromuscular system of Pycnophyes kielensis (Kinorhyncha: Allomalorhagida) investigated by confocal laser scanning microscopy. EvoDevo 2016; 7:25. [PMID: 27933139 PMCID: PMC5126839 DOI: 10.1186/s13227-016-0062-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/17/2016] [Indexed: 11/10/2022] Open
Abstract
Background Kinorhynchs are ecdysozoan animals with a phylogenetic position close to priapulids and loriciferans. To understand the nature of segmentation within Kinorhyncha and to infer a probable ancestry of segmentation within the last common ancestor of Ecdysozoa, the musculature and the nervous system of the allomalorhagid kinorhynch Pycnophyes kielensis were investigated by use of immunohistochemistry, confocal laser scanning microscopy, and 3D reconstruction software. Results The kinorhynch body plan comprises 11 trunk segments. Trunk musculature consists of paired ventral and dorsal longitudinal muscles in segments 1–10 as well as dorsoventral muscles in segments 1–11. Dorsal and ventral longitudinal muscles insert on apodemes of the cuticle inside the animal within each segment. Strands of longitudinal musculature extend over segment borders in segments 1–6. In segments 7–10, the trunk musculature is confined to the segments. Musculature of the digestive system comprises a strong pharyngeal bulb with attached mouth cone muscles as well as pharyngeal bulb protractors and retractors. The musculature of the digestive system shows no sign of segmentation. Judged by the size of the pharyngeal bulb protractors and retractors, the pharyngeal bulb, as well as the introvert, is moved passively by internal pressure caused by concerted action of the dorsoventral muscles. The nervous system comprises a neuropil ring anterior to the pharyngeal bulb. Associated with the neuropil ring are flask-shaped serotonergic somata extending anteriorly and posteriorly. A ventral nerve cord is connected to the neuropil ring and runs toward the anterior until an attachment point in segment 1, and from there toward the posterior with one ganglion in segment 6. Conclusions Segmentation within Kinorhyncha likely evolved from an unsegmented ancestor. This conclusion is supported by continuous trunk musculature in the anterior segments 1–6, continuous pharyngeal bulb protractors and retractors throughout the anterior segments, no sign of segmentation within the digestive system, and the absence of ganglia in most segments. The musculature shows evidence of segmentation that fit the definition of an anteroposteriorly repeated body unit only in segments 7–10. Electronic supplementary material The online version of this article (doi:10.1186/s13227-016-0062-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andreas Altenburger
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83, 1307 Copenhagen, Denmark
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50
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Chesmore KN, Watson WH, Chabot CC. Identification of putative circadian clock genes in the American horseshoe crab, Limulus polyphemus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2016; 19:45-61. [PMID: 27341138 PMCID: PMC10935561 DOI: 10.1016/j.cbd.2016.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 03/22/2016] [Accepted: 06/02/2016] [Indexed: 02/02/2023]
Abstract
While the American horseshoe crab, Limulus polyphemus, has robust circadian and circatidal rhythms, virtually nothing is known about the molecular basis of these rhythms in this species or any other chelicerate. In this study, next generation sequencing was used to assemble transcriptomic reads and then putative homologs of known core and accessory circadian genes were identified in these databases. Homologous transcripts were discovered for one circadian clock input gene, five core genes, 22 accessory genes, and two possible output pathways. Alignments and functional domain analyses showed generally high conservation between the putative L. polyphemus clock genes and homologs from Drosophila melanogaster and Daphnia pulex. The presence of both cry1 and cry2 in the L. polyphemus transcriptome would classify its system as an "ancestral", type 2 clock system. In addition, a novel duplication of CYCLE, and a novel triplication of PERIOD were found. Investigations are currently underway to determine if any of these "circadian" genes also participate in the molecular processes that drive the Limulus circatidal clock.
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Affiliation(s)
- Kevin N Chesmore
- Department of Genetics, Dartmouth, College Hanover, NH 03755, USA.
| | - Winsor H Watson
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Christopher C Chabot
- Department of Biological Sciences, MSC#64, Plymouth State University, Plymouth, NH 03264, USA
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