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Lin Z, Agarwal V, Cong Y, Pomponi SA, Schmidt EW. Short macrocyclic peptides in sponge genomes. Proc Natl Acad Sci U S A 2024; 121:e2314383121. [PMID: 38442178 PMCID: PMC10945851 DOI: 10.1073/pnas.2314383121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/19/2024] [Indexed: 03/07/2024] Open
Abstract
Sponges (Porifera) contain many peptide-specialized metabolites with potent biological activities and significant roles in shaping marine ecology. It is well established that symbiotic bacteria produce bioactive "sponge" peptides, both on the ribosome (RiPPs) and nonribosomally. Here, we demonstrate that sponges themselves also produce many bioactive macrocyclic peptides, such as phakellistatins and related proline-rich macrocyclic peptides (PRMPs). Using the Stylissa carteri sponge transcriptome, methods were developed to find sequences encoding 46 distinct RiPP-type core peptides, of which ten encoded previously identified PRMP sequences. With this basis set, the genome and transcriptome of the sponge Axinella corrugata was interrogated to find 35 PRMP precursor peptides encoding 31 unique core peptide sequences. At least 11 of these produced cyclic peptides that were present in the sponge and could be characterized by mass spectrometry, including stylissamides A-D and seven previously undescribed compounds. Precursor peptides were encoded in the A. corrugata genome, confirming their animal origin. The peptides contained signal peptide sequences and highly repetitive recognition sequence-core peptide elements with up to 25 PRMP copies in a single precursor. In comparison to sponges without PRMPs, PRMP sponges are incredibly enriched in potentially secreted polypeptides, with >23,000 individual signal peptide encoding genes found in a single transcriptome. The similarities between PRMP biosynthetic genes and neuropeptides in terms of their biosynthetic logic suggest a fundamental biology linked to circular peptides, possibly indicating a widespread and underappreciated diversity of signaling peptide post-translational modifications across the animal kingdom.
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Affiliation(s)
- Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA30332
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332
| | - Ying Cong
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL34946
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
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2
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Galitz A, Nakao Y, Schupp PJ, Wörheide G, Erpenbeck D. A Soft Spot for Chemistry-Current Taxonomic and Evolutionary Implications of Sponge Secondary Metabolite Distribution. Mar Drugs 2021; 19:448. [PMID: 34436287 PMCID: PMC8398655 DOI: 10.3390/md19080448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/17/2022] Open
Abstract
Marine sponges are the most prolific marine sources for discovery of novel bioactive compounds. Sponge secondary metabolites are sought-after for their potential in pharmaceutical applications, and in the past, they were also used as taxonomic markers alongside the difficult and homoplasy-prone sponge morphology for species delineation (chemotaxonomy). The understanding of phylogenetic distribution and distinctiveness of metabolites to sponge lineages is pivotal to reveal pathways and evolution of compound production in sponges. This benefits the discovery rate and yield of bioprospecting for novel marine natural products by identifying lineages with high potential of being new sources of valuable sponge compounds. In this review, we summarize the current biochemical data on sponges and compare the metabolite distribution against a sponge phylogeny. We assess compound specificity to lineages, potential convergences, and suitability as diagnostic phylogenetic markers. Our study finds compound distribution corroborating current (molecular) phylogenetic hypotheses, which include yet unaccepted polyphyly of several demosponge orders and families. Likewise, several compounds and compound groups display a high degree of lineage specificity, which suggests homologous biosynthetic pathways among their taxa, which identifies yet unstudied species of this lineage as promising bioprospecting targets.
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Affiliation(s)
- Adrian Galitz
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany; (A.G.); (G.W.)
| | - Yoichi Nakao
- Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan;
| | - Peter J. Schupp
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl-von-Ossietzky University Oldenburg, 26111 Wilhelmshaven, Germany;
- Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg (HIFMB), 26129 Oldenburg, Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany; (A.G.); (G.W.)
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
- SNSB-Bavarian State Collection of Palaeontology and Geology, 80333 Munich, Germany
| | - Dirk Erpenbeck
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany; (A.G.); (G.W.)
- GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
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3
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Hardoim CCP, Ramaglia ACM, Lôbo-Hajdu G, Custódio MR. Community composition and functional prediction of prokaryotes associated with sympatric sponge species of southwestern Atlantic coast. Sci Rep 2021; 11:9576. [PMID: 33953214 PMCID: PMC8100286 DOI: 10.1038/s41598-021-88288-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 04/07/2021] [Indexed: 02/03/2023] Open
Abstract
Prokaryotes contribute to the health of marine sponges. However, there is lack of data on the assembly rules of sponge-associated prokaryotic communities, especially for those inhabiting biodiversity hotspots, such as ecoregions between tropical and warm temperate southwestern Atlantic waters. The sympatric species Aplysina caissara, Axinella corrugata, and Dragmacidon reticulatum were collected along with environmental samples from the north coast of São Paulo (Brazil). Overall, 64 prokaryotic phyla were detected; 51 were associated with sponge species, and the dominant were Proteobacteria, Bacteria (unclassified), Cyanobacteria, Crenarchaeota, and Chloroflexi. Around 64% and 89% of the unclassified operational taxonomical units (OTUs) associated with Brazilian sponge species showed a sequence similarity below 97%, with sequences in the Silva and NCBI Type Strain databases, respectively, indicating the presence of a large number of unidentified taxa. The prokaryotic communities were species-specific, ranging 56%-80% of the OTUs and distinct from the environmental samples. Fifty-four lineages were responsible for the differences detected among the categories. Functional prediction demonstrated that Ap. caissara was enriched for energy metabolism and biosynthesis of secondary metabolites, whereas D. reticulatum was enhanced for metabolism of terpenoids and polyketides, as well as xenobiotics' biodegradation and metabolism. This survey revealed a high level of novelty associated with Brazilian sponge species and that distinct members responsible from the differences among Brazilian sponge species could be correlated to the predicted functions.
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Affiliation(s)
- C C P Hardoim
- Institute of Biosciences, São Paulo State University, Coastal Campus of São Vicente, São Paulo, Brazil.
| | - A C M Ramaglia
- Institute of Biosciences, São Paulo State University, Coastal Campus of São Vicente, São Paulo, Brazil
| | - G Lôbo-Hajdu
- Department of Genetic, Biology Institute Roberto Alcântara Gomes, Rio de Janeiro State University, Rio de Janeiro, Brazil
| | - M R Custódio
- Department of Physiology, Center for Marine Biology, Biosciences Institute and NP-Biomar, São Paulo University, São Paulo, Brazil
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4
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Das S, Patel B. Marine resources and animals in modern biotechnology. Anim Biotechnol 2020. [DOI: 10.1016/b978-0-12-811710-1.00027-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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5
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Santodomingo N, Becking LE. Unravelling the moons: review of the genera Paratetilla and Cinachyrella in the Indo-Pacific (Demospongiae, Tetractinellida, Tetillidae). Zookeys 2018. [DOI: 10.3897/zookeys.786.27546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Paratetillabacca(Selenka, 1867) andCinachyrellaaustraliensis(Carter, 1886) occur in a broad range of marine environments and are allegedly widely distributed species in the Indo-Pacific. We coin the term ‘moon sponges’ for these species as they are spherical in shape with numerous porocalices resembling the lunar surface. Both species have a complex taxonomic history with high synonymization, in particular by Burton (1934, 1959). An examination of the junior synonyms proposed by Burton (1934, 1959) was conducted to establish the validity of the names. More than 230 specimens from Naturalis Biodiversity Center were reviewed that belong to the generaParatetillaandCinachyrellafrom marine lakes, coral reefs, and mangroves in Indonesia. The aim of the current study was to untangle the taxonomic history, describe the collection of moon sponges from Indonesia, and develop a key. We extensively reviewed the taxonomic literature as well as holotypes of most of the species synonymized by Burton. The taxonomic history ofParatetillaspp. andCinachyrellaaustraliensisshowed some cases of misinterpreted synonyms, misidentifications, and lack of detailed descriptions for some species. The conclusion of the revision is that there are three valid species ofParatetilla(P.arcifera,P.bacca, andP.corrugata) and four valid species ofCinachyrella(C.australiensis,C.porosa,C.paterifera, andC.schulzei) in Indonesia. This is furthermore corroborated by molecular work from previous studies.ParatetillaarciferaWilson 1925 andC.porosa(Lendenfeld, 1888) are resurrected. A full review of taxonomic history is provided as well as a key for identification of moon sponges from Indonesia. All species are sympatric and we expect that there are undescribed species remaining within the Tetillidae from the Indo-Pacific. Our current review provides the framework from which to describe new species in the generaParatetillaandCinachyrellafrom the Indo-Pacific.
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6
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Santodomingo N, Becking LE. Unravelling the moons: review of the genera Paratetilla and Cinachyrella in the Indo-Pacific (Demospongiae, Tetractinellida, Tetillidae). Zookeys 2018:1-46. [PMID: 30386152 PMCID: PMC6209763 DOI: 10.3897/zookeys.791.27546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/20/2018] [Indexed: 01/19/2023] Open
Abstract
Paratetillabacca (Selenka, 1867) and Cinachyrellaaustraliensis (Carter, 1886) occur in a broad range of marine environments and are allegedly widely distributed species in the Indo-Pacific. We coin the term ‘moon sponges’ for these species as they are spherical in shape with numerous porocalices resembling the lunar surface. Both species have a complex taxonomic history with high synonymization, in particular by Burton (1934, 1959). An examination of the junior synonyms proposed by Burton (1934, 1959) was conducted to establish the validity of the names. More than 230 specimens from Naturalis Biodiversity Center were reviewed that belong to the genera Paratetilla and Cinachyrella from marine lakes, coral reefs, and mangroves in Indonesia. The aim of the current study was to untangle the taxonomic history, describe the collection of moon sponges from Indonesia, and develop a key. We extensively reviewed the taxonomic literature as well as holotypes of most of the species synonymized by Burton. The taxonomic history of Paratetilla spp. and Cinachyrellaaustraliensis showed some cases of misinterpreted synonyms, misidentifications, and lack of detailed descriptions for some species. The conclusion of the revision is that there are three valid species of Paratetilla (P.arcifera, P.bacca, and P.corrugata) and four valid species of Cinachyrella (C.australiensis, C.porosa, C.paterifera, and C.schulzei) in Indonesia. This is furthermore corroborated by molecular work from previous studies. ParatetillaarciferaWilson 1925 and C.porosa (Lendenfeld, 1888) are resurrected. A full review of taxonomic history is provided as well as a key for identification of moon sponges from Indonesia. All species are sympatric and we expect that there are undescribed species remaining within the Tetillidae from the Indo-Pacific. Our current review provides the framework from which to describe new species in the genera Paratetilla and Cinachyrella from the Indo-Pacific.
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Affiliation(s)
- Nadiezhda Santodomingo
- Department of Life Sciences, The Natural History Museum, Cromwell Road, SW7 5BD London, UK The Natural History Museum London United Kingdom.,Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands Wageningen University Wageningen Netherlands
| | - Leontine E Becking
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands Wageningen University Wageningen Netherlands.,Marine Animal Ecology, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands Naturalis Biodiversity Center Leiden Netherlands.,Wageningen Marine Research, Ankerpark 27, Den Helder, The Netherlands Wageningen Marine Research Den Helder Netherlands
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7
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Shaffer MR, Davy SK, Bell JJ. Hidden diversity in the genus Tethya: comparing molecular and morphological techniques for species identification. Heredity (Edinb) 2018; 122:354-369. [PMID: 30131516 DOI: 10.1038/s41437-018-0134-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/25/2018] [Accepted: 07/29/2018] [Indexed: 11/09/2022] Open
Abstract
Correctly determining species' identity is critical for estimating biodiversity and effectively managing marine populations, but is difficult for species that have few morphological traits or are highly plastic. Sponges are considered a taxonomically difficult group because they lack multiple consistent diagnostic features, which coupled with their common phenotypic plasticity, makes the presence of species complexes likely, but difficult to detect. Here, we investigated the evolutionary relationship of Tethya spp. in central New Zealand using both molecular and morphological techniques to highlight the potential for cryptic speciation in sponges. Phylogenetic reconstructions based on two mitochondrial markers (rnl, COI-ext) and one nuclear marker (18S) revealed three genetic clades, with one clade representing Tethya bergquistae and two clades belonging to what was a priori thought to be a single species, Tethya burtoni. Eleven microsatellite markers were also used to further resolve the T. burtoni group, revealing a division consistent with the 18S and rnl data. Morphological analysis based on spicule characteristics allowed T. bergquistae to be distinguished from T. burtoni, but revealed no apparent differences between the T. burtoni clades. Here, we highlight hidden genetic diversity within T. burtoni, likely representing a group consisting of incipient species that have undergone speciation but have yet to express clear morphological differences. Our study supports the notion that cryptic speciation in sponges may go undetected and diversity underestimated when using only morphology-based taxonomy, which has broad scale implications for conservation and management of marine systems.
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Affiliation(s)
- Megan R Shaffer
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand.
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
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8
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da Silva-Júnior R, Paiva TDS. Evaluating the role of morphological characters in the phylogeny of some trypanosomatid genera (Excavata, Kinetoplastea, Trypanosomatida). Cladistics 2017; 34:167-180. [DOI: 10.1111/cla.12199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2017] [Indexed: 11/29/2022] Open
Affiliation(s)
- Renato da Silva-Júnior
- Laboratório Interdisciplinar de Vigilância Entomológica em Diptera e Hemiptera; FIOCRUZ; Instituto Oswaldo Cruz; 21040-900 Rio de Janeiro RJ Brazil
- Programa de Pós-graduação em Ciências e Biotecnologia; Universidade Federal Fluminense; Niterói RJ Brazil
| | - Thiago da Silva Paiva
- Laboratory of Evolutionary Protistology; Instituto de Biociências; Universidade de São Paulo; 05508-090 São Paulo SP Brazil
- Laboratório de Biologia Molecular “Francisco Mauro Salzano”; Instituto de Ciências Biológicas; Universidade Federal do Pará; 66075-110 Belém PA Brazil
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9
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Yang Q, Franco CMM, Sorokin SJ, Zhang W. Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations. Sci Rep 2017; 7:41422. [PMID: 28150727 PMCID: PMC5288722 DOI: 10.1038/srep41422] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/19/2016] [Indexed: 01/29/2023] Open
Abstract
For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3-D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity. The reliability of SIP was validated by phylogenetic analysis. The 28S rRNA gene and COI mtDNA performed better than the ITS region in classifying sponges at various taxonomic levels. A major limitation is that the databases are not well populated and possess low diversity, making it difficult to conduct the molecular identification protocol. The identification is also impacted by the accuracy of the morphological classification of the sponges whose sequences have been submitted to the database. Re-examination of the morphological identification further demonstrated and improved the reliability of sponge identification by SIP. Integrated with morphological identification, the multilocus-based SIP offers an improved protocol for more reliable and effective sponge identification, by coupling the accuracy of different DNA markers.
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Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia
| | - Shirley J Sorokin
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia.,SARDI Aquatic Sciences, 2 Hamra Ave, West Beach, SA 5024, Australia
| | - Wei Zhang
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Centre for Marine Drugs, Renji Hospital, Shanghai Jiaotong University, Shanghai, 200240, China
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10
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Das S. Biotechnological Exploitation of Marine Animals. Anim Biotechnol 2014. [DOI: 10.1016/b978-0-12-416002-6.00029-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Haber M, Ilan M. Diversity and antibacterial activity of bacteria cultured from Mediterranean Axinella
spp. sponges. J Appl Microbiol 2013; 116:519-32. [DOI: 10.1111/jam.12401] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/23/2013] [Accepted: 11/15/2013] [Indexed: 12/01/2022]
Affiliation(s)
- M. Haber
- Department of Zoology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Tel Aviv Israel
| | - M. Ilan
- Department of Zoology; George S. Wise Faculty of Life Sciences; Tel Aviv University; Tel Aviv Israel
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12
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Redmond NE, Morrow CC, Thacker RW, Diaz MC, Boury-Esnault N, Cardenas P, Hajdu E, Lobo-Hajdu G, Picton BE, Pomponi SA, Kayal E, Collins AG. Phylogeny and Systematics of Demospongiae in Light of New Small-Subunit Ribosomal DNA (18S) Sequences. Integr Comp Biol 2013; 53:388-415. [DOI: 10.1093/icb/ict078] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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13
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Gazave E, Lavrov DV, Cabrol J, Renard E, Rocher C, Vacelet J, Adamska M, Borchiellini C, Ereskovsky AV. Systematics and molecular phylogeny of the family oscarellidae (homoscleromorpha) with description of two new oscarella species. PLoS One 2013; 8:e63976. [PMID: 23737959 PMCID: PMC3667853 DOI: 10.1371/journal.pone.0063976] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 04/06/2013] [Indexed: 11/19/2022] Open
Abstract
The family Oscarellidae is one of the two families in the class Homoscleromorpha (phylum Porifera) and is characterized by the absence of a skeleton and the presence of a specific mitochondrial gene, tatC. This family currently encompasses sponges in two genera: Oscarella with 17 described species and Pseudocorticium with one described species. Although sponges in this group are relatively well-studied, phylogenetic relationships among members of Oscarellidae and the validity of genus Pseudocorticium remain open questions. Here we present a phylogenetic analysis of Oscarellidae using four markers (18S rDNA, 28S rDNA, atp6, tatC), and argue that it should become a mono-generic family, with Pseudocorticium being synonymized with Oscarella, and with the transfer of Pseudocorticium jarrei to Oscarella jarrei. We show that the genus Oscarella can be subdivided into four clades, each of which is supported by either a small number of morphological characters or by molecular synapomorphies. In addition, we describe two new species of Oscarella from Norwegian fjords: O. bergenensis sp. nov. and O. nicolae sp. nov., and we compare their morphology, anatomy, and cytology with other species in this genus. Internal anatomical characters are similar in both species, but details of external morphology and particularly of cytological characters provide diagnostic features. Our study also confirms that O. lobularis and O. tuberculata are two distinct polychromic sibling species. This study highlights the difficulties of species identification in skeleton-less sponges and, more generally, in groups where morphological characters are scarce. Adopting a multi-marker approach is thus highly suitable for these groups.
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Affiliation(s)
- Eve Gazave
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
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14
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Itskovich V, Kaluzhnaya O, Ostrovsky I, McCormack G. The number of endemic species of freshwater sponges (Malawispongiidae; Spongillina; Porifera) from Lake Kinneret is overestimated. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Valeria Itskovich
- Limnological Institute of the Siberian Branch of The Russian Academy of Sciences; Irkutsk Russia
| | - Oxana Kaluzhnaya
- Limnological Institute of the Siberian Branch of The Russian Academy of Sciences; Irkutsk Russia
| | - Ilia Ostrovsky
- Israel Oceanographic and Limnological Research; Kinneret Limnological Laboratory; Migdal Israel
| | - Grace McCormack
- Zoology Department; Molecular Evolution and Systematics Laboratory; Ryan Institute; School of Natural Sciences; National University of Ireland; Galway Ireland
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15
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Hill MS, Hill AL, Lopez J, Peterson KJ, Pomponi S, Diaz MC, Thacker RW, Adamska M, Boury-Esnault N, Cárdenas P, Chaves-Fonnegra A, Danka E, De Laine BO, Formica D, Hajdu E, Lobo-Hajdu G, Klontz S, Morrow CC, Patel J, Picton B, Pisani D, Pohlmann D, Redmond NE, Reed J, Richey S, Riesgo A, Rubin E, Russell Z, Rützler K, Sperling EA, di Stefano M, Tarver JE, Collins AG. Reconstruction of family-level phylogenetic relationships within Demospongiae (Porifera) using nuclear encoded housekeeping genes. PLoS One 2013; 8:e50437. [PMID: 23372644 PMCID: PMC3553142 DOI: 10.1371/journal.pone.0050437] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 10/22/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. METHODOLOGY/PRINCIPAL FINDINGS We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosa(p), Myxospongiae(p), Spongillida(p), Haploscleromorpha(p) (the marine haplosclerids) and Democlavia(p). We found conflicting results concerning the relationships of Keratosa(p) and Myxospongiae(p) to the remaining demosponges, but our results strongly supported a clade of Haploscleromorpha(p)+Spongillida(p)+Democlavia(p). In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillida(p)) are sister to Haploscleromorpha(p) rather than part of Democlavia(p). Within Keratosa(p), we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiae(p), Chondrosida and Verongida were monophyletic. A well-supported clade within Democlavia(p), Tetractinellida(p), composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlavia(p). Within Tetractinellida(p), we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. CONCLUSIONS/SIGNIFICANCE These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets.
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Affiliation(s)
- Malcolm S. Hill
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - April L. Hill
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - Jose Lopez
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Shirley Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Maria C. Diaz
- Museo Marino de Margarita, Boulevard de Boca Del Rio, Boca del Rio, Nueva Esparta, Venezuela
| | - Robert W. Thacker
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Maja Adamska
- Sars International Centre for Marine Molecular Biology, Thormøhlensgt, Bergen, Norway
| | - Nicole Boury-Esnault
- IMBE-UMR7263 CNRS, Université d'Aix-Marseille, Station marine d'Endoume, Marseille, France
| | - Paco Cárdenas
- Department of Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Andia Chaves-Fonnegra
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
| | - Elizabeth Danka
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - Bre-Onna De Laine
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - Dawn Formica
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
| | - Eduardo Hajdu
- Departamento de Invertebrados, Museu Nacional/Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gisele Lobo-Hajdu
- Departamento de Genética, IBRAG, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sarah Klontz
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Christine C. Morrow
- School of Biological Sciences, MBC, Queen's University, Belfast, United Kingdom
| | - Jignasa Patel
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
| | - Bernard Picton
- National Museums Northern Ireland, Holywood, Northern Ireland, United Kingdom
| | - Davide Pisani
- School of Earth Sciences and School of Biological Sciences, The University of Bristol, Bristol, United Kingdom
| | - Deborah Pohlmann
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - Niamh E. Redmond
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - John Reed
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, Florida, United States of America
| | - Stacy Richey
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - Ana Riesgo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Ewelina Rubin
- Nova Southeastern University Oceanographic Center, Dania Beach, Florida, United States of America
| | - Zach Russell
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - Klaus Rützler
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
| | - Erik A. Sperling
- Harvard University, Department of Earth and Planetary Science, Cambridge, Massachusetts, United States of America
| | - Michael di Stefano
- Gottwald Science Center, University of Richmond, Richmond, Virginia, United States of America
| | - James E. Tarver
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Allen G. Collins
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
- National Systematics Laboratory of NOAA's Fisheries Service, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
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16
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The phylogeny of halichondrid demosponges: past and present re-visited with DNA-barcoding data. ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-011-0068-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Cárdenas P, Pérez T, Boury-Esnault N. Sponge systematics facing new challenges. ADVANCES IN MARINE BIOLOGY 2012; 61:79-209. [PMID: 22560778 DOI: 10.1016/b978-0-12-387787-1.00010-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Systematics is nowadays facing new challenges with the introduction of new concepts and new techniques. Compared to most other phyla, phylogenetic relationships among sponges are still largely unresolved. In the past 10 years, the classical taxonomy has been completely overturned and a review of the state of the art appears necessary. The field of taxonomy remains a prominent discipline of sponge research and studies related to sponge systematics were in greater number in the Eighth World Sponge Conference (Girona, Spain, September 2010) than in any previous world sponge conferences. To understand the state of this rapidly growing field, this chapter proposes to review studies, mainly from the past decade, in sponge taxonomy, nomenclature and phylogeny. In a first part, we analyse the reasons of the current success of this field. In a second part, we establish the current sponge systematics theoretical framework, with the use of (1) cladistics, (2) different codes of nomenclature (PhyloCode vs. Linnaean system) and (3) integrative taxonomy. Sponges are infamous for their lack of characters. However, by listing and discussing in a third part all characters available to taxonomists, we show how diverse characters are and that new ones are being used and tested, while old ones should be revisited. We then review the systematics of the four main classes of sponges (Hexactinellida, Calcispongiae, Homoscleromorpha and Demospongiae), each time focusing on current issues and case studies. We present a review of the taxonomic changes since the publication of the Systema Porifera (2002), and point to problems a sponge taxonomist is still faced with nowadays. To conclude, we make a series of proposals for the future of sponge systematics. In the light of recent studies, we establish a series of taxonomic changes that the sponge community may be ready to accept. We also propose a series of sponge new names and definitions following the PhyloCode. The issue of phantom species (potential new species revealed by molecular studies) is raised, and we show how they could be dealt with. Finally, we present a general strategy to help us succeed in building a Porifera tree along with the corresponding revised Porifera classification.
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Affiliation(s)
- P Cárdenas
- Département Milieux et Peuplements Aquatiques, Muséum National d'Histoire Naturelle, UMR 7208 "BOrEA", Paris, France
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18
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Wörheide G, Dohrmann M, Erpenbeck D, Larroux C, Maldonado M, Voigt O, Borchiellini C, Lavrov DV. Deep phylogeny and evolution of sponges (phylum Porifera). ADVANCES IN MARINE BIOLOGY 2012; 61:1-78. [PMID: 22560777 DOI: 10.1016/b978-0-12-387787-1.00007-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Sponges (phylum Porifera) are a diverse taxon of benthic aquatic animals of great ecological, commercial, and biopharmaceutical importance. They are arguably the earliest-branching metazoan taxon, and therefore, they have great significance in the reconstruction of early metazoan evolution. Yet, the phylogeny and systematics of sponges are to some extent still unresolved, and there is an on-going debate about the exact branching pattern of their main clades and their relationships to the other non-bilaterian animals. Here, we review the current state of the deep phylogeny of sponges. Several studies have suggested that sponges are paraphyletic. However, based on recent phylogenomic analyses, we suggest that the phylum Porifera could well be monophyletic, in accordance with cladistic analyses based on morphology. This finding has many implications for the evolutionary interpretation of early animal traits and sponge development. We further review the contribution that mitochondrial genes and genomes have made to sponge phylogenetics and explore the current state of the molecular phylogenies of the four main sponge lineages (Classes), that is, Demospongiae, Hexactinellida, Calcarea, and Homoscleromorpha, in detail. While classical systematic systems are largely congruent with molecular phylogenies in the class Hexactinellida and in certain parts of Demospongiae and Homoscleromorpha, the high degree of incongruence in the class Calcarea still represents a challenge. We highlight future areas of research to fill existing gaps in our knowledge. By reviewing sponge development in an evolutionary and phylogenetic context, we support previous suggestions that sponge larvae share traits and complexity with eumetazoans and that the simple sedentary adult lifestyle of sponges probably reflects some degree of secondary simplification. In summary, while deep sponge phylogenetics has made many advances in the past years, considerable efforts are still required to achieve a comprehensive understanding of the relationships among and within the main sponge lineages to fully appreciate the evolution of this extraordinary metazoan phylum.
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Affiliation(s)
- G Wörheide
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, München, Germany.
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19
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Congruence between nuclear and mitochondrial genes in Demospongiae: A new hypothesis for relationships within the G4 clade (Porifera: Demospongiae). Mol Phylogenet Evol 2012; 62:174-90. [PMID: 22001855 DOI: 10.1016/j.ympev.2011.09.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 09/22/2011] [Accepted: 09/23/2011] [Indexed: 01/06/2023]
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20
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Lira NS, Montes RC, Tavares JF, da Silva MS, da Cunha EVL, de Athayde-Filho PF, Rodrigues LC, da Silva Dias C, Barbosa-Filho JM. Brominated compounds from marine sponges of the genus Aplysina and a compilation of their 13C NMR spectral data. Mar Drugs 2011; 9:2316-2368. [PMID: 22163189 PMCID: PMC3229238 DOI: 10.3390/md9112316] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/24/2011] [Accepted: 10/31/2011] [Indexed: 12/20/2022] Open
Abstract
Aplysina is the best representative genus of the family Aplysinidae. Halogenated substances are its main class of metabolites. These substances contribute greatly to the chemotaxonomy and characterization of the sponges belonging to this genus. Due to their pharmacological activities, these alkaloids are of special interest. The chemistry of halogenated substances and of the alkaloids has long been extensively studied in terrestrial organisms, while the number of marine organisms studied has just started to increase in the last decades. This review describes 101 halogenated substances from 14 species of Aplysina from different parts of the world. These substances can be divided into the following classes: bromotyramines (A), cavernicolins (B), hydroverongiaquinols (C), bromotyrosineketals (D), bromotyrosine lactone derivatives (E), oxazolidones (F), spiroisoxazolines (G), verongiabenzenoids (H), verongiaquinols (I), and dibromocyclohexadienes (J). A compilation of their (13)C NMR data is also part of the review. For this purpose 138 references were consulted.
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Affiliation(s)
- Narlize Silva Lira
- Laboratory of Pharmaceutical Technology, Federal University of Paraiba, Joao Pessoa 58051-900, PB, Brazil; E-Mails: (N.S.L.); (R.C.M.); (J.F.T.); (M.S.d.S.); (P.F.d.A.-F.); (L.C.R.)
| | - Ricardo Carneiro Montes
- Laboratory of Pharmaceutical Technology, Federal University of Paraiba, Joao Pessoa 58051-900, PB, Brazil; E-Mails: (N.S.L.); (R.C.M.); (J.F.T.); (M.S.d.S.); (P.F.d.A.-F.); (L.C.R.)
| | - Josean Fechine Tavares
- Laboratory of Pharmaceutical Technology, Federal University of Paraiba, Joao Pessoa 58051-900, PB, Brazil; E-Mails: (N.S.L.); (R.C.M.); (J.F.T.); (M.S.d.S.); (P.F.d.A.-F.); (L.C.R.)
| | - Marcelo Sobral da Silva
- Laboratory of Pharmaceutical Technology, Federal University of Paraiba, Joao Pessoa 58051-900, PB, Brazil; E-Mails: (N.S.L.); (R.C.M.); (J.F.T.); (M.S.d.S.); (P.F.d.A.-F.); (L.C.R.)
| | - Emidio V. L. da Cunha
- Department of Pharmacy, State University of Paraiba, Campina Grande 58100-000, PB, Brazil; E-Mail:
| | - Petronio Filgueiras de Athayde-Filho
- Laboratory of Pharmaceutical Technology, Federal University of Paraiba, Joao Pessoa 58051-900, PB, Brazil; E-Mails: (N.S.L.); (R.C.M.); (J.F.T.); (M.S.d.S.); (P.F.d.A.-F.); (L.C.R.)
| | - Luis Cezar Rodrigues
- Laboratory of Pharmaceutical Technology, Federal University of Paraiba, Joao Pessoa 58051-900, PB, Brazil; E-Mails: (N.S.L.); (R.C.M.); (J.F.T.); (M.S.d.S.); (P.F.d.A.-F.); (L.C.R.)
| | - Celidarque da Silva Dias
- Laboratory of Pharmaceutical Technology, Federal University of Paraiba, Joao Pessoa 58051-900, PB, Brazil; E-Mails: (N.S.L.); (R.C.M.); (J.F.T.); (M.S.d.S.); (P.F.d.A.-F.); (L.C.R.)
| | - Jose Maria Barbosa-Filho
- Laboratory of Pharmaceutical Technology, Federal University of Paraiba, Joao Pessoa 58051-900, PB, Brazil; E-Mails: (N.S.L.); (R.C.M.); (J.F.T.); (M.S.d.S.); (P.F.d.A.-F.); (L.C.R.)
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21
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McCormack GP, Kelly M. New indications of the phylogenetic affinity of Spongosorites suberitoides Diaz et al., 1993 (Porifera, Demospongiae) as revealed by 28S ribosomal DNA. J NAT HIST 2010. [DOI: 10.1080/00222930110040394] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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22
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Gazave E, Carteron S, Chenuil A, Richelle-Maurer E, Boury-Esnault N, Borchiellini C. Polyphyly of the genus Axinella and of the family Axinellidae (Porifera: Demospongiaep). Mol Phylogenet Evol 2010; 57:35-47. [DOI: 10.1016/j.ympev.2010.05.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 05/20/2010] [Accepted: 05/31/2010] [Indexed: 10/19/2022]
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23
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Thomas TRA, Kavlekar DP, LokaBharathi PA. Marine drugs from sponge-microbe association--a review. Mar Drugs 2010; 8:1417-68. [PMID: 20479984 PMCID: PMC2866492 DOI: 10.3390/md8041417] [Citation(s) in RCA: 245] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 04/13/2010] [Accepted: 04/19/2010] [Indexed: 12/31/2022] Open
Abstract
The subject of this review is the biodiversity of marine sponges and associated microbes which have been reported to produce therapeutically important compounds, along with the contextual information on their geographic distribution. Class Demospongiae and the orders Halichondrida, Poecilosclerida and Dictyoceratida are the richest sources of these compounds. Among the microbial associates, members of the bacterial phylum Actinobacteria and fungal division Ascomycota have been identified to be the dominant producers of therapeutics. Though the number of bacterial associates outnumber the fungal associates, the documented potential of fungi to produce clinically active compounds is currently more important than that of bacteria. Interestingly, production of a few identical compounds by entirely different host-microbial associations has been detected in both terrestrial and marine environments. In the Demospongiae, microbial association is highly specific and so to the production of compounds. Besides, persistent production of bioactive compounds has also been encountered in highly specific host-symbiont associations. Though spatial and temporal variations are known to have a marked effect on the quality and quantity of bioactive compounds, only a few studies have covered these dimensions. The need to augment production of these compounds through tissue culture and mariculture has also been stressed. The reviewed database of these compounds is available at www.niobioinformatics.in/drug.php.
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Affiliation(s)
- Tresa Remya A. Thomas
- Biological Oceanography, National Institute of Oceanography, Dona Paula, Goa, Pin-403004, India; E-Mails:
(T.R.A.T.);
(D.P.K.)
| | - Devanand P. Kavlekar
- Biological Oceanography, National Institute of Oceanography, Dona Paula, Goa, Pin-403004, India; E-Mails:
(T.R.A.T.);
(D.P.K.)
| | - Ponnapakkam A. LokaBharathi
- Biological Oceanography, National Institute of Oceanography, Dona Paula, Goa, Pin-403004, India; E-Mails:
(T.R.A.T.);
(D.P.K.)
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24
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De Bivort BL, Clouse RM, Giribet G. A morphometrics-based phylogeny of the temperate Gondwanan mite harvestmen (Opiliones, Cyphophthalmi, Pettalidae). J ZOOL SYST EVOL RES 2010. [DOI: 10.1111/j.1439-0469.2009.00562.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Large expansion segments in 18S rDNA support a new sponge clade (Class Demospongiae, Order Haplosclerida). Mol Phylogenet Evol 2008; 47:1090-9. [PMID: 18406630 DOI: 10.1016/j.ympev.2008.02.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 02/14/2008] [Accepted: 02/17/2008] [Indexed: 11/21/2022]
Abstract
Newly emerging molecular phylogenetic hypotheses involving the sponge Order Haplosclerida (Class Demospongiae) are far removed from traditional views on their classification using morphology. In the new grouping of marine haplosclerid taxa by molecular data all members of one highly supported clade were found to have three large indels in the 18S rRNA gene. These indels were not found in this gene in other marine haplosclerids or in any other demosponges analysed. These indels were found in the variable V4 and V7 region of the gene, had high GC contents and formed stable double stranded helices in the 18S rRNA secondary structure. These indels are very important synapomorphies, provide high support for an alternative taxonomic scheme and could help resolve the phylogeny of this order in conjunction with other phylogenetically informative characters.
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26
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Holmes B, Blanch H. Possible taxonomic trends in the success of primary aggregate formation in marine sponge cell cultures. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2008; 10:99-109. [PMID: 18196339 DOI: 10.1007/s10126-007-9047-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 07/31/2007] [Accepted: 08/09/2007] [Indexed: 05/25/2023]
Abstract
A large number of novel compounds with significant medical potential have been isolated from sponges, motivating efforts to develop techniques for the sustainable cultivation of sponge biomass. To date, 33 sponges from nine different orders have been examined to assess their ability to be cultured in vitro. However, little consideration has been given to the relationships between these sponges; only one report has considering the phylogenetic relationships between the species. On the basis of morphological data, no taxonomic specificity was apparent as an indicator for the successful cultivation of the sponges. As the systematic classification of the Demospongiae is poorly understood, we collated available information on the success of in vitro sponge cell cultivation reports and examined the phylogenetic relationships of these sponges through the use of 18S and 28S rDNA sequence data. Based on molecular data, the ability of sponges to form primary aggregates from the dissociated cells of marine demosponges indicates that taxonomic trends may exist, emphasizing the need to better characterize sponges being investigated for biotechnological applications.
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Affiliation(s)
- Bradley Holmes
- Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA,
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27
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Taylor MW, Radax R, Steger D, Wagner M. Sponge-associated microorganisms: evolution, ecology, and biotechnological potential. Microbiol Mol Biol Rev 2007; 71:295-347. [PMID: 17554047 PMCID: PMC1899876 DOI: 10.1128/mmbr.00040-06] [Citation(s) in RCA: 794] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine sponges often contain diverse and abundant microbial communities, including bacteria, archaea, microalgae, and fungi. In some cases, these microbial associates comprise as much as 40% of the sponge volume and can contribute significantly to host metabolism (e.g., via photosynthesis or nitrogen fixation). We review in detail the diversity of microbes associated with sponges, including extensive 16S rRNA-based phylogenetic analyses which support the previously suggested existence of a sponge-specific microbiota. These analyses provide a suitable vantage point from which to consider the potential evolutionary and ecological ramifications of these widespread, sponge-specific microorganisms. Subsequently, we examine the ecology of sponge-microbe associations, including the establishment and maintenance of these sometimes intimate partnerships, the varied nature of the interactions (ranging from mutualism to host-pathogen relationships), and the broad-scale patterns of symbiont distribution. The ecological and evolutionary importance of sponge-microbe associations is mirrored by their enormous biotechnological potential: marine sponges are among the animal kingdom's most prolific producers of bioactive metabolites, and in at least some cases, the compounds are of microbial rather than sponge origin. We review the status of this important field, outlining the various approaches (e.g., cultivation, cell separation, and metagenomics) which have been employed to access the chemical wealth of sponge-microbe associations.
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Affiliation(s)
- Michael W Taylor
- Department of Microbial Ecology, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria.
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28
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Erpenbeck D, Nichols SA, Voigt O, Dohrmann M, Degnan BM, Hooper JNA, Wörheide G. Phylogenetic Analyses Under Secondary Structure-Specific Substitution Models Outperform Traditional Approaches: Case Studies with Diploblast LSU. J Mol Evol 2007; 64:543-57. [PMID: 17460808 DOI: 10.1007/s00239-006-0146-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Accepted: 11/22/2006] [Indexed: 10/23/2022]
Abstract
Many rDNA molecular phylogenetic studies result in trees that are incongruent to either alternative gene tree reconstructions and/or morphological assumptions. One reason for this outcome might be the application of suboptimal phylogenetic substitution models. While the most commonly implemented models describe the evolution of independently evolving characters fairly well, they do not account for character dependencies such as rRNA strands that form a helix in the ribosome. Such nonindependent sites require the use of models that take into account the coevolution of the complete nucleotide pair (doublet). We analyzed 28S rDNA (LSU) demosponge phylogenies using a "doublet" model for pairing sites (rRNA-helices) and compared our findings with the results of "standard" approaches using Bayes factors. We demonstrate that paired and unpaired sites of the same gene result in different reconstructions and that usage of a doublet model leads to more reliable demosponge trees. We show the influence of more sophisticated models on phylogenetic reconstructions of early-branching metazoans and the phylogenetic relationships of demosponge orders.
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Affiliation(s)
- Dirk Erpenbeck
- Biodiversity Program, Queensland Museum, P.O. Box 3300, South Brisbane, Queensland 4101, Australia.
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29
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Erpenbeck D, Breeuwer JAJ, Parra-Velandia FJ, van Soest RWM. Speculation with spiculation?—Three independent gene fragments and biochemical characters versus morphology in demosponge higher classification. Mol Phylogenet Evol 2006; 38:293-305. [PMID: 16325431 DOI: 10.1016/j.ympev.2005.11.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2004] [Revised: 09/22/2005] [Accepted: 10/04/2005] [Indexed: 11/28/2022]
Abstract
Demosponge higher-level systematics is currently a subject of major changes due to the simplicity and paucity of complex morphological characters. Still, sponge classification is primarily based on morphological features. The systematics of the demosponge order Agelasida has been exceptionally problematic in the past. Here, we present the first molecular phylogenetic analysis based on three partially independent genes in demosponges in combination with a comprehensive search for biochemical synapomorphies to indicate their phylogenetic relationships. We show how sponges with fundamentally different skeletons can be in fact closely related and discuss examples of the misleading nature of morphological systematics in sponges.
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Affiliation(s)
- D Erpenbeck
- IBED, University of Amsterdam, P.O. Box 94766, 1090GT Amsterdam, The Netherlands.
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30
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Abstract
Systematic and evolutionary studies of Demospongiae Sollas, 1885 are a very dynamic field of research. The scientific knowledge pertaining to Demospongiae systematics has been recently assembled in the collective book Systema Porifera. However, a general consensus among spongologists has not yet been achieved regarding this group and the phylogenetic relationships within Demospongiae and between Demospongiae and other clades of Porifera and metazoans are still unresolved. The two traditional subclasses Tetractinomorpha and Ceractinomorpha are polyphyletic and it is proposed that they be abandoned. Since the publication of Systema Porifera, several works have suggested the polyphyly of Halichondrida and the paraphyly of Haplosclerida, as well as the monophyly of Tetractinellida (Astrophorida + Spirophorida), Keratosa (Dictyoceratida + Dendroceratida), and Myxospongiae (Chondrosida + Verongida + Halisarcida). Within all the classical orders, whether they are monophyletic or not, families and even genera have also been found to be polyphyletic. For example, Ancorinidae, Geodiidae, and Axinellidae are clearly polyphyletic. No single data set is able to resolve all the problems; thus, it is absolutely necessary that the classification of Demospongiae be examined from all angles and with as many data sets as possible.
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31
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Schmitt S, Hentschel U, Zea S, Dandekar T, Wolf M. ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae). J Mol Evol 2005; 60:327-36. [PMID: 15871043 DOI: 10.1007/s00239-004-0162-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2004] [Accepted: 10/01/2004] [Indexed: 10/25/2022]
Abstract
18S ribosomal DNA and internal transcribed spacer 2 (ITS-2) full-length sequences, each of which was sequenced three times, were used to construct phylogenetic trees with alignments based on secondary structures, in order to elucidate genealogical relationships within the Aplysinidae (Verongida). The first poriferan ITS-2 secondary structures are reported. Altogether 11 Aplysina sponges and 3 additional sponges (Verongula gigantea, Aiolochroia crassa, Smenospongia aurea) from tropical and subtropical oceans were analyzed. Based on these molecular studies, S. aurea, which is currently affiliated with the Dictyoceratida, should be reclassified to the Verongida. Aplysina appears as monophyletic. A soft form of Aplysina lacunosa was separated from other Aplysina and stands at a basal position in both 18S and ITS-2 trees. Based on ITS-2 sequence information, the Aplysina sponges could be distinguished into a single Caribbean-Eastern Pacific cluster and a Mediterranean cluster. The species concept for Aplysina sponges as well as a phylogenetic history with a possibly Tethyan origin is discussed.
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Affiliation(s)
- Susanne Schmitt
- Research Center for Infectious Diseases, University of Würzburg, Germany
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Erpenbeck D, Breeuwer JAJ, van Soest RWM. Identification, characterization and phylogenetic signal of an elongation factor-1 alpha fragment in demosponges (Metazoa, Porifera, Demospongiae). ZOOL SCR 2005. [DOI: 10.1111/j.1463-6409.2005.00186.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Erpenbeck D, van Soest RW. A survey for biochemical synapomorphies to reveal phylogenetic relationships of halichondrid demosponges (Metazoa: Porifera). BIOCHEM SYST ECOL 2005. [DOI: 10.1016/j.bse.2004.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Erpenbeck D, Breeuwer JAJ, Soest RWM. Implications from a 28S rRNA gene fragment for the phylogenetic relationships of halichondrid sponges (Porifera: Demospongiae). J ZOOL SYST EVOL RES 2005. [DOI: 10.1111/j.1439-0469.2005.00306.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Borchiellini C, Chombard C, Manuel M, Alivon E, Vacelet J, Boury-Esnault N. Molecular phylogeny of Demospongiae: implications for classification and scenarios of character evolution. Mol Phylogenet Evol 2005; 32:823-37. [PMID: 15288059 DOI: 10.1016/j.ympev.2004.02.021] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2003] [Revised: 02/20/2004] [Indexed: 11/23/2022]
Abstract
An analysis of the phylogenetic relationships of the 13 orders of Demospongiae, based on 18S and C1, D1 and C2 domains of 28S rRNA (for, respectively, 26 and 32 taxa) has been performed. The class Demospongiae as traditionally defined is not found to be monophyletic. Instead, a clade comprising all demosponges except Homoscleromorpha is well-supported, and we define phylogenetically the name Demospongiae in this more restricted sense to preclude the possibility of drastic alterations of the meaning of Demospongiae in the future, depending on the position of Homoscleromorpha. Within this clade Demospongiae s.s., ceractinomorphs and tetractinomorphs are polyphyletic, implying homoplastic evolution of characters such as reproductive strategies (viviparity vs. oviparity) and skeleton architecture (reticulate vs. radiate). The topology derived from our molecular data provides a basis for proposing a new classification of Demospongiae s.s., and suggests a reverse polarity of some characters, with respect to traditional conceptions: viviparity, presence of monaxon spicules and of spongin appear to be ancestral, whereas oviparity, and presence of tetraxon spicules appear as derived characters.
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Affiliation(s)
- Carole Borchiellini
- Centre d'Océanologie de Marseille, Université de la Méditerranée, UMR-CNRS 6540, Station marine d'Endoume, rue de la Batterie des Lions, 13007 Marseille, France.
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Erpenbeck D, McCormack GP, Breeuwer JAJ, van Soest RWM. Order level differences in the structure of partial LSU across demosponges (Porifera): new insights into an old taxon. Mol Phylogenet Evol 2005; 32:388-95. [PMID: 15186823 DOI: 10.1016/j.ympev.2004.02.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2003] [Revised: 01/28/2004] [Indexed: 11/30/2022]
Affiliation(s)
- D Erpenbeck
- IBED, University of Amsterdam, P.O. Box 94766, 1090GT Amsterdam, The Netherlands.
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Richelle-Maurer E, De Kluijver M, Feio S, Gaudêncio S, Gaspar H, Gomez R, Tavares R, Van de Vyver G, Van Soest R. Localization and ecological significance of oroidin and sceptrin in the Caribbean sponge Agelas conifera. BIOCHEM SYST ECOL 2003. [DOI: 10.1016/s0305-1978(03)00072-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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McCormack GP, Erpenbeck D, van Soest RWM. Major discrepancy between phylogenetic hypotheses based on molecular and morphological criteria within the Order Haplosclerida (Phylum Porifera: Class Demospongiae). J ZOOL SYST EVOL RES 2002. [DOI: 10.1046/j.1439-0469.2002.00204.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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