Settlement Patterns in Ascidians Concerning Have Been
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Ciona Intestinalis and Comparative Analysis with Ciona Savignyi
Downloaded from genome.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Methods Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi Jong Hyun Kim,1,4 Michael S. Waterman,2,3 and Lei M. Li2,3 1Department of Computer Science, Yonsei University, Seoul, 120-749, Republic of Korea; 2Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA; 3Department of Mathematics, University of Southern California, Los Angeles, California 90089, USA One of the main goals in genome sequencing projects is to determine a haploid consensus sequence even when clone libraries are constructed from homologous chromosomes. However, it has been noticed that haplotypes can be inferred from genome assemblies by investigating phase conservation in sequenced reads. In this study, we seek to infer haplotypes, a diploid consensus sequence, from the genome assembly of an organism, Ciona intestinalis. The Ciona intestinalis genome is an ideal resource from which haplotypes can be inferred because of the high polymorphism rate (1.2%). The haplotype estimation scheme consists of polymorphism detection and phase estimation. The core step of our method is a Gibbs sampling procedure. The mate-pair information from two-end sequenced clone inserts is exploited to provide long-range continuity. We estimate the polymorphism rate of Ciona intestinalis to be 1.2% and 1.5%, according to two different polymorphism counting schemes. The distribution of heterozygosity number is well fit by a compound Poisson distribution. The N50 length of haplotype segments is 37.9 kb in our assembly, while the N50 scaffold length of the Ciona intestinalis assembly is 190 kb. -
Phlebobranchia of CTAW
PHLEBOBRANCHIA PHLEBOBRANCHIA The suborder Phlebobranchia (order Enterogona) is characterised by having unpaired gonads present only on the same side of the body as the gut. As in Stolidobranchia, the body is not divided into different sections (such as thorax, abdomen and posterior abdomen) as the gut is folded up in the parietal body wall outside the pharynx and the large branchial sac occupies the whole length of the body. Usually the branchial sac (which is flat, without folds) has internal longitudinal vessels (although only vestiges remain in Agneziidae). Epicardial sacs do not persist in adults as they do in Aplousobranchia, although excretory vesicles (nephrocytes) embedded in the body wall over the gut are known to originate from the embryonic epicardium in Ascidiidae and Corellidae. Most phlebobranchs are solitary. However, Plurellidae Kott, 1973 includes both solitary and colonial forms, and Perophoridae Giard, 1872 are all colonial. Replication in Perophoridae is from ectodermal epithelium (rather than endodermal or mesodermal tissue the mesodermal tissue of the vascular stolon (rather than the endodermal tissue as in most as in Aplousobranchia). The process of replication has not been investigated in Plurellidae. Phlebobranch taxa occurring in Australia are documented in Kott (1985). Family level taxa are characterised principally by the size and form of the branchial sac including the number of branchial vessels and form of the stigmata; the form, size and position of the gonads; and the habit (colonial or solitary) of the taxon. Berrill (1950) has discussed problems in assessing the phylogeny of Perophoridae. References Berrill, N.J. (1950). The Tunicata. Ray Soc. Publs 133: 1–354 Giard, A.M. -
Cionin, a Vertebrate Cholecystokinin/Gastrin
www.nature.com/scientificreports OPEN Cionin, a vertebrate cholecystokinin/gastrin homolog, induces ovulation in the ascidian Ciona intestinalis type A Tomohiro Osugi, Natsuko Miyasaka, Akira Shiraishi, Shin Matsubara & Honoo Satake* Cionin is a homolog of vertebrate cholecystokinin/gastrin that has been identifed in the ascidian Ciona intestinalis type A. The phylogenetic position of ascidians as the closest living relatives of vertebrates suggests that cionin can provide clues to the evolution of endocrine/neuroendocrine systems throughout chordates. Here, we show the biological role of cionin in the regulation of ovulation. In situ hybridization demonstrated that the mRNA of the cionin receptor, Cior2, was expressed specifcally in the inner follicular cells of pre-ovulatory follicles in the Ciona ovary. Cionin was found to signifcantly stimulate ovulation after 24-h incubation. Transcriptome and subsequent Real-time PCR analyses confrmed that the expression levels of receptor tyrosine kinase (RTK) signaling genes and a matrix metalloproteinase (MMP) gene were signifcantly elevated in the cionin-treated follicles. Of particular interest is that an RTK inhibitor and MMP inhibitor markedly suppressed the stimulatory efect of cionin on ovulation. Furthermore, inhibition of RTK signaling reduced the MMP gene expression in the cionin-treated follicles. These results provide evidence that cionin induces ovulation by stimulating MMP gene expression via the RTK signaling pathway. This is the frst report on the endogenous roles of cionin and the induction of ovulation by cholecystokinin/gastrin family peptides in an organism. Ascidians are the closest living relatives of vertebrates in the Chordata superphylum, and thus they provide important insights into the evolution of peptidergic systems in chordates. -
Ciona Intestinalis
UC Berkeley UC Berkeley Previously Published Works Title Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis Permalink https://escholarship.org/uc/item/6531j4jb Journal Genome Research, 15(12) ISSN 1088-9051 Authors Shi, Weiyang Levine, Michael Davidson, Brad Publication Date 2005-12-01 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Perspective Unraveling genomic regulatory networks in the simple chordate, Ciona intestinalis Weiyang Shi, Michael Levine, and Brad Davidson1 Department of Molecular and Cell Biology, Division of Genetics and Development, Center for Integrative Genomics, University of California, Berkeley, California 94720, USA The draft genome of the primitive chordate, Ciona intestinalis, was published three years ago. Since then, significant progress has been made in utilizing Ciona’s genomic and morphological simplicity to better understand conserved chordate developmental processes. Extensive annotation and sequencing of staged EST libraries make the Ciona genome one of the best annotated among those that are publicly available. The formation of the Ciona tadpole depends on simple, well-defined cellular lineages, and it is possible to trace the lineages of key chordate tissues such as the notochord and neural tube to the fertilized egg. Electroporation methods permit the targeted expression of regulatory genes and signaling molecules in defined cell lineages, as well as the rapid identification of regulatory DNAs underlying cell-specific gene expression. The recent sequencing of a second Ciona genome (C. savignyi) permits the use of simple alignment algorithms for the identification of conserved noncoding sequences, including microRNA genes and enhancers. Detailed expression profiles are now available for almost every gene that encodes a regulatory protein or cell-signaling molecule. -
Biology of the Invasive Ascidian Ascidiella Aspersa in Its Native Habitat: Reproductive Patterns and Parasite Load
Estuarine, Coastal and Shelf Science 181 (2016) 249e255 Contents lists available at ScienceDirect Estuarine, Coastal and Shelf Science journal homepage: www.elsevier.com/locate/ecss Biology of the invasive ascidian Ascidiella aspersa in its native habitat: Reproductive patterns and parasite load * Sharon A. Lynch , Grainne Darmody, Katie O'Dwyer, Mary Catherine Gallagher, Sinead Nolan, Rob McAllen, Sarah C. Culloty School of Biological, Earth and Environmental Sciences, Aquaculture and Fisheries Development Centre and Environmental Research Institute, University College Cork, The Cooperage, Distillery Fields, North Mall, Cork, Ireland article info abstract Article history: The European sea squirt Ascidiella aspersa is a solitary tunicate native to the northeastern Atlantic, Received 4 February 2016 commonly found in shallow and sheltered marine ecosystems where it is capable of forming large Received in revised form clumps and outcompeting other invertebrate fauna at settlement. To date, there have been relatively few 28 July 2016 studies looking at the reproductive biology and health status of this invasive species. Between 2006 and Accepted 29 August 2016 2010 sampling of a native population took place to investigate gametogenesis and reproductive cycle and Available online 31 August 2016 to determine the impact of settlement depth on reproduction. In addition, parasite diversity and impact was assessed. A staging system to assess reproductive development was determined. The study high- Keywords: Ascidiella aspersa lighted that from year to year the tunicate could change its reproductive strategy from single sex to Gametogenesis hermaphrodite, with spawning possible throughout the year. Depth did not impact on sex determination, Parasites however, gonad maturation and spawning occurred earlier in individuals in deeper waters compared to Invasives shallow depth and it also occurred later in A. -
And Description of a New Species, Ciona Interme
An integrative taxonomic framework for the study of the genus Ciona (Ascidiacea) and description of a new species, Ciona intermedia Francesco Mastrototaro, Federica Montesanto, Marika Salonna, Frédérique Viard, Giovanni Chimienti, Egidio Trainito, Carmela Gissi To cite this version: Francesco Mastrototaro, Federica Montesanto, Marika Salonna, Frédérique Viard, Giovanni Chimi- enti, et al.. An integrative taxonomic framework for the study of the genus Ciona (Ascidiacea) and description of a new species, Ciona intermedia. Zoological Journal of the Linnean Society, Linnean Society of London, 2020, 10.1093/zoolinnean/zlaa042. hal-02861027 HAL Id: hal-02861027 https://hal.archives-ouvertes.fr/hal-02861027 Submitted on 8 Jun 2020 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. Doi: 10.1093/zoolinnean/zlaa042 An integrative taxonomy framework for the study of the genus Ciona (Ascidiacea) and the description of the new species Ciona intermedia Francesco Mastrototaro1, Federica Montesanto1*, Marika Salonna2, Frédérique Viard3, Giovanni Chimienti1, Egidio Trainito4, Carmela Gissi2,5,* 1 Department of Biology and CoNISMa LRU, University of Bari “Aldo Moro” Via Orabona, 4 - 70125 Bari, Italy 2 Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Via Orabona, 4 - 70125 Bari, Italy 3 Sorbonne Université, CNRS, Lab. -
Repertoires of G Protein-Coupled Receptors for Ciona-Specific Neuropeptides
Repertoires of G protein-coupled receptors for Ciona-specific neuropeptides Akira Shiraishia, Toshimi Okudaa, Natsuko Miyasakaa, Tomohiro Osugia, Yasushi Okunob, Jun Inouec, and Honoo Satakea,1 aBioorganic Research Institute, Suntory Foundation for Life Sciences, 619-0284 Kyoto, Japan; bDepartment of Biomedical Intelligence, Graduate School of Medicine, Kyoto University, 606-8507 Kyoto, Japan; and cMarine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 904-0495 Okinawa, Japan Edited by Thomas P. Sakmar, The Rockefeller University, New York, NY, and accepted by Editorial Board Member Jeremy Nathans March 11, 2019 (received for review September 26, 2018) Neuropeptides play pivotal roles in various biological events in the conservesagreaternumberofneuropeptide homologs than proto- nervous, neuroendocrine, and endocrine systems, and are corre- stomes (e.g., Caenorhabditis elegans and Drosophila melanogaster) lated with both physiological functions and unique behavioral and other invertebrate deuterostomes (7–13), confirming the evo- traits of animals. Elucidation of functional interaction between lutionary and phylogenetic relatedness of ascidians to vertebrates. neuropeptides and receptors is a crucial step for the verification of The second group includes Ciona-specific novel neuropeptides, their biological roles and evolutionary processes. However, most namely Ci-NTLPs, Ci-LFs, and Ci-YFV/Ls (SI Appendix,Fig. receptors for novel peptides remain to be identified. Here, we S1 and Table S1), which share neither consensus motifs nor se- show the identification of multiple G protein-coupled receptors quence similarity with any other peptides (8, 9). The presence of (GPCRs) for species-specific neuropeptides of the vertebrate sister both homologous and species-specific neuropeptides highlights this group, Ciona intestinalis Type A, by combining machine learning phylogenetic relative of vertebrates as a prominent model organism and experimental validation. -
Title Occurrence of the European Ascidian Ascidiella Scabra (Müller
Occurrence of the European ascidian Ascidiella scabra (Müller, Title 1776) in the 19 century in Nagasaki, Japan, probably as an ephemeral alien species Author(s) NISHIKAWA, Teruaki; OTANI, Michio Contributions from the Biological Laboratory, Kyoto Citation University (2004), 29(4): 401-408 Issue Date 2004-07-21 URL http://hdl.handle.net/2433/156412 Right Type Departmental Bulletin Paper Textversion publisher Kyoto University Contr. biol. lab. Kyoto Univ., Vol. 29, pp. 401ZK)8. Issued 21 July 2004 Occurrence of the European ascidian Ascidiella scabra (Milller, 1776) in the 19 century in Nagasaki, Japan, probably as an ephemeral alien species Teruaki NISHIKAWA' and Michio OTANI2 Thei Nagoya University Museum, Chikusa-ku, Nagoya, 464-8601 Japan 2Marine Ecological Institute Inc., 3-3-4 Harada Moto-machi, Toyonaka, 561 -0808 Japan ABSTRACT The generic affiliation of the single Japanese record of the ascidian genus Ascidietta, as "A. virginea (MtiIIer)" by Hartmeyer in 1902, was questioned by Nishikawa in 1995 because of the genus's natura1 distribution being confined to Atlantic waters, the somewhat confused history of taxonomy in the genus and allies, and of the insufficient description. Our personal reexamination of the material collected from Nagasaki and deposited in the Museum fUr Naturkunde der Humboldt-Universitat zu Berlin reyeals that it is identical to Ascidietla scabra (Mti11er, 1776), so far recorded exclusively from European boreal to warm-temperate waters. Combining imperfect label information of the material with historical knowledge, the material is supposed to have been collected in February, 1861, by Mr. Otto SchottmUller, a member of the Prussian East Asia Expedition led by Graf zu Eulenburg. -
Bering Sea Marine Invasive Species Assessment Alaska Center for Conservation Science
Bering Sea Marine Invasive Species Assessment Alaska Center for Conservation Science Scientific Name: Ciona savignyi Phylum Chordata Common Name Pacific transparent sea squirt Class Ascidiacea Order Enterogona Family Cionidae Z:\GAP\NPRB Marine Invasives\NPRB_DB\SppMaps\CIOSAV.png 73 Final Rank 52.25 Data Deficiency: 0.00 Category Scores and Data Deficiencies Total Data Deficient Category Score Possible Points Distribution and Habitat: 20.5 30 0 Anthropogenic Influence: 6 10 0 Biological Characteristics: 21.25 30 0 Impacts: 4.5 30 0 Figure 1. Occurrence records for non-native species, and their geographic proximity to the Bering Sea. Ecoregions are based on the classification system by Spalding et al. (2007). Totals: 52.25 100.00 0.00 Occurrence record data source(s): NEMESIS and NAS databases. General Biological Information Tolerances and Thresholds Minimum Temperature (°C) -1.7 Minimum Salinity (ppt) 24 Maximum Temperature (°C) 27 Maximum Salinity (ppt) 37 Minimum Reproductive Temperature (°C) 12 Minimum Reproductive Salinity (ppt) 31* Maximum Reproductive Temperature (°C) 25 Maximum Reproductive Salinity (ppt) 35* Additional Notes Ciona savignyi is a solitary, tube-shaped tunicate that is white to almost clear in colour. It has two siphons of unequal length, with small yellow or orange flecks on the siphons’ rim. Although C. savignyi is considered solitary, individuals are most often found in groups, and can form dense aggregations (Jiang and Smith 2005). Report updated on Wednesday, December 06, 2017 Page 1 of 14 1. Distribution and Habitat 1.1 Survival requirements - Water temperature Choice: Moderate overlap – A moderate area (≥25%) of the Bering Sea has temperatures suitable for year-round survival Score: B 2.5 of 3.75 Ranking Rationale: Background Information: Temperatures required for year-round survival occur in a moderate Based on this species' geographic distribution, it is estimated to tolerate area (≥25%) of the Bering Sea. -
The Role of Metalloproteases in Fertilisation in the Ascidian Ciona
www.nature.com/scientificreports OPEN The role of metalloproteases in fertilisation in the ascidian Ciona robusta Received: 8 August 2018 Shiori Nakazawa 1,2, Maki Shirae-Kurabayashi1 & Hitoshi Sawada1 Accepted: 12 December 2018 In the ascidian Ciona robusta (formerly C. intestinalis type A), the mechanism underlying sperm Published: xx xx xxxx penetration through the egg investment remains unknown. We previously reported that proteins containing both an astacin metalloprotease domain and thrombospondin type 1 repeats are abundant in the sperm surface protein-enriched fraction of C. robusta. Here we investigated the involvement of those proteins in fertilisation. We refned the sequences of astacin metalloproteases, confrmed that fve of them are present in the sperm, and labelled them as tunicate astacin and thrombospondin type 1 repeat-containing (Tast) proteins. Fertilisation of C. robusta eggs was potently inhibited by a metalloprotease inhibitor GM6001. The eggs cleaved normally when they were vitelline coat-free or the inhibitor was added after insemination. Furthermore, vitelline coat proteins were degraded after incubation with intact sperm. These results suggest that sperm metalloproteases are indispensable for fertilisation, probably owing to direct or indirect mediation of vitelline-coat digestion during sperm penetration. TALEN-mediated knockout of Tast genes and the presence of GM6001 impaired larval development at the metamorphic stage, suggesting that Tast gene products play a key role in late development. Egg fertilisation is key to achieving genetic diversity in the next generation. In most animals, the eggs are covered with an acellular investment called the egg coat, also called the vitelline coat (VC) in some marine invertebrates, including ascidians and zona pellucida in mammals. -
Record of a Bypass on the Oral Siphon of Ascidia Sydneiensis (Tunicata: Ascidiacea) in a Tropical Bay from South-Eastern Brazil
OCEAN AND COASTAL NOTE https://doi.org/10.1590/s2675-28242020068344 RESEARCH Record of a bypass on the oral siphon of Ascidia sydneiensis (Tunicata: Ascidiacea) in a tropical bay from south-eastern Brazil Paulo Cezar Azevedo Silva1 , Géssica Cristine Maia Oliveira1,2 , Danielle Fernandes Barboza1,2 , Luís Felipe Skinner1,2* 1 Universidade do Estado do Rio de Janeiro (UERJ/FFP) Departamento de Ciências, Rio de Janeiro, Brasil (Rua Dr. Francisco Portela, 1470 - Patronato - São Gonçalo - 24435-005 - RJ - Brazil) 2 Programa de Pós-Graduação em Oceanografia (PPG-OCN/UERJ), Rio de Janeiro, Brasil (Rua São Francisco Xavier, 524 - sala 4018/bloco E - Maracanã, 20550-013 - RJ - Brazil) *Corresponding author: [email protected] Ascidia sydneiensis Stimpson, 1855 is a solitary natural substrate at Ilha da Amarração, next to Ilha ascidian (Order Phlebobranchia) first described in the Grande, Rio de Janeiro state, Brazil (23°10’58.0”S, China Sea and Japan. Recently, it has been recorded 44°10’47.7” W). This atypical individual had a small in subtropical and tropical regions and is abundant projection with rims and other morphological in the Caribbean (Rocha et al., 2005; Worms, 2020). features, on the tunic next to a larger oral siphon. In Brazil, it was first recorded in the São Paulo State After collection, the animal was anesthetized with (Bjornberg, 1956) and ranges from Ceará to Santa menthol and fixed in 10% formaldehyde. The Catarina (Rodrigues, 1962; Rocha and Nasser, 1998; presence of the third opening was not noticed during Rocha and Costa, 2005; Rocha and Kremmer, 2005; the removal of the animal from the substrate but was Rocha et al., 2012). -
Ascidiella Aspersa Global Invasive
FULL ACCOUNT FOR: Ascidiella aspersa Ascidiella aspersa System: Marine Kingdom Phylum Class Order Family Animalia Chordata Ascidiacea Enterogona Ascidiidae Common name dirty sea squirt (English), European sea squirt (English), ascidie sale (French), vuilwitte zakpijp (Dutch), Spritz-Ascidie (German), ruwe zakpijp (Dutch) Synonym Ascidia aculeata , (Alder, 1863) Ascidia affinis , (Hancock, 1870) Ascidia albida , (Alder & Hancock, 1848) Ascidia aspersa , (M?ller, 1776) Ascidia elliptica , (Alder & Hancock, 1848) Acidia expansa , (Kiaer, 1893) Ascidia minuta , (Kiaer, 1893) Ascidia normanni , (Alder & Hancock, 1870) Ascidia opalina , (Macgillivray, 1843) Ascidia patula , (M?ller, 1776) Ascidia pedunculata , (Hoffman, 1829) Ascidia pellucida , (Alder & Hancock, 1848) Ascidia pustulosa , (Alder, 1863) Ascidia scabra , (M?ller, 1776) Ascidia sordida , (Alder & Hancock, 1848) Ascidia triangularis , (Herdman, 1881) Ascidia truncata , (Herdman, 1881) Ascidiella aspersa , (Kiaer, 1893) Ascidiella cristata , (Roule, 1884) Phallusia aspersa , (Traustedt, 1883) Phallusia cristata , (Risso, 1826) Similar species Styela clava, Ciona intestinalis, Molgula spp., Ascidiella scabra Summary Ascidiella aspersa (European sea squirt) is a solitary marine and estuarine tunicate that is native from Norway to the Mediterranean. It is a suspension filter-feeder and was introduced via foulling on the hulls of ships to the northwest coast of the Atlantic, India, Australia and New Zealand. Commonly called the European sea squirt, it has become a moderate to serious threat by displacing native fauna. view this species on IUCN Red List Global Invasive Species Database (GISD) 2021. Species profile Ascidiella aspersa. Pag. 1 Available from: http://www.iucngisd.org/gisd/species.php?sc=1126 [Accessed 25 September 2021] FULL ACCOUNT FOR: Ascidiella aspersa Species Description Ascidiella aspersa (European sea squirt) is a marine organism classified as a tunicate.