Trophic Dynamics of Filter Feeding Bivalves in the Yangtze Estuarine Intertidal Marsh: Stable Isotope and Fatty Acid Analyses
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Analysis of Synonymous Codon Usage Patterns in Sixty-Four Different Bivalve Species
Analysis of synonymous codon usage patterns in sixty-four diVerent bivalve species Marco Gerdol1, Gianluca De Moro1, Paola Venier2 and Alberto Pallavicini1 1 Department of Life Sciences, University of Trieste, Trieste, Italy 2 Department of Biology, University of Padova, Padova, Italy ABSTRACT Synonymous codon usage bias (CUB) is a defined as the non-random usage of codons encoding the same amino acid across diVerent genomes. This phenomenon is common to all organisms and the real weight of the many factors involved in its shaping still remains to be fully determined. So far, relatively little attention has been put in the analysis of CUB in bivalve mollusks due to the limited genomic data available. Taking advantage of the massive sequence data generated from next generation sequencing projects, we explored codon preferences in 64 diVerent species pertaining to the six major evolutionary lineages in Bivalvia. We detected remarkable diVerences across species, which are only partially dependent on phylogeny. While the intensity of CUB is mild in most organisms, a heterogeneous group of species (including Arcida and Mytilida, among the others) display higher bias and a strong preference for AT-ending codons. We show that the relative strength and direction of mutational bias, selection for translational eYciency and for translational accuracy contribute to the establishment of synonymous codon usage in bivalves. Although many aspects underlying bivalve CUB still remain obscure, we provide for the first time an overview of this phenomenon -
Shell Morphology and Sperm Ultrastructure of Solen Tehuelchus Hanley, 1842 (Bivalvia: Solenidae): New Taxonomic Characters Author(S): Amanda Bonini, Gisele O
CORE Metadata, citation and similar papers at core.ac.uk Provided by Repositorio da Producao Cientifica e Intelectual da Unicamp Shell Morphology and Sperm Ultrastructure of Solen tehuelchus Hanley, 1842 (Bivalvia: Solenidae): New Taxonomic Characters Author(s): Amanda Bonini, Gisele O. Introíni Lenita F. Tallarico, Fabrizio M. Machado and Shirlei M. Recco-Pimentel Source: American Malacological Bulletin, 34(2):73-78. Published By: American Malacological Society https://doi.org/10.4003/006.034.0202 URL: http://www.bioone.org/doi/full/10.4003/006.034.0202 BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/page/terms_of_use. Usage of BioOne content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. Amer. Malac. Bull. 34(2): 73–78 (2016) RESEARCH NOTE Shell morphology and sperm ultrastructure of Solen tehuelchus Hanley, 1842 (Bivalvia: Solenidae): New taxonomic characters Amanda Bonini1, Gisele O. Introíni1, 3, Lenita F. Tallarico1, Fabrizio M. Machado2 and Shirlei M. Recco-Pimentel1 1Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas, Rua Charles Darwin, s/n. -
Xerces Society's
Conserving the Gems of Our Waters Best Management Practices for Protecting Native Western Freshwater Mussels During Aquatic and Riparian Restoration, Construction, and Land Management Projects and Activities Emilie Blevins, Laura McMullen, Sarina Jepsen, Michele Blackburn, Aimée Code, and Scott Homan Black CONSERVING THE GEMS OF OUR WATERS Best Management Practices for Protecting Native Western Freshwater Mussels During Aquatic and Riparian Restoration, Construction, and Land Management Projects and Activities Emilie Blevins Laura McMullen Sarina Jepsen Michele Blackburn Aimée Code Scott Hoffman Black The Xerces Society for Invertebrate Conservation www.xerces.org The Xerces® Society for Invertebrate Conservation is a nonprot organization that protects wildlife through the conservation of invertebrates and their habitat. Established in 1971, the Society is at the forefront of invertebrate protection, harnessing the knowledge of scientists and the enthusiasm of citizens to implement conservation programs worldwide. The Society uses advocacy, education, and applied research to promote invertebrate conservation. The Xerces Society for Invertebrate Conservation 628 NE Broadway, Suite 200, Portland, OR 97232 Tel (855) 232-6639 Fax (503) 233-6794 www.xerces.org Regional oces from coast to coast. The Xerces Society is an equal opportunity employer and provider. Xerces® is a trademark registered in the U.S. Patent and Trademark Oce © 2018 by The Xerces Society for Invertebrate Conservation Primary Authors and Contributors The Xerces Society for Invertebrate Conservation: Emilie Blevins, Laura McMullen, Sarina Jepsen, Michele Blackburn, Aimée Code, and Scott Homan Black. Acknowledgements Funding for this report was provided by the Oregon Watershed Enhancement Board, The Nature Conservancy and Portland General Electric Salmon Habitat Fund, the Charlotte Martin Foundation, Meyer Memorial Trust, and Xerces Society members and supporters. -
Evolutionary History of DNA Methylation Related Genes in Bivalvia: New Insights from Mytilus Galloprovincialis
fevo-09-698561 July 3, 2021 Time: 17:34 # 1 ORIGINAL RESEARCH published: 09 July 2021 doi: 10.3389/fevo.2021.698561 Evolutionary History of DNA Methylation Related Genes in Bivalvia: New Insights From Mytilus galloprovincialis Marco Gerdol1, Claudia La Vecchia2, Maria Strazzullo2, Pasquale De Luca3, Stefania Gorbi4, Francesco Regoli4, Alberto Pallavicini1,2 and Enrico D’Aniello2* 1 Department of Life Sciences, University of Trieste, Trieste, Italy, 2 Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy, 3 Research Infrastructures for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, Naples, Italy, 4 Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy DNA methylation is an essential epigenetic mechanism influencing gene expression in all organisms. In metazoans, the pattern of DNA methylation changes during embryogenesis and adult life. Consequently, differentiated cells develop a stable Edited by: and unique DNA methylation pattern that finely regulates mRNA transcription Giulia Furfaro, during development and determines tissue-specific gene expression. Currently, DNA University of Salento, Italy methylation remains poorly investigated in mollusks and completely unexplored in Reviewed by: Celine Cosseau, Mytilus galloprovincialis. To shed light on this process in this ecologically and Université de Perpignan Via Domitia, economically important bivalve, we screened its genome, detecting sequences France Ricard Albalat, homologous to DNA methyltransferases (DNMTs), methyl-CpG-binding domain (MBD) University of Barcelona, Spain proteins and Ten-eleven translocation methylcytosine dioxygenase (TET) previously *Correspondence: described in other organisms. We characterized the gene architecture and protein Enrico D’Aniello domains of the mussel sequences and studied their phylogenetic relationships with [email protected] the ortholog sequences from other bivalve species. -
Data on Intertidal and Subtidal Assemblages
Annex 9C Data on Intertidal and Subtidal Assemblages Table 9C.1 Relative Abundance of Intertidal Biota Recorded on the LPS Seawall, Tau Lo Chau and Pak Chau within the Assessment Area in the Wet Season 2016 and Dry Season 2017 Class Species LPS Seawall Tau Lo Chau Pak Chau Wet Dry Wet Dry Wet Dry Season Season Season Season Season Season (2016) (2017) (2016) (2017) (2016) (2017) Gastropoda Echinolittorina radiata 1 3 3 2 2 3 Echinolittorina pascua 1 1 2 0 0 0 Echinolittorina vidua 0 1 1 2 0 0 Littoraria articulata 0 0 0 0 3 3 Nerita albicilla 1 1 1 1 2 1 Nerita costata 0 0 0 0 1 1 Lunella coronata 0 0 0 0 0 1 Monodonta labio 1 1 1 1 1 2 Tenguella musiva 1 1 0 0 0 0 Planaxis sulcatus 1 0 1 1 0 0 Reishia clavigera 1 1 2 1 1 0 Reishia luteostoma 0 0 1 0 1 0 Siphonaria japonica 1 1 1 1 0 0 Siphonaria laciniosa 0 0 0 1 0 0 Cellana grata 1 2 1 1 0 0 Cellana toreuma 1 1 1 2 0 0 Mangelia dorsuosa 1 1 0 0 0 0 Nipponacmea concinna 0 1 1 1 0 1 Patelloida saccharina 3 4 3 1 0 0 Patelloida pygmaea 0 1 0 0 0 0 Polyplacophora Liolophura japonica 1 1 1 1 0 1 Onithochiton hirasei 1 1 1 1 0 1 Malacostraca Ligia exotica 2 0 2 2 1 0 Grapsus albolineatus 1 0 1 1 0 0 Hemigrapsus sanguineus 0 0 1 0 1 1 Plagusia depressa 0 0 1 0 0 0 Diogenes dubiu 0 0 1 1 0 0 Polychaeta Spirorbis spp. -
Distribution of DTHS3 Satellite DNA Across 12 Bivalve Species
Research Note Distribution of DTHS3 satellite DNA across 12 bivalve species Eva Šatović1* and Miroslav Plohl1 1 Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10 000 Zagreb, Croatia * Corresponding Author: Eva Šatović, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia, e- mail: [email protected] Running (short) title: DTHS3 satellite DNA Keywords: satellite DNA, Bivalvia, evolution Abstract In this work, characterization of DTHS3 satellite DNA was further expanded within the Class Bivalvia. Monomer variants of DTHS3 satDNA were compared in 12 bivalve species belonging to two different Subclasses, Heterodonta and Pteriomorphia. This satDNA, whose age is estimated to a minimum of 516 Ma, is contributing to the concept of the dual character of satDNA sequences: their sequence preservation throughout long evolutionary periods and generation of species-specific variants of the same satDNA family. Introduction Class Bivalvia is represented by a large number of marine and freshwater mollusks, found in aquatic habitats throughout the world. Despite their significant ecological and commercial value, genomic studies on these organisms are not abundant, and information is still limited to a few species. Genome sequencing projects have been performed only for the pearl oyster Pinctada fucata (Takeuchi et al. 2012), pacific oyster Crassostrea gigas (Zhang et al. 2012), and filter-feeder mussel Mytillus galloprovincialis (Murgarella et al. 2016). Significant fraction of all eukaryotic genomes is made of repetitive sequences. Among them are satellite DNA (satDNA) sequences, organized in arrays of tandemly repeated monomers (Miklos 1985). Donax trunculus is an example of a bivalve species harboring a number of different satDNAs: DTE (Plohl and Cornudella 1996), DTHS1, DTHS2, DTHS3, DTHS4 (Plohl and Cornudella 1997), DTF1 (Petrović and Plohl 2005), DTF2 (Petrović et al. -
Genome Sizes and Karyotypes in the Razor Clams Ensis Arcuatus (Jeffreys, 1865) and E
Cah. Biol. Mar. (2008) 49 : 79-85 Genome sizes and karyotypes in the razor clams Ensis arcuatus (Jeffreys, 1865) and E. siliqua (Linnaeus, 1758) Juan FERNÁNDEZ-TAJES1, Andrés MARTÍNEZ-LAGE1, Ruth FREIRE1, Alejandro GUERRA2, Josefina MÉNDEZ1 and Ana M. GONZÁLEZ-TIZÓN*1 (1) Departamento de Biología Celular y Molecular, Facultade de Ciencias, Universidade da Coruña, 15071 La Coruña, Spain (2) Centro de Investigaciones Marinas, Xunta de Galicia, Pontevedra, Spain *Corresponding author: Tel.: +34 981 167 000, Fax: +34 981 167 065. E-mail: [email protected] Abstract: The razor clams Ensis arcuatus and E. siliqua show a diploid DNA content of 3.85 ± 0.049 pg and 4.00 ± 0.050 pg, respectively. Both have a diploid chromosome number of 38 although their karyotypes show remarkable differences. The karyotype of E. arcuatus consists of 4 metacentric, 1 metacentric-submetacentric, 7 submetacentric and 7 telocentric chromosome pairs, whereas that of E. siliqua possesses 3 metacentric, 7 submetacentric and 9 telocentric pairs. In situ hybridization using an 18S-5.8S-28S rDNA probe located this ribosomal locus on one chromosome pair for both species. Results demonstrate that large differences exist between them, probably caused by chromosome rearrangements along evolution of these two species, and increase the number of studies on bivalve cytogenetics. Résumé : Taille du génome et caryotype chez les couteaux Ensis arcuatus (Jeffreys, 1865) et E. siliqua (L., 1758). Le contenu de l’ADN diploïde des couteaux Ensis arcuatus et E. siliqua est de 3,85 ± 0,049 pg et 4,00 ± 0,050 pg, respective- ment. Ils ont tous les deux un nombre de chromosomes diploïdes de 38 bien que leurs caryotypes présentent des différences. -
Extensive Tandem Duplication Events Drive the Expansion of the C1q-Domain-Containing Gene Family in Bivalves
marine drugs Article Extensive Tandem Duplication Events Drive the Expansion of the C1q-Domain-Containing Gene Family in Bivalves Marco Gerdol 1,* , Samuele Greco 1 and Alberto Pallavicini 1,2 1 Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; [email protected] (S.G.); [email protected] (A.P.) 2 National Institute of Oceanography and Applied Geophysics, 34151 Trieste, Italy * Correspondence: [email protected]; Tel.: +39-040-5588676 Received: 30 August 2019; Accepted: 12 October 2019; Published: 14 October 2019 Abstract: C1q-domain-containing (C1qDC) proteins are rapidly emerging as key players in the innate immune response of bivalve mollusks. Growing experimental evidence suggests that these highly abundant secretory proteins are involved in the recognition of microbe-associated molecular patterns, serving as lectin-like molecules in the bivalve proto-complement system. While a large amount of functional data concerning the binding specificity of the globular head C1q domain and on the regulation of these molecules in response to infection are quickly accumulating, the genetic mechanisms that have led to the extraordinary lineage-specific expansion of the C1qDC gene family in bivalves are still largely unknown. The analysis of the chromosome-scale genome assembly of the Eastern oyster Crassostrea virginica revealed that the 476 oyster C1qDC genes, far from being uniformly distributed along the genome, are located in large clusters of tandemly duplicated paralogs, mostly found on chromosomes 7 and 8. Our observations point out that the evolutionary process behind the development of a large arsenal of C1qDC lectin-like molecules in marine bivalves is still ongoing and likely based on an unequal crossing over. -
Significant Genetic Differentiation Among Ten Populations of The
Zoological Studies 51(3): 406-414 (2012) Significant Genetic Differentiation among Ten Populations of the Razor Clam Sinonovacula constricta along the Coast of China Revealed by a Microsatellite Analysis Dong-Hong Niu1, Bing-Bing Feng1, Da-Bo Liu1, Yu-Min Zhong1, He-Ding Shen1, and Jia-Le Li1,2,* 1Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, 999 Hucheng Huan Road, Shanghai 201306, China 2Aquaculture Division, E-Institute of Shanghai Universities, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai 201306, China (Accepted November 9, 2011) Dong-Hong Niu, Bing-Bing Feng, Da-Bo Liu, Yu-Min Zhong, He-Ding Shen, and Jia-Le Li (2012) Significant genetic differentiation among ten populations of the razor clam Sinonovacula constricta along the coast of China revealed by a microsatellite analysis. Zoological Studies 51(3): 406-414. The razor clam Sinonovacula constricta is a common shellfish in human seafood diets. Little is known about the genetic structure of the species on the coast of China. In this study, the genetic diversity and differentiation of S. constricta from the northern, middle, and southern coasts of China were estimated using 8 microsatellites. The 10 populations possessed high allelic (Ar = 6.0-7.0) and genetic diversities (Ho = 0.737-0.909 and He = 0.836-0.882) across the 8 microsatellite loci. The FST analysis indicated significant genetic differentiation (FST = 0.044, p < 0.05) among the 10 populations. Two populations in the middle region significantly differed from the remaining populations (FST = 0.039-0.125, p < 0.05). -
Discovery of a Silicate Rock-Boring Organism and Macrobioerosion in Fresh Water
ARTICLE DOI: 10.1038/s41467-018-05133-4 OPEN Discovery of a silicate rock-boring organism and macrobioerosion in fresh water Ivan N. Bolotov 1,2, Olga V. Aksenova1,2, Torkild Bakken3, Christopher J. Glasby4, Mikhail Yu. Gofarov1,2, Alexander V. Kondakov1,2, Ekaterina S. Konopleva1,2, Manuel Lopes-Lima 5,6, Artyom A. Lyubas1,2, Yu Wang7,8, Andrey Yu. Bychkov9,10, Agniya M. Sokolova11,12, Kitti Tanmuangpak13, Sakboworn Tumpeesuwan14, Ilya V. Vikhrev1,2, J. Bruce H. Shyu8, Than Win 15 & Oleg S. Pokrovsky 16,17 1234567890():,; Macrobioerosion is a common process in marine ecosystems. Many types of rock-boring organisms break down hard substrates, particularly carbonate rocks and calcareous struc- tures such as dead corals and shells. In paleontology, the presence of rocks with boreholes and fossil macroboring assemblage members is one of the primary diagnostic features of shallow marine paleo-environments. Here we describe a silicate rock-boring organism and an associated community in submerged siltstone rock outcrops in Kaladan River, Myanmar. The rock-boring mussel Lignopholas fluminalis is a close relative of the marine piddocks, and its borings belong to the ichnospecies Gastrochaenolites anauchen. The neotectonic uplift of the area leading to gradual decrease of the sea level with subsequent shift from estuarine to freshwater environment was the most likely driver for the origin of this community. Our findings highlight that rocks with macroborings are not an exclusive indicator of marine paleo-ecosystems, but may also reflect freshwater habitats. 1 Northern Arctic Federal University, Arkhangelsk, Russia 163002. 2 Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russia 163000. -
The Complete Mitochondrial Genomes of Six Heterodont Bivalves (Tellinoidea and Solenoidea): Variable Gene Arrangements and Phylogenetic Implications
CORE Metadata, citation and similar papers at core.ac.uk Provided by PubMed Central The Complete Mitochondrial Genomes of Six Heterodont Bivalves (Tellinoidea and Solenoidea): Variable Gene Arrangements and Phylogenetic Implications Yang Yuan, Qi Li*, Hong Yu, Lingfeng Kong Fisheries College, Ocean University of China, Qingdao, Shandong, China Abstract Background: Taxonomy and phylogeny of subclass Heterodonta including Tellinoidea are long-debated issues and a complete agreement has not been reached yet. Mitochondrial (mt) genomes have been proved to be a powerful tool in resolving phylogenetic relationship. However, to date, only ten complete mitochondrial genomes of Heterodonta, which is by far the most diverse major group of Bivalvia, have been determined. In this paper, we newly sequenced the complete mt genomes of six species belonging to Heterodonta in order to resolve some problematical relationships among this subclass. Principal Findings: The complete mt genomes of six species vary in size from 16,352 bp to 18,182. Hairpin-like secondary structures are found in the largest non-coding regions of six freshly sequenced mt genomes, five of which contain tandem repeats. It is noteworthy that two species belonging to the same genus show different gene arrangements with three translocations. The phylogenetic analysis of Heterodonta indicates that Sinonovacula constricta, distant from the Solecurtidae belonging to Tellinoidea, is as a sister group with Solen grandis of family Solenidae. Besides, all five species of Tellinoidea cluster together, while Sanguinolaria diphos has closer relationship with Solecurtus divaricatus, Moerella iridescens and Semele scaba rather than with Sanguinolaria olivacea. Conclusions/Significance: By comparative study of gene order rearrangements and phylogenetic relationships of the five species belonging to Tellinoidea, our results support that comparisons of mt gene order rearrangements, to some extent, are a useful tool for phylogenetic studies. -
Systematic Utility and Unusual Properties of Anomalodesmatan Mitochondrial Genomes
Title Curious bivalves: Systematic utility and unusual properties of anomalodesmatan mitochondrial genomes Authors Williams, ST; Foster, PG; Hughes, C; Harper, EM; Taylor, JD; Littlewood, T; Dyal, P; Hopkins, KP; Briscoe, AG Description publisher: Elsevier articletitle: Curious bivalves: Systematic utility and unusual properties of anomalodesmatan mitochondrial genomes journaltitle: Molecular Phylogenetics and Evolution articlelink: http://dx.doi.org/10.1016/j.ympev.2017.03.004 content_type: article copyright: Crown Copyright © 2017 Published by Elsevier Inc. All rights reserved. Date Submitted 2017-05-22 *Manuscript Click here to view linked References 1 2 3 4 5 6 7 Curious bivalves: systematic utility and unusual properties of anomalodesmatan mitochondrial 8 genomes 9 10 11 12 S. T. Williamsa*, P. G. Fostera, C. Hughesa, E. M. Harperb, J. D. Taylora, D. T. J. Littlewooda, 13 P. Dyala, K. P. Hopkinsa,c & A. G. Briscoea 14 15 a Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom 16 b Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EQ, 17 United Kingdom 18 c Present address: Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 19 4RY, United Kingdom 20 21 22 23 24 25 26 27 *Corresponding author: S. T. Williams, email: [email protected] 1 28 Highlights 29 The addition of seven anomalodesmatans improves relationships in bivalve mitogenomic 30 tree 31 Non-monophyly of Bivalvia may in part be the result of compositional heterogeneity 32 Transcriptomic data helped determine boundaries for protein-coding genes 33 We identified a possible case of gene duplication of ND5 in Myadora brevis 34 We identified possible pseudogenes in published anomalodesmatan transcriptomic data 35 36 37 Abstract 38 Mitogenomic trees for Bivalvia have proved problematic in the past, but several highly divergent 39 lineages were missing from these analyses and increased representation of these groups may yet 40 improve resolution.