Sterol and Genomic Analyses Validate the Sponge Biomarker Hypothesis
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Appendix: Some Important Early Collections of West Indian Type Specimens, with Historical Notes
Appendix: Some important early collections of West Indian type specimens, with historical notes Duchassaing & Michelotti, 1864 between 1841 and 1864, we gain additional information concerning the sponge memoir, starting with the letter dated 8 May 1855. Jacob Gysbert Samuel van Breda A biography of Placide Duchassaing de Fonbressin was (1788-1867) was professor of botany in Franeker (Hol published by his friend Sagot (1873). Although an aristo land), of botany and zoology in Gent (Belgium), and crat by birth, as we learn from Michelotti's last extant then of zoology and geology in Leyden. Later he went to letter to van Breda, Duchassaing did not add de Fon Haarlem, where he was secretary of the Hollandsche bressin to his name until 1864. Duchassaing was born Maatschappij der Wetenschappen, curator of its cabinet around 1819 on Guadeloupe, in a French-Creole family of natural history, and director of Teyler's Museum of of planters. He was sent to school in Paris, first to the minerals, fossils and physical instruments. Van Breda Lycee Louis-le-Grand, then to University. He finished traveled extensively in Europe collecting fossils, especial his studies in 1844 with a doctorate in medicine and two ly in Italy. Michelotti exchanged collections of fossils additional theses in geology and zoology. He then settled with him over a long period of time, and was received as on Guadeloupe as physician. Because of social unrest foreign member of the Hollandsche Maatschappij der after the freeing of native labor, he left Guadeloupe W etenschappen in 1842. The two chief papers of Miche around 1848, and visited several islands of the Antilles lotti on fossils were published by the Hollandsche Maat (notably Nevis, Sint Eustatius, St. -
Proposal for a Revised Classification of the Demospongiae (Porifera) Christine Morrow1 and Paco Cárdenas2,3*
Morrow and Cárdenas Frontiers in Zoology (2015) 12:7 DOI 10.1186/s12983-015-0099-8 DEBATE Open Access Proposal for a revised classification of the Demospongiae (Porifera) Christine Morrow1 and Paco Cárdenas2,3* Abstract Background: Demospongiae is the largest sponge class including 81% of all living sponges with nearly 7,000 species worldwide. Systema Porifera (2002) was the result of a large international collaboration to update the Demospongiae higher taxa classification, essentially based on morphological data. Since then, an increasing number of molecular phylogenetic studies have considerably shaken this taxonomic framework, with numerous polyphyletic groups revealed or confirmed and new clades discovered. And yet, despite a few taxonomical changes, the overall framework of the Systema Porifera classification still stands and is used as it is by the scientific community. This has led to a widening phylogeny/classification gap which creates biases and inconsistencies for the many end-users of this classification and ultimately impedes our understanding of today’s marine ecosystems and evolutionary processes. In an attempt to bridge this phylogeny/classification gap, we propose to officially revise the higher taxa Demospongiae classification. Discussion: We propose a revision of the Demospongiae higher taxa classification, essentially based on molecular data of the last ten years. We recommend the use of three subclasses: Verongimorpha, Keratosa and Heteroscleromorpha. We retain seven (Agelasida, Chondrosiida, Dendroceratida, Dictyoceratida, Haplosclerida, Poecilosclerida, Verongiida) of the 13 orders from Systema Porifera. We recommend the abandonment of five order names (Hadromerida, Halichondrida, Halisarcida, lithistids, Verticillitida) and resurrect or upgrade six order names (Axinellida, Merliida, Spongillida, Sphaerocladina, Suberitida, Tetractinellida). Finally, we create seven new orders (Bubarida, Desmacellida, Polymastiida, Scopalinida, Clionaida, Tethyida, Trachycladida). -
Transcriptome Sequencing, Characterization and Overview of the Gene Expression Along Three Life Cycle Stages
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC Molecular Ecology Resources (2013) doi: 10.1111/1755-0998.12085 A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages A. R. PEREZ-PORRO,*† D. NAVARRO-GOMEZ,† M. J. URIZ* and G. GIRIBET† *Center for Advanced Studies of Blanes (CEAB-CSIC), c/Acces a la Cala St. Francesc 14, Girona, Blanes 17300, Spain, †Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA Abstract Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing tech- nologies–such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. -
Ereskovsky Et 2018 Bulgarie.Pd
Sponge community of the western Black Sea shallow water caves: diversity and spatial distribution Alexander Ereskovsky, Oleg Kovtun, Konstantin Pronin, Apostol Apostolov, Dirk Erpenbeck, Viatcheslav Ivanenko To cite this version: Alexander Ereskovsky, Oleg Kovtun, Konstantin Pronin, Apostol Apostolov, Dirk Erpenbeck, et al.. Sponge community of the western Black Sea shallow water caves: diversity and spatial distribution. PeerJ, PeerJ, 2018, 6, pp.e4596. 10.7717/peerj.4596. hal-01789010 HAL Id: hal-01789010 https://hal.archives-ouvertes.fr/hal-01789010 Submitted on 14 May 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Sponge community of the western Black Sea shallow water caves: diversity and spatial distribution Alexander Ereskovsky1,2, Oleg A. Kovtun3, Konstantin K. Pronin4, Apostol Apostolov5, Dirk Erpenbeck6 and Viatcheslav Ivanenko7 1 Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale (IMBE), Aix Marseille University, CNRS, IRD, Avignon Université, Marseille, France 2 Department of Embryology, Faculty of Biology, -
Računalna Analiza Dugih Nekodirajućih RNA Ogulinske Špiljske Spužvice (Eunapius Subterraneus)
Računalna analiza dugih nekodirajućih RNA ogulinske špiljske spužvice (Eunapius subterraneus) Bodulić, Kristian Master's thesis / Diplomski rad 2020 Degree Grantor / Ustanova koja je dodijelila akademski / stručni stupanj: University of Zagreb, Faculty of Science / Sveučilište u Zagrebu, Prirodoslovno-matematički fakultet Permanent link / Trajna poveznica: https://urn.nsk.hr/urn:nbn:hr:217:310016 Rights / Prava: In copyright Download date / Datum preuzimanja: 2021-10-04 Repository / Repozitorij: Repository of Faculty of Science - University of Zagreb Sveučilište u Zagrebu Prirodoslovno-matematički fakultet Biološki odsjek Kristian Bodulić Računalna analiza dugih nekodirajućih RNA ogulinske špiljske spužvice (Eunapius subterraneus) Diplomski rad Zagreb, 2020. Ovaj rad izrađen je u Grupi za bioinformatiku na Zavodu za molekularnu biologiju Prirodoslovno-matematičkog fakulteta Sveučilišta u Zagrebu pod vodstvom prof. dr. sc. Kristiana Vlahovičeka. Rad je predan na ocjenu Biološkom odsjeku Prirodoslovno- matematičkog fakulteta Sveučilišta u Zagrebu radi stjecanja zvanja magistar molekularne biologije. Zahvaljujem mentoru prof. dr. sc. Kristianu Vlahovičeku na stručnom vodstvu te pruženim savjetima, znanju i vremenu. Zahvaljujem Grupi za bioinformatiku na stečenom znanju i iskustvu te ugodnim trenutcima provedenim u uredu u posljednje dvije godine. Posebno zahvaljujem obitelji i prijateljima na velikoj podršci. TEMELJNA DOKUMENTACIJSKA KARTICA Sveučilište u Zagrebu Prirodoslovno-matematički fakultet Biološki odsjek Diplomski rad RAČUNALNA ANALIZA DUGIH NEKODIRAJUĆIH RNA OGULINSKE ŠPILJSKE SPUŽVICE (EUNAPIUS SUBTERRANEUS) Kristian Bodulić Rooseveltov trg 6, 10000 Zagreb. Hrvatska Pojavom metoda sekvenciranja druge generacije, duge nekodirajuće RNA postale su vrlo zanimljiv predmet bioloških istraživanja. Njihove uloge dokazane su u velikom broju bioloških procesa, od kojih je najvažnije spomenuti regulaciju ekspresije brojnih gena. Ipak, ova skupina RNA još uvijek nije istražena u brojnim koljenima životinja, uključujući i spužve. -
(Familia: Halichondriidae) Para Un Sistema Lagunar Del Golfo De México Revista Ciencias Marinas Y Costeras, Vol
Revista Ciencias Marinas y Costeras ISSN: 1659-455X ISSN: 1659-407X Universidad Nacional, Costa Rica de la Cruz-Francisco, Vicencio; Rodríguez Muñoz, Salvador; León Méndez, Ramses Giovanni; Duran López, Aarón; Argüelles-Jiménez, Jimmy Primer registro de Amorphinopsis atlantica Carvalho, Hadju, Mothes & van Soest, 2004 (Familia: Halichondriidae) para un sistema lagunar del golfo de México Revista Ciencias Marinas y Costeras, vol. 11, núm. 1, 2019, -Junio, pp. 61-70 Universidad Nacional, Costa Rica DOI: https://doi.org/10.15359/revmar.11-1.5 Disponible en: https://www.redalyc.org/articulo.oa?id=633766165005 Cómo citar el artículo Número completo Sistema de Información Científica Redalyc Más información del artículo Red de Revistas Científicas de América Latina y el Caribe, España y Portugal Página de la revista en redalyc.org Proyecto académico sin fines de lucro, desarrollado bajo la iniciativa de acceso abierto Primer registro de Amorphinopsis atlantica Carvalho, Hadju, Mothes & van Soest, 2004 (Familia: Halichondriidae) para un sistema lagunar del golfo de México First record of Amorphinopsis atlantica Carvalho, Hadju, Mothes & van Soest, 2004 (Family: Halichondriidae) for a lagoon system in the Gulf of Mexico Vicencio de la Cruz-Francisco1*, Jimmy Argüelles-Jiménez2, Salvador Rodríguez Muñoz1, Ramses Giovanni León Méndez1 y Aarón Duran López1 RESUMEN Se registra por primera vez la presencia de Amorphinopsis atlantica en un sistema lagunar del golfo de México. Esta esponja fue reportada en Brasil donde prefiere asentarse sobre costas rocosas y en estuarios. Las observaciones y recolecta de especímenes provienen de la laguna de Tampamachoco, ubicada al norte de Veracruz, México. Los ejemplares registrados se contemplaron como epibiontes en bancos ostrícolas de Isognomon alatus, donde destacaron por su coloración amarilla, y su forma incrustante ahí masiva con ramificaciones prolongadas. -
Studio Dei Fattori Di Crescita Coinvolti Nello Sviluppo Tissutale E Nella
Università degli Studi di Genova Dipartimento di Scienze della terra, dell’ambiente e della vita (DISTAV) Dottorato in: SCIENZE E TECNOLOGIE PER L’AMBIENTE E IL TERRITORIO (STAT) Curriculum: SCIENZE DEL MARE XXXI CICLO Dottorando: Dott. Gallus Lorenzo ssa Tutore: Prof. Scarfì Sonia Studio dei fattori di crescita coinvolti nello sviluppo tissutale e nella deposizione di matrice extracellulare del porifero Chondrosia reniformis (Nardo, 1847) con metodi immunoistochimici e di biologia molecolare. 1 “ […] alcuni animali sono stazionari e alcuni sono erratici. Gli animali stazionari si trovano nell'acqua, ma nessuna di queste creature si trova sulla terraferma. Nell'acqua ci sono molte creature che vivono in stretta adesione ad un oggetto esterno, come nel caso di diversi tipi di ostriche. E, a proposito, la spugna sembra essere dotata di una certa sensibilità: come prova di ciò si riporta che la difficoltà nel distaccarla dai suoi ormeggi aumenta se il movimento per distaccarla non viene applicato di nascosto.” (Immagine 1) Aristotele, Historia Animalium. The works of Aristotle, by Aristotle; Ross, W. D. (William David), 1877-; Smith, J. A. (John Alexander), 1863-1939. 1910-1931. Publisher Oxford : Clarendon Press Contributions to Zoology, 76 (2) 103-120 (2007) Marine invertebrate diversity in Aristotle’s zoology Eleni Voultsiadou, Dimitris Vafidis. (Immagine 1) Costantinopoli, aristotele, historia animalium e altri scritti, xii sec., pluteo 87,4.JPG https://creativecommons.org/licenses/by/3.0/legalcode https://commons.wikimedia.org/wiki/User:Sailko 2 “Nel 1847, (Giandomenico Nardo) lesse al nostro Istituto (Istituto Veneto di Scienze Lettere ed Arti, ndr), nell’adunanza del 23 marzo, un’altra Memoria (Immagine 2) intorno ad un prodotto marino da lui raccolto per la prima volta sulle coste dell’Istria fino dal 1823, e conosciuto dai pescatori sotto il nome di Carnume de mar o di Rognone di mare. -
Horizontal Gene Transfer in the Sponge Amphimedon Queenslandica
Horizontal gene transfer in the sponge Amphimedon queenslandica Simone Summer Higgie BEnvSc (Honours) A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2018 School of Biological Sciences Abstract Horizontal gene transfer (HGT) is the nonsexual transfer of genetic sequence across species boundaries. Historically, HGT has been assumed largely irrelevant to animal evolution, though widely recognised as an important evolutionary force in bacteria. From the recent boom in whole genome sequencing, many cases have emerged strongly supporting the occurrence of HGT in a wide range of animals. However, the extent, nature and mechanisms of HGT in animals remain poorly understood. Here, I explore these uncertainties using 576 HGTs previously reported in the genome of the demosponge Amphimedon queenslandica. The HGTs derive from bacterial, plant and fungal sources, contain a broad range of domain types, and many are differentially expressed throughout development. Some domains are highly enriched; phylogenetic analyses of the two largest groups, the Aspzincin_M35 and the PNP_UDP_1 domain groups, suggest that each results from one or few transfer events followed by post-transfer duplication. Their differential expression through development, and the conservation of domains and duplicates, together suggest that many of the HGT-derived genes are functioning in A. queenslandica. The largest group consists of aspzincins, a metallopeptidase found in bacteria and fungi, but not typically in animals. I detected aspzincins in representatives of all four of the sponge classes, suggesting that the original sponge aspzincin was transferred after sponges diverged from their last common ancestor with the Eumetazoa, but before the contemporary sponge classes emerged. -
Collation and Validation of Museum Collection Databases Related to the Distribution of Marine Sponges in Northern Australia
1 COLLATION AND VALIDATION OF MUSEUM COLLECTION DATABASES RELATED TO THE DISTRIBUTION OF MARINE SPONGES IN NORTHERN AUSTRALIA. JOHN N.A. HOOPER & MERRICK EKINS 2 3 Collation and validation of museum collection databases related to the distribution of marine sponges in Northern Australia (Contract National Oceans Office C2004/020) John N.A. Hooper & Merrick Ekins Queensland Museum, PO Box 3300, South Brisbane, Queensland, 4101, Australia ([email protected], [email protected]) CONTENTS SUMMARY ......................................................................................................................... 6 1. INTRODUCTION ......................................................................................................... 10 1.1. General Introduction ..................................................................................... 10 1.2. Definitions of Australia’s marine bioregions ............................................... 12 2. MATERIALS & METHODS ....................................................................................... 16 2.1. Specimen point-data conversion ................................................................... 16 2.2. Geographic coverage and scales of analysis................................................. 18 2.3. Species distributions....................................................................................... 19 2.4. Modelled distribution datasets and historical sponge data ........................ 20 2.5. Identification of useful datasets and gaps in data, prioritised -
Transcriptome Sequencing, Characterization and Overview of the Gene Expression Along Three Life Cycle Stages
Molecular Ecology Resources (2013) doi: 10.1111/1755-0998.12085 A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages A. R. PEREZ-PORRO,*† D. NAVARRO-GOMEZ,† M. J. URIZ* and G. GIRIBET† *Center for Advanced Studies of Blanes (CEAB-CSIC), c/Acces a la Cala St. Francesc 14, Girona, Blanes 17300, Spain, †Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA Abstract Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing tech- nologies–such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. -
Molecular Phylogenies Confirm the Presence of Two Cryptic Hemimycale
Molecular phylogenies confirm the presence of two cryptic Hemimycale species in the Mediterranean and reveal the polyphyly of the genera Crella and Hemimycale (Demospongiae: Poecilosclerida) Maria J. Uriz, Leire Garate and Gemma Agell Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Blanes, Girona, Spain ABSTRACT Background: Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. Hemimycale is a sponge genus (Family Hymedesmiidae, Order Poecilosclerida) with four formally described species, from which only Hemimycale columella has been recorded in the Atlanto-Mediterranean basin, on shallow to 80 m deep bottoms. Contrasting biological features between shallow and deep individuals of Hemimycale columella suggested larger genetic differences than those expected between sponge populations. To assess whether shallow and deep populations indeed belong to different species, we performed a phylogenetic study of Hemimycale columella across the Mediterranean. We also included other Hemimycale and Crella species from the Red Sea, with the additional aim of clarifying the relationships of the genus Hemimycale. Methods: Hemimycale columella was sampled across the Mediterranean, and Adriatic Seas. Hemimycale arabica and Crella cyathophora were collected from Submitted 19 November 2016 the Red Sea and Pacific. From two to three specimens per species and locality Accepted 4 January 2017 were extracted, amplified for Cytochrome C Oxidase I (COI) (M1–M6 partition), Published 7 March 2017 18S rRNA, and 28S (D3–D5 partition) and sequenced. Sequences were aligned using Corresponding author Clustal W v.1.81. Phylogenetic trees were constructed under neighbor joining (NJ), Maria J. -
Transcriptomic Analysis of Differential Host Gene
Riesgo et al. BMC Genomics 2014, 15:376 http://www.biomedcentral.com/1471-2164/15/376 RESEARCH ARTICLE Open Access Transcriptomic analysis of differential host gene expression upon uptake of symbionts: a case study with Symbiodinium and the major bioeroding sponge Cliona varians Ana Riesgo1,2†, Kristin Peterson3,4, Crystal Richardson3,5,TylerHeist3,BrianStrehlow3,6, Mark McCauley3,7, Carlos Cotman3, Malcolm Hill3*† and April Hill3*† Abstract Background: We have a limited understanding of genomic interactions that occur among partners for many symbioses. One of the most important symbioses in tropical reef habitats involves Symbiodinium. Most work examining Symbiodinium-host interactions involves cnidarian partners. To fully and broadly understand the conditions that permit Symbiodinium to procure intracellular residency, we must explore hosts from different taxa to help uncover universal cellular and genetic strategies for invading and persisting in host cells. Here, we present data from gene expression analyses involving the bioeroding sponge Cliona varians that harbors Clade G Symbiodinium. Results: Patterns of differential gene expression from distinct symbiont states (“normal”, “reinfected”,and“aposymbiotic”) of the sponge host are presented based on two comparative approaches (transcriptome sequencing and suppressive subtractive hybridization (SSH)). Transcriptomic profiles were different when reinfected tissue was compared to normal and aposymbiotic tissue. We characterized a set of 40 genes drawn from a pool of differentially expressed