DOCSLIB.ORG

The Common Dragonet, Callionymus Lyra 4 5 Authors 6 Sven Winter1,2*, Stefan Prost3,4, Jordi De Raad1,2,3, Raphael T

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Common Dragonet, Callionymus Lyra 4 5 Authors 6 Sven Winter1,2*, Stefan Prost3,4, Jordi De Raad1,2,3, Raphael T bioRxiv preprint doi: https://doi.org/10.1101/2020.09.08.287078; this version posted September 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Title 2 Chromosome-level genome assembly of a benthic associated 3 Syngnathiformes species: the common dragonet, Callionymus lyra 4 5 Authors 6 Sven Winter1,2*, Stefan Prost3,4, Jordi de Raad1,2,3, Raphael T. F. Coimbra1,2, Magnus Wolf1,2, 7 Marcel Nebenführ1, Annika Held1, Melina Kurzawe1, Ramona Papapostolou1, Jade Tessien1, 8 Julian Bludau1, Andreas Kelch1, Sarah Gronefeld1, Yannis Schöneberg1, Christian Zeitz1, 9 Konstantin Zapf1, David Prochotta1, Maximilian Murphy1, Monica M. Sheffer5, Moritz 10 Sonnewald6, Maria A. Nilsson2,3, Axel Janke1,2,3 11 12 Affiliations 13 1Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany 14 2Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany 15 3LOEWE-Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany 16 4South African National Biodiversity Institute, National Zoological Garden, Pretoria, South 17 Africa 18 5Zoological Institute and Museum, University of Greifswald, Greifswald, Germany. 19 6Senckenberg Research Institute, Department of Marine Zoology, Section Ichthyology, 20 Frankfurt am Main, Germany 21 *Correspondence: [email protected] 22 23 Email and Orcid: Name e-mail ORCID Sven Winter [email protected] 0000-0002-1890-0977 Stefan Prost [email protected] 0000-0002-6229-3596 Jordi de Raad [email protected] 0000-0002-4991-4431 Raphael T.F. Coimbra [email protected] 0000-0002-6075-7203 Magnus Wolf [email protected] 0000-0001-9212-9861 Marcel Nebenführ [email protected] Annika Held [email protected] Melina Kurzawe [email protected] Ramona Papapostolou [email protected] frankfurt.de Jade Tessien [email protected] Julian Bludau [email protected] Andreas Kelch [email protected] 0000-0002-8265-4643 Sarah Gronefeld [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.08.287078; this version posted September 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Yannis Schöneberg [email protected] 0000-0003-1113- 973X Christian Zeitz [email protected] Konstantin Zapf [email protected] David Prochotta [email protected] Maximilian Murphy [email protected] Monica M. Sheffer [email protected] 0000-0002-6527-4198 Moritz Sonnewald [email protected] Maria A. Nilsson [email protected] 0000-0002-8136-7263 Axel Janke [email protected] 0000-0002-9394-1904 24 25 Abstract 26 Background 27 The common dragonet, Callionymus lyra, is one of three Callionymus species inhabiting the 28 North Sea. All three species show strong sexual dimorphism. The males show strong 29 morphological differentiation, e.g., species-specific colouration and size relations, while the 30 females of different species have few distinguishing characters. Callionymus belongs to the 31 ‘benthic associated clade’ of the order Syngnathiformes. The ‘benthic associated clade’ so far 32 is not represented by genome data and serves as an important outgroup to understand the 33 morphological transformation in ‘long-snouted’ syngnatiforms such as seahorses and 34 pipefishes. 35 Findings 36 Here, we present the chromosome-level genome assembly of C. lyra. We applied Oxford 37 Nanopore Technologies’ long-read sequencing, short-read DNBseq, and proximity-ligation- 38 based scaffolding to generate a high-quality genome assembly. The resulting assembly has a 39 contig N50 of 2.2 Mbp, a scaffold N50 of 26.7 Mbp. The total assembly length is 568.7 Mbp, 40 of which over 538 Mbp were scaffolded into 19 chromosome-length scaffolds. The 41 identification of 94.5% of complete BUSCO genes indicates high assembly completeness. 42 Additionally, we sequenced and assembled a multi-tissue transcriptome with a total length of 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.08.287078; this version posted September 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 43 255.5 Mbp that was used to aid the annotation of the genome assembly. The annotation 44 resulted in 19,849 annotated transcripts and identified a repeat content of 27.66%. 45 Conclusions 46 The chromosome-level assembly of C. lyra provides a high-quality reference genome for 47 future population genomic, phylogenomic, and phylogeographic analyses. 48 49 Keywords 50 Callionymidae, genome annotation, genome assembly, Hi-C, Nanopore, Syngnathiformes 51 52 Data Description 53 Background information 54 Until recently, the family Callionymidae was placed into the order Perciformes, which is often 55 considered a “polyphyletic taxonomic wastebasket for families not placed in other orders” [1]. 56 However, recent phylogenetic analyses suggest a placement of Callionymidae within the order 57 Syngnathiformes, which currently contains ten families with highly derived morphological 58 characters such as the pipefish and seahorses [1]. Syngnathiformes has recently been divided 59 into two clades, a ‘long-snouted clade’ and a ‘benthic associated clade,’ each comprising five 60 families [2]. The ‘long-snouted clade’ (Syngnathidae, Solenostomidae, Aulostomidae, 61 Centriscidae, and Fistulariidae) is currently represented by genomes from the Gulf pipefish 62 (Syngnathus scovelli) and the tiger tail seahorse (Hippocampus comes) [3,4] and additional 63 draft assemblies of pipefish [5]. A genome of the ‘benthic associated clade’ (Callionymidae, 64 Draconettidae, Dactylopteridae, Mullidae, and Pegasidae) has not been sequenced and 65 analysed yet. Callionymidae comprises 196 species [6], of which the common dragonet, 66 Callionymus lyra (Linnaeus, 1758) (Fig. 1), is one of three Callionymus species inhabiting the 67 North Sea [7]. All three species also occur in the East Atlantic, and the Mediterranean Sea [6]. 68 They represent essential prey fish for commercially important fish species such as the cod 69 (Gadus morhua) [8]. The males of the North Sea dragonet species (C. lyra, C. maculatus, C. 70 reticulatus) show strong morphological differentiation in the form of species-specific 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.08.287078; this version posted September 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 71 colouration and size relations. The much less conspicuous females can be distinguished 72 morphologically, with rather high inaccuracy, by the presence or absence of their preopercular, 73 basal spine and by various percentual length ratios. The great resemblance among the 74 different species’ females, together with the fact that all three species can be found in 75 sympatry, suggest the possibility of hybridization among them. 76 77 Here, we present the chromosome-level genome of the common dragonet, representing the 78 first genome of the ‘benthic associated’ Syngnathiformes clade as a reference for future 79 population genomic, phylogenomic, and comparative genomic analyses. The chromosome- 80 level genome assembly was generated as part of a six-week university master’s course. For 81 a detailed description and outline of the course, see [9]. 82 83 Sampling, DNA extraction, and Sequencing 84 We sampled two Callionymus lyra individuals (one of each sex) during a yearly monitoring 85 expedition to the Dogger Bank in the North Sea (Female: 54°59.189'N 1°37.586'E; Male: 86 54°48.271'N 1°25.077'E) with the permission of the Maritime Policy Unit of the UK Foreign 87 and Commonwealth Office in 2019. The samples were initially frozen at -20°C on the ship and 88 later stored at -80°C until further processing. The study was conducted in compliance with the 89 ‘Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of 90 Benefits Arising from Their Utilization’. 91 We extracted high molecular weight genomic DNA (hmwDNA) from muscle tissue of the 92 female individual following the protocol by [10]. Quantity and quality of the DNA was evaluated 93 using the Genomic DNA ScreenTape on the Agilent 2200 TapeStation system (Agilent 94 Technologies). Library preparation for long-read sequencing followed the associated protocols 95 for Oxford Nanopore Technologies (ONT, Oxford, UK) Rapid Sequencing Kit (SQK-RAD004). 96 A total of seven sequencing runs were performed using individual flow cells (FLO-MIN106 97 v.9.41) on a ONT MinION v.Mk1B. 4 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.08.287078; this version posted September 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 98 Additionally, we sent tissue samples to BGI Genomics (Shenzhen, China) to generate 99 additional sequencing data. A 100 bp paired-end short-read genomic DNA sequencing library 100 was prepared from the muscle tissue of the female individual. This library was later used for 101 genome assembly polishing. Moreover, a 100 bp paired-end RNAseq library was prepared for 102 pooled RNA isolates derived from kidney, liver, gill, gonad, and brain tissue of the male 103 individual. Both libraries were sequenced on BGI’s DNBseq platform.
Load more

Recommended publications
  • Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary Megan E
    University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School November 2017 Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary Megan E. Hepner University of South Florida, [email protected] Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the Biology Commons, Ecology and Evolutionary Biology Commons, and the Other Oceanography and Atmospheric Sciences and Meteorology Commons Scholar Commons Citation Hepner, Megan E., "Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary" (2017). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/7408 This Thesis is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Reef Fish Biodiversity in the Florida Keys National Marine Sanctuary by Megan E. Hepner A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science Marine Science with a concentration in Marine Resource Assessment College of Marine Science University of South Florida Major Professor: Frank Muller-Karger, Ph.D. Christopher Stallings, Ph.D. Steve Gittings, Ph.D. Date of Approval: October 31st, 2017 Keywords: Species richness, biodiversity, functional diversity, species traits Copyright © 2017, Megan E. Hepner ACKNOWLEDGMENTS I am indebted to my major advisor, Dr. Frank Muller-Karger, who provided opportunities for me to strengthen my skills as a researcher on research cruises, dive surveys, and in the laboratory, and as a communicator through oral and presentations at conferences, and for encouraging my participation as a full team member in various meetings of the Marine Biodiversity Observation Network (MBON) and other science meetings.
    [Show full text]
  • First Record of the Reticulated Dragonet, Callionymus Reticulatus
    ACTA ICHTHYOLOGICA ET PISCATORIA (2017) 47 (2): 163–171 DOI: 10.3750/AIEP/02098 FIRST RECORD OF THE RETICULATED DRAGONET, CALLIONYMUS RETICULATUS VALENCIENNES, 1837 (ACTINOPTERYGII: CALLIONYMIFORMES: CALLIONYMIDAE), FROM THE BALEARIC ISLANDS, WESTERN MEDITERRANEAN Ronald FRICKE1* and Francesc ORDINES2 1Lauda-Königshofen, Germany 2Instituto Español de Oceanografía, Centre Oceanogràfic de les Balears, Palma de Mallorca, Spain Fricke R., Ordines F. 2017. First record of the reticulated dragonet, Callionymus reticulatus Valenciennes, 1837 (Actinopterygii: Callionymiformes: Callionymidae), from the Balearic Islands, western Mediterranean. Acta Ichthyol. Piscat. 47 (2): 163–171. Background. The reticulated dragonet, Callionymus reticulatus, was originally described based on a single specimen, the holotype from Malaga, Spain, south-western Mediterranean, probably collected before 1831. The holotype is now disintegrated; the specific characteristics are no longer discernible. The species was subsequently recorded from several north-eastern Atlantic localities (Western Sahara to central Norway), but missing in the Mediterranean. Material and methods. Specimens of C. reticulatus were observed and collected during two cruises in 2014 and 2016 in the Balearic Islands off Mallorca and Menorca. The collected specimens (8 females) have been deposited in the collection of the Hebrew University of Jerusalem (HUJ). All individuals of C. reticulatus were collected from beam trawl samples carried out during the DRAGONSAL0914 in September 2014, and during the MEDITS_ES05_16 bottom trawl survey in June 2016, on shelf and slope bottoms around the Balearic Islands. Both surveys used a ‘Jennings’ beam trawl to sample the epi-benthic communities, which was the main objective of the DRAGONSAL0914 and a complementary objective in the MEDITS_ES05_16. The ‘Jennings’ beam trawl has a 2 m horizontal opening, 0.5 m vertical opening and a 5 mm diamond mesh in the codend.
    [Show full text]
  • Biodiversity: the UK Overseas Territories. Peterborough, Joint Nature Conservation Committee
    Biodiversity: the UK Overseas Territories Compiled by S. Oldfield Edited by D. Procter and L.V. Fleming ISBN: 1 86107 502 2 © Copyright Joint Nature Conservation Committee 1999 Illustrations and layout by Barry Larking Cover design Tracey Weeks Printed by CLE Citation. Procter, D., & Fleming, L.V., eds. 1999. Biodiversity: the UK Overseas Territories. Peterborough, Joint Nature Conservation Committee. Disclaimer: reference to legislation and convention texts in this document are correct to the best of our knowledge but must not be taken to infer definitive legal obligation. Cover photographs Front cover: Top right: Southern rockhopper penguin Eudyptes chrysocome chrysocome (Richard White/JNCC). The world’s largest concentrations of southern rockhopper penguin are found on the Falkland Islands. Centre left: Down Rope, Pitcairn Island, South Pacific (Deborah Procter/JNCC). The introduced rat population of Pitcairn Island has successfully been eradicated in a programme funded by the UK Government. Centre right: Male Anegada rock iguana Cyclura pinguis (Glen Gerber/FFI). The Anegada rock iguana has been the subject of a successful breeding and re-introduction programme funded by FCO and FFI in collaboration with the National Parks Trust of the British Virgin Islands. Back cover: Black-browed albatross Diomedea melanophris (Richard White/JNCC). Of the global breeding population of black-browed albatross, 80 % is found on the Falkland Islands and 10% on South Georgia. Background image on front and back cover: Shoal of fish (Charles Sheppard/Warwick
    [Show full text]
  • Distribution and Relative Abundance of Demersal Fishes from Beam Trawl
    CENTRE FOR ENVIRONMENT, FISHERIES AND AQUACULTURE SCI ENCE SCIENCE SERIES TECHNICAL REPORT Number 124 Distribution and relative abundance of demersal fi shes from beam trawl surveys in the eastern English Channel (ICES division VIId) and the southern North Sea (ICES division IVc) 1993-2001 M. Parker-Humphreys LOWESTOFT 2005 1 This report should be cited as: Parker-Humphreys, M. (2005). Distribution and relative abundance of demersal fishes from beam trawl surveys in eastern English Channel (ICES division VIId) and the southern North Sea (ICES division IVc) 1993-2001. Sci. Ser. Tech Rep., CEFAS Lowestoft, 124: 92pp. © Crown copyright, 2005 This publication (excluding the logos) may be re-used free of charge in any format or medium for research for non-commercial purposes, private study or for internal circulation within an organisation. This is subject to it being re-used accurately and not used in a misleading context. The material must be acknowledged as Crown copyright and the title of the publication specified. This publication is also available at www.cefas.co.uk For any other use of this material please apply for a Click-Use Licence for core material at www.hmso.gov.uk/ copyright/licences/core/core_licence.htm, or by writing to: HMSO’s Licensing Division St Clements House 2-16 Colegate Norwich NR3 1BQ Fax: 01603 723000 E-mail: [email protected] 2 CONTENTS ........................................................................................Page 1. Eastern English Channel Fisheries .............................................................................................
    [Show full text]
  • Lincolnshire Time and Tide Bell Community Interest Company The
    To bid, visit #200Fish www.bit.ly/200FishAuction Art inspired by each species of fish found in the North Sea : mail - il,com Auction The At the exhibition and by e and exhibition At the biffvernon@gma Lincolnshire Time and Tide Bell Community Interest Company Bidding is open now by e-mail and at the gallery during the exhibition’s opening hours. Bidding ends 6 pm Monday 3rd September 2018 The #200Fish Auction Thanks to the many artists who have so generously donated their works to the Lincolnshire Time and Tide Bell Community Interest Company to raise funds for our future art and environmental projects, we are selling some of the artworks in the #200Fish exhibition by auction. Here’s how it works. Take a look through this catalogue and if you would like to buy a piece send us an email giving the Fish Number and how much you are willing to pay. Or if you visit the North Sea Observatory during the exhibition, 23rd August to 3rd September, you can hand in your bid on paper. Along with your bid amount, please include your e-mail address and postal address. After the auction closes, at 6pm Monday 3rd September 2018, the person who has bid the highest price wins and we’ll send you an e-mail. Sold works can be collected from the gallery on Tuesday the 4th or from my house in North Somercotes any time later. We can post them to you but will charge whatever it costs us. Bear in mind that the images displayed here are a bit rubbish, just low resolution versions of snapshots as often as not taken on a camera phone rather than in a professional art photo studio.
    [Show full text]
  • Updated Checklist of Marine Fishes (Chordata: Craniata) from Portugal and the Proposed Extension of the Portuguese Continental Shelf
    European Journal of Taxonomy 73: 1-73 ISSN 2118-9773 http://dx.doi.org/10.5852/ejt.2014.73 www.europeanjournaloftaxonomy.eu 2014 · Carneiro M. et al. This work is licensed under a Creative Commons Attribution 3.0 License. Monograph urn:lsid:zoobank.org:pub:9A5F217D-8E7B-448A-9CAB-2CCC9CC6F857 Updated checklist of marine fishes (Chordata: Craniata) from Portugal and the proposed extension of the Portuguese continental shelf Miguel CARNEIRO1,5, Rogélia MARTINS2,6, Monica LANDI*,3,7 & Filipe O. COSTA4,8 1,2 DIV-RP (Modelling and Management Fishery Resources Division), Instituto Português do Mar e da Atmosfera, Av. Brasilia 1449-006 Lisboa, Portugal. E-mail: [email protected], [email protected] 3,4 CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal. E-mail: [email protected], [email protected] * corresponding author: [email protected] 5 urn:lsid:zoobank.org:author:90A98A50-327E-4648-9DCE-75709C7A2472 6 urn:lsid:zoobank.org:author:1EB6DE00-9E91-407C-B7C4-34F31F29FD88 7 urn:lsid:zoobank.org:author:6D3AC760-77F2-4CFA-B5C7-665CB07F4CEB 8 urn:lsid:zoobank.org:author:48E53CF3-71C8-403C-BECD-10B20B3C15B4 Abstract. The study of the Portuguese marine ichthyofauna has a long historical tradition, rooted back in the 18th Century. Here we present an annotated checklist of the marine fishes from Portuguese waters, including the area encompassed by the proposed extension of the Portuguese continental shelf and the Economic Exclusive Zone (EEZ). The list is based on historical literature records and taxon occurrence data obtained from natural history collections, together with new revisions and occurrences.
    [Show full text]
  • Appendix 13.2 Marine Ecology and Biodiversity Baseline Conditions
    THE LONDON RESORT PRELIMINARY ENVIRONMENTAL INFORMATION REPORT Appendix 13.2 Marine Ecology and Biodiversity Baseline Conditions WATER QUALITY 13.2.1. The principal water quality data sources that have been used to inform this study are: • Environment Agency (EA) WFD classification status and reporting (e.g. EA 2015); and • EA long-term water quality monitoring data for the tidal Thames. Environment Agency WFD Classification Status 13.2.2. The tidal River Thames is divided into three transitional water bodies as part of the Thames River Basin Management Plan (EA 2015) (Thames Upper [ID GB530603911403], Thames Middle [ID GB53060391140] and Thames Lower [ID GB530603911401]. Each of these waterbodies are classified as heavily modified waterbodies (HMWBs). The most recent EA assessment carried out in 2016, confirms that all three of these water bodies are classified as being at Moderate ecological potential (EA 2018). 13.2.3. The Thames Estuary at the London Resort Project Site is located within the Thames Middle Transitional water body, which is a heavily modified water body on account of the following designated uses (Cycle 2 2015-2021): • Coastal protection; • Flood protection; and • Navigation. 13.2.4. The downstream extent of the Thames Middle transitional water body is located approximately 12 km downstream of the Kent Project Site and 8 km downstream of the Essex Project Site near Lower Hope Point. Downstream of this location is the Thames Lower water body which extends to the outer Thames Estuary. 13.2.5. A summary of the current Thames Middle water body WFD status is presented in Table A13.2.1, together with those supporting elements that do not currently meet at least Good status and their associated objectives.
    [Show full text]
  • New Zealand Fishes a Field Guide to Common Species Caught by Bottom, Midwater, and Surface Fishing Cover Photos: Top – Kingfish (Seriola Lalandi), Malcolm Francis
    New Zealand fishes A field guide to common species caught by bottom, midwater, and surface fishing Cover photos: Top – Kingfish (Seriola lalandi), Malcolm Francis. Top left – Snapper (Chrysophrys auratus), Malcolm Francis. Centre – Catch of hoki (Macruronus novaezelandiae), Neil Bagley (NIWA). Bottom left – Jack mackerel (Trachurus sp.), Malcolm Francis. Bottom – Orange roughy (Hoplostethus atlanticus), NIWA. New Zealand fishes A field guide to common species caught by bottom, midwater, and surface fishing New Zealand Aquatic Environment and Biodiversity Report No: 208 Prepared for Fisheries New Zealand by P. J. McMillan M. P. Francis G. D. James L. J. Paul P. Marriott E. J. Mackay B. A. Wood D. W. Stevens L. H. Griggs S. J. Baird C. D. Roberts‡ A. L. Stewart‡ C. D. Struthers‡ J. E. Robbins NIWA, Private Bag 14901, Wellington 6241 ‡ Museum of New Zealand Te Papa Tongarewa, PO Box 467, Wellington, 6011Wellington ISSN 1176-9440 (print) ISSN 1179-6480 (online) ISBN 978-1-98-859425-5 (print) ISBN 978-1-98-859426-2 (online) 2019 Disclaimer While every effort was made to ensure the information in this publication is accurate, Fisheries New Zealand does not accept any responsibility or liability for error of fact, omission, interpretation or opinion that may be present, nor for the consequences of any decisions based on this information. Requests for further copies should be directed to: Publications Logistics Officer Ministry for Primary Industries PO Box 2526 WELLINGTON 6140 Email: [email protected] Telephone: 0800 00 83 33 Facsimile: 04-894 0300 This publication is also available on the Ministry for Primary Industries website at http://www.mpi.govt.nz/news-and-resources/publications/ A higher resolution (larger) PDF of this guide is also available by application to: [email protected] Citation: McMillan, P.J.; Francis, M.P.; James, G.D.; Paul, L.J.; Marriott, P.; Mackay, E.; Wood, B.A.; Stevens, D.W.; Griggs, L.H.; Baird, S.J.; Roberts, C.D.; Stewart, A.L.; Struthers, C.D.; Robbins, J.E.
    [Show full text]
  • Aqua, International Journal of Ichthyology AQUA19(1):AQUA 24/01/13 12:37 Pagina 1
    AQUA19(1):AQUA 24/01/13 12:37 Pagina 101 aqua International Journal of Ichthyology Vol. 19 (1), 21 January 2013 Aquapress ISSN 0945-9871 AQUA19(1):AQUA 24/01/13 12:37 Pagina 102 aqua - International Journal of Ichthyology Managing Editor: Scope aqua is an international journal which publishes original Heiko Bleher scientific articles in the fields of systematics, taxonomy, Via G. Falcone 11, bio geography, ethology, ecology, and general biology of 27010 Miradolo Terme (PV), Italy fishes. Papers on freshwater, brackish, and marine fishes Tel. & Fax: +39-0382-754129 will be considered. aqua is fully refereed and aims at pub- E-mail: [email protected] lishing manuscripts within 2-4 months of acceptance. In www.aqua-aquapress.com view of the importance of color patterns in species identi - fication and animal ethology, authors are encouraged to submit color illustrations in addition to descriptions of Scientific Editor: coloration. It is our aim to provide the international sci- entific community with an efficiently published journal Frank Pezold meeting high scientific and technical standards. College of Science & Engineering Texas A&M University – Corpus Christi Call for papers 6300 Ocean Drive – Corpus Christi, TX 78412-5806 The editors welcome the submission of original manu- Tel. 361-825-2349 scripts which should be sent in digital format to the scien- E-mail: [email protected] tific editor. Full length research papers and short notes will be considered for publication. There are no page charges and color illustrations will be published free of charge. Authors will receive one free copy of the issue in which Editorial Board: their paper is published and an e-print in PDF format.
    [Show full text]
  • The Genome of the Gulf Pipefish Enables Understanding of Evolutionary Innovations C
    Small et al. Genome Biology (2016) 17:258 DOI 10.1186/s13059-016-1126-6 RESEARCH Open Access The genome of the Gulf pipefish enables understanding of evolutionary innovations C. M. Small1†, S. Bassham1†, J. Catchen1,2†, A. Amores3, A. M. Fuiten1, R. S. Brown1,4, A. G. Jones5 and W. A. Cresko1* Abstract Background: Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuing these molecular phenomena underlying phenotypic evolution. We explored the genome of the Gulf pipefish (Syngnathus scovelli), which belongs to family Syngnathidae (pipefishes, seahorses, and seadragons). These fishes have dramatically derived bodies and a remarkable novelty among vertebrates, the male brood pouch. Results: We produce a reference genome, condensed into chromosomes, for the Gulf pipefish. Gene losses and other changes have occurred in pipefish hox and dlx clusters and in the tbx and pitx gene families, candidate mechanisms for the evolution of syngnathid traits, including an elongated axis and the loss of ribs, pelvic fins, and teeth. We measure gene expression changes in pregnant versus non-pregnant brood pouch tissue and characterize the genomic organization of duplicated metalloprotease genes (patristacins) recruited into the function of this novel structure. Phylogenetic inference using ultraconserved sequences provides an alternative hypothesis for the relationship between orders Syngnathiformes and Scombriformes. Comparisons of chromosome structure among percomorphs show that chromosome number in a pipefish ancestor became reduced via chromosomal fusions. Conclusions: The collected findings from this first syngnathid reference genome open a window into the genomic underpinnings of highly derived morphologies, demonstrating that de novo production of high quality and useful reference genomes is within reach of even small research groups.
    [Show full text]
  • Louisiana's Animal Species of Greatest Conservation Need (SGCN)
    Louisiana's Animal Species of Greatest Conservation Need (SGCN) ‐ Rare, Threatened, and Endangered Animals ‐ 2020 MOLLUSKS Common Name Scientific Name G‐Rank S‐Rank Federal Status State Status Mucket Actinonaias ligamentina G5 S1 Rayed Creekshell Anodontoides radiatus G3 S2 Western Fanshell Cyprogenia aberti G2G3Q SH Butterfly Ellipsaria lineolata G4G5 S1 Elephant‐ear Elliptio crassidens G5 S3 Spike Elliptio dilatata G5 S2S3 Texas Pigtoe Fusconaia askewi G2G3 S3 Ebonyshell Fusconaia ebena G4G5 S3 Round Pearlshell Glebula rotundata G4G5 S4 Pink Mucket Lampsilis abrupta G2 S1 Endangered Endangered Plain Pocketbook Lampsilis cardium G5 S1 Southern Pocketbook Lampsilis ornata G5 S3 Sandbank Pocketbook Lampsilis satura G2 S2 Fatmucket Lampsilis siliquoidea G5 S2 White Heelsplitter Lasmigona complanata G5 S1 Black Sandshell Ligumia recta G4G5 S1 Louisiana Pearlshell Margaritifera hembeli G1 S1 Threatened Threatened Southern Hickorynut Obovaria jacksoniana G2 S1S2 Hickorynut Obovaria olivaria G4 S1 Alabama Hickorynut Obovaria unicolor G3 S1 Mississippi Pigtoe Pleurobema beadleianum G3 S2 Louisiana Pigtoe Pleurobema riddellii G1G2 S1S2 Pyramid Pigtoe Pleurobema rubrum G2G3 S2 Texas Heelsplitter Potamilus amphichaenus G1G2 SH Fat Pocketbook Potamilus capax G2 S1 Endangered Endangered Inflated Heelsplitter Potamilus inflatus G1G2Q S1 Threatened Threatened Ouachita Kidneyshell Ptychobranchus occidentalis G3G4 S1 Rabbitsfoot Quadrula cylindrica G3G4 S1 Threatened Threatened Monkeyface Quadrula metanevra G4 S1 Southern Creekmussel Strophitus subvexus
    [Show full text]
  • Morphological Variations in the Scleral Ossicles of 172 Families Of
    Zoological Studies 51(8): 1490-1506 (2012) Morphological Variations in the Scleral Ossicles of 172 Families of Actinopterygian Fishes with Notes on their Phylogenetic Implications Hin-kui Mok1 and Shu-Hui Liu2,* 1Institute of Marine Biology and Asia-Pacific Ocean Research Center, National Sun Yat-sen University, Kaohsiung 804, Taiwan 2Institute of Oceanography, National Taiwan University, 1 Roosevelt Road, Sec. 4, Taipei 106, Taiwan (Accepted August 15, 2012) Hin-kui Mok and Shu-Hui Liu (2012) Morphological variations in the scleral ossicles of 172 families of actinopterygian fishes with notes on their phylogenetic implications. Zoological Studies 51(8): 1490-1506. This study reports on (1) variations in the number and position of scleral ossicles in 283 actinopterygian species representing 172 families, (2) the distribution of the morphological variants of these bony elements, (3) the phylogenetic significance of these variations, and (4) a phylogenetic hypothesis relevant to the position of the Callionymoidei, Dactylopteridae, and Syngnathoidei based on these osteological variations. The results suggest that the Callionymoidei (not including the Gobiesocidae), Dactylopteridae, and Syngnathoidei are closely related. This conclusion was based on the apomorphic character state of having only the anterior scleral ossicle. Having only the anterior scleral ossicle should have evolved independently in the Syngnathioidei + Dactylopteridae + Callionymoidei, Gobioidei + Apogonidae, and Pleuronectiformes among the actinopterygians studied in this paper. http://zoolstud.sinica.edu.tw/Journals/51.8/1490.pdf Key words: Scleral ossicle, Actinopterygii, Phylogeny. Scleral ossicles of the teleostome fish eye scleral ossicles and scleral cartilage have received comprise a ring of cartilage supporting the eye little attention. It was not until a recent paper by internally (i.e., the sclerotic ring; Moy-Thomas Franz-Odendaal and Hall (2006) that the homology and Miles 1971).
    [Show full text]