DOCSLIB.ORG

Transcriptome Analysis of the New Zealand Sea Urchin Kina (Evechinus Chloroticus)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Transcriptome Analysis of the New Zealand Sea Urchin Kina (Evechinus Chloroticus) Transcriptome analysis of the New Zealand sea urchin Kina (Evechinus chloroticus) Gareth B Gillard A thesis submitted for the degree of Master of Science at the University of Otago, Dunedin, New Zealand. February 4th 2014 1 Abstract Sea urchins are studied as model organisms for developmental and systems biology, and the sequencing of one species’ genome revealed many avenues for further studies. Sea urchins’ highly expanded innate immune system is a valuable resource for antimicrobials. Furthermore, the gonads of male and female sea urchins, referred to as the roe, are a highly valued food product internationally, with the largest demand from Asian countries such as Japan. The price of roe is greatly influenced by sensory qualities such as colour, texture and flavour, and research has focused on increasing roe quality to give it higher value. Evechinus chloroticus (Kina) is a sea urchin species that is indigenous to New Zealand. It is the type member of the Evechinus genus based on its morphological characteristics. Previous research has focused on identifying physical factors affecting the commercial roe quality of E. chloroticus, including protein and metabolite analysis, but there is almost no genetic information available for this species. E. chloroticus is the only species in its genus and has yet to be subjected to molecular phylogenetic analysis. This study aimed to increase the amount of genetic data available for the E. chloroticus species through transcriptome assembly and analysis, which would aid current and future research on E. chloroticus. In this study, a de novo transcriptome assembly of Illumina sequencing data was carried out. A total of 123 million 100 base length paired-end reads were generated using RNA-Seq libraries from a range of E. chloroticus tissues from two individuals obtained from Fiordland, New Zealand. The assembly resulted in a set of 75,002 transcripts with an accepted read coverage and length, of which 24,655 transcripts could be functionally annotated using protein similarity. Transcripts were further annotated with Gene Ontology, KEGG Orthology and InterPro terms. The first molecular phylogenetic analysis of E. chloroticus to other species of its family was done using multiple genes. When sequences for the mitochondrial NADH dehydrogenase genes were compared, E. chloroticus remained outside of a family level clade, which indicated E. chloroticus is indeed a genetically distinct genus within its family. A differential gene expression analysis was carried out using the new reference transcriptome data. RNA-Seq libraries were generated from the roe of individual E. chloroticus females that showed a distinct grade of roe colour (light, medium or dark) and the expression of genes between different coloured roe was analysed. The results showed most gene expression 2 in the roe remains consistent regardless of the roe colour, with a small proportion of genes shown to have differential expression. Differentially expressed genes could now be investigated to understand the role of genes whose expression correlates with colour. This study has produced a large set of E. chloroticus transcripts (and predicted proteins) along with functional annotations, vastly increasing the amount of genomic data available for this species. This provides a resource for current and future studies on E. chloroticus, either to increase its commercial value, or its use as a model organism. The phylogenetic results provide a basis for further analysis of relationships between E. chloroticus and its family members, and its evolutionary history. The differential gene expression results provide the first transcriptome analysis of differences in roe colour and the data will be valuable for current and future molecular research on roe colour qualities. 3 Table of contents Abstract .................................................................................. 2 Table of contents .................................................................... 4 List of figures ......................................................................... 7 List of tables ........................................................................... 8 List of Abbreviations .............................................................. 8 Chapter 1 - Introduction ....................................................... 10 1.1 The sea urchin ......................................................................................... 10 1.1.1 The Echinodermata phylum ..................................................................................... 10 1.1.2 The sea urchin as a model organism ........................................................................ 10 1.1.3 Biology of the sea urchin ......................................................................................... 11 1.1.4 Sea urchin roe as a valued food product .................................................................. 13 1.2 Evechinus chloroticus, the New Zealand sea urchin ................................ 14 1.2.1 Ecology of E. chloroticus ........................................................................................ 14 1.2.2 The marketplace and roe quality .............................................................................. 15 1.2.3 Pigmentation in E. chloroticus roe .......................................................................... 16 1.2.4 Phylogeny of E. chloroticus .................................................................................... 18 1.3 Transcriptome analysis study .................................................................. 19 1.3.1 Transcriptome analysis of E. chloroticus ................................................................ 19 1.3.2 RNA-Seq.................................................................................................................. 19 1.3.3 De novo assembly analysis ...................................................................................... 20 1.3.4 Function annotation ................................................................................................. 22 1.3.5 Phylogenetic analysis............................................................................................... 22 1.5.6 Differential expression analysis using RNA-Seq .................................................... 23 1.4 Research goals ........................................................................................ 24 1.5 Aims ....................................................................................................... 24 Chapter 2 - Methods ............................................................. 25 2.1 Transcriptome assembly .......................................................................... 25 2.1.1 Sample collection..................................................................................................... 25 2.1.2 RNA extraction and sequencing .............................................................................. 26 4 2.1.3 Quality analysis ........................................................................................................ 27 2.1.4 De novo assembly..................................................................................................... 29 2.1.5 Post-processing transcripts ....................................................................................... 30 2.1.6 Assembly completeness ........................................................................................... 31 2.2 Functional annotation .............................................................................. 32 2.2.1 Protein similarity search ........................................................................................... 32 2.2.2 Functional term annotations ..................................................................................... 33 2.2.3 Unannotated transcript analysis ............................................................................... 34 2.3 Phylogenetic analysis .............................................................................. 35 2.3.1 Identification of evolutionary conserved genes for E. chloroticus .......................... 35 2.3.2 Sequence alignments ................................................................................................ 36 2.3.3 Phylogenetic trees .................................................................................................... 37 2.4 Gene expression analysis in different coloured roe .................................. 37 2.4.1 Sample selection and RNA sequencing ................................................................... 38 2.4.2 Pooled sample analysis............................................................................................. 38 2.4.3 Quality analysis ........................................................................................................ 39 2.4.4 Read alignment and novel transcript assembly ........................................................ 39 2.4.5 Count data generation............................................................................................... 40 2.4.6 Most abundant transcripts in female roe .................................................................. 41 2.4.7 Differential expression analysis of genes ................................................................. 41 2.4.8 Gene set analysis of functional terms ....................................................................... 42 2.4.9 Cluster analysis of gene expression ........................................................................
Load more

Recommended publications
  • Risk Analysis: Vessel Biofouling
    Risk Analysis: Vessel Biofouling ISBN 978-0-478-37548-0 (print) ISBN 978-0-478-37549-7 (online) 15 February 2011 Risk Analysis: Vessel Biofouling 15 February 2011 Approved for general release Christine Reed Manager, Risk Analysis Ministry of Agriculture and Forestry Requests for further copies should be directed to: Publication Adviser MAF Information Bureau P O Box 2526 WELLINGTON Telephone: 0800 00 83 33 Facsimile: 04-894 0300 This publication is also available on the MAF website at http://www.biosecurity.govt.nz/regs/imports/ihs/risk © Crown Copyright - Ministry of Agriculture and Forestry i Contributors to this risk analysis 1. Primary author/s Dr Andrew Bell Senior Adviser MAF Biosecurity New Zealand Risk Analysis, Marine Wellington Simon Phillips Adviser MAF Biosecurity New Zealand Risk Analysis, Marine Wellington Dr Eugene Georgiades Senior Adviser MAF Biosecurity New Zealand Risk Analysis, Marine Wellington Dr Daniel Kluza Senior Adviser MAF Biosecurity New Zealand Risk Analysis, Marine Wellington 2. Secondary contributors Dr Christopher Denny Adviser MAF Biosecurity New Zealand Border Standards Wellington 3. External peer review John Lewis Principal Marine Consultant ES Link Services Pty Ltd Melbourne, Victoria, Australia Richard Piola Senior Scientist Cawthron Institute Nelson, New Zealand The draft risk analysis has also been internally reviewed by: Liz Jones (Border Standards); Justin McDonald (Post-Clearance); Melanie Newfield (Risk Analysis); Howard Pharo (Risk Analysis); Sandy Toy (Risk Analysis). The contribution of all the reviewers is gratefully acknowledged. ii Contents Page Executive summary 1 Definitions 7 1. Introduction 8 1.1. Background 8 1.2. Scope 13 1.3. References 14 2. Methodology 19 2.1.
    [Show full text]
  • Growth, Regeneration, and Damage Repair of Spines of the Slate-Pencil Sea Urchin Heterocentrotus Mammillatus (L.) (Echinodermata: Echinoidea)!
    Pacific Science (1988), vol. 42, nos. 3-4 © 1988 by the University of Hawaii Press. All rights reserved Growth, Regeneration, and Damage Repair of Spines of the Slate-Pencil Sea Urchin Heterocentrotus mammillatus (L.) (Echinodermata: Echinoidea)! THOMAS A. EBERT2 ABSTRACT: Spines of sea urchins are appendages that are associated with defense, locomotion, and food gathering. Spines are repaired when damaged, and the dynamics of repair was studied in the slate-pencil sea urchin Hetero­ centrotus mammillatus to provide insights not only into the processes of healing . but also into the normal growth of spines and the formation of growth lines. Regeneration of spines on tubercles following complete removal of a spine was slow and depended upon the size of the original spine. The maximum amount of regeneration occurred on tubercles with spines of intermediate size (1.6 g), which, on average, developed regenerated spines weighing 0.1, 0.3, and 0.7 g after 4, 8, and 12 months, respectively. Some large tubercles, which had original spines weighing over 3 g, failed to develop a new spine even after 8-12 months. Regeneration ofa new tip on a cut stump was more rapid than production of a new spine on a tubercle . Regeneration to original size was more rapid for small spines than for large spines, but large stumps produced more calcite per unit time. In 4 months, a small spine with a removed tip weighing 0.15 g regenerated a new tip weighing 0.09 g, or 63% of its original weight. In the same time, a large spine with 2.35 g of tip removed regenerated 0.40 g of new tip, or 17% of the original weight.
    [Show full text]
  • Scientific and Biodiversity Values of Marine Reserves: a Review.DOC Research and Development Series 340
    Scientific and biodiversity values of marine reserves A review DOC RESEARCH AND DEVELOPMENT SERIES 340 Trevor J. Willis DOC Research & Development Series is a published record of scientific research carried out, or advice given, by Department of Conservation staff or external contractors funded by DOC. It comprises reports and short communications that are peer-reviewed. This report is available from the departmental website in pdf form. Titles are listed in our catalogue on the website, refer www.doc.govt.nz under Publications, then Science & technical. © Copyright October 2013, New Zealand Department of Conservation ISSN 1177–9306 (web PDF) ISBN 978–0–478–14999–9 (web PDF) This report was prepared for publication by the Publishing Team; editing by Sue Hallas and layout by Lynette Clelland. Publication was approved by the Deputy Director-General, Science and Capability Group, Department of Conservation, Wellington, New Zealand. Published by Publishing Team, Department of Conservation, PO Box 10420, The Terrace, Wellington 6143, New Zealand. In the interest of forest conservation, we support paperless electronic publishing. CONTENTS Abstract 1 1. Introduction 2 2. Research in New Zealand marine reserves 4 2.1 Peer-reviewed literature 5 2.2 University theses 7 2.3 Unpublished reports 9 2.4 Monitoring in New Zealand marine reserves 9 2.4.1 What is ‘monitoring’? 9 2.4.2 Comments on survey designs for monitoring 9 2.4.3 Trends in biological indicators 14 2.4.4 Understanding the biology of targeted species—a cautionary tale for meta-analysts 15 3. The value of marine reserves 17 3.1 Scientific research 17 3.1.1 Safety of in situ experiments and apparatus 17 3.1.2 Access to depleted species 17 3.1.3 Marine reserves as reference points for environmental and fishery management 21 3.2 Biodiversity values of marine reserves 25 3.3 Concluding remarks 26 4.
    [Show full text]
  • Endemic Species of Christmas Island, Indian Ocean D.J
    RECORDS OF THE WESTERN AUSTRALIAN MUSEUM 34 055–114 (2019) DOI: 10.18195/issn.0312-3162.34(2).2019.055-114 Endemic species of Christmas Island, Indian Ocean D.J. James1, P.T. Green2, W.F. Humphreys3,4 and J.C.Z. Woinarski5 1 73 Pozieres Ave, Milperra, New South Wales 2214, Australia. 2 Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria 3083, Australia. 3 Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia. 4 School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia. 5 NESP Threatened Species Recovery Hub, Charles Darwin University, Casuarina, Northern Territory 0909, Australia, Corresponding author: [email protected] ABSTRACT – Many oceanic islands have high levels of endemism, but also high rates of extinction, such that island species constitute a markedly disproportionate share of the world’s extinctions. One important foundation for the conservation of biodiversity on islands is an inventory of endemic species. In the absence of a comprehensive inventory, conservation effort often defaults to a focus on the better-known and more conspicuous species (typically mammals and birds). Although this component of island biota often needs such conservation attention, such focus may mean that less conspicuous endemic species (especially invertebrates) are neglected and suffer high rates of loss. In this paper, we review the available literature and online resources to compile a list of endemic species that is as comprehensive as possible for the 137 km2 oceanic Christmas Island, an Australian territory in the north-eastern Indian Ocean.
    [Show full text]
  • The Effects of Oxygen Supply When Immersed on the Thermal Limits and Performance of the Wave Zone Echinoderm Colobocentrotus Atratus
    THE EFFECTS OF OXYGEN SUPPLY WHEN IMMERSED ON THE THERMAL LIMITS AND PERFORMANCE OF THE WAVE ZONE ECHINODERM COLOBOCENTROTUS ATRATUS A THESIS SUBMITTED TO THE GRADUATE DIVISION OF THE UNIVERSITY OF HAWAI‘I AT MĀNOA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTERS OF SCIENCE IN ZOOLOGY AUGUST 2017 By Sean L. Wilbur Thesis Committee: Amy L. Moran, Chairperson Amber N. Wright Celia M. Smith ACKNOWLEDGMENTS I would like to thank those who have provided their support and guidance during my stint in graduate school. First and foremost, I would like to thank my major advisor Amy Moran for taking a chance on me from the beginning and always providing support, both intellectual and material. The entire Moran lab played a huge part in helping me develop as a scientist and refine my research goals. I want to thank all my colleagues in both the Moran lab and at Kewalo marine lab, who both helped provide guidance and were critical in assisting in dangerous field work. I would also like to thank my committee members Amber Wright and Celia Smith for providing assistance with data analysis and intellectual input into my research. Additionally, I would like to acknowledge my undergraduate advisor, Michael Hadfield, who helped mold me as a young scientist and encouraged me to continue my intellectual pursuits. Lastly, I would like to thank my family for never doubting my resolve and always supporting me in my endeavors. I would like to thank my wife, Ashley Wilbur, for all she has sacrificed to support me and being patient with me.
    [Show full text]
  • Māhā'ulepū, Island of Kaua'i Reconnaissance Survey
    National Park Service U.S. Department of the Interior Pacific West Region, Honolulu Office February 2008 Māhā‘ulepū, Island of Kaua‘i Reconnaissance Survey THIS PAGE INTENTIONALLY LEFT BLANK TABLE OF CONTENTS 1 SUMMARY………………………………………………………………………………. 1 2 BACKGROUND OF THE STUDY……………………………………………………..3 2.1 Background of the Study…………………………………………………………………..……… 3 2.2 Purpose and Scope of an NPS Reconnaissance Survey………………………………………4 2.2.1 Criterion 1: National Significance………………………………………………………..4 2.2.2 Criterion 2: Suitability…………………………………………………………………….. 4 2.2.3 Criterion 3: Feasibility……………………………………………………………………. 4 2.2.4 Criterion 4: Management Options………………………………………………………. 4 3 OVERVIEW OF THE STUDY AREA…………………………………………………. 5 3.1 Regional Context………………………………………………………………………………….. 5 3.2 Geography and Climate…………………………………………………………………………… 6 3.3 Land Use and Ownership………………………………………………………………….……… 8 3.4. Maps……………………………………………………………………………………………….. 10 4 STUDY AREA RESOURCES………………………………………..………………. 11 4.1 Geological Resources……………………………………………………………………………. 11 4.2 Vegetation………………………….……………………………………………………...……… 16 4.2.1 Coastal Vegetation……………………………………………………………………… 16 4.2.2 Upper Elevation…………………………………………………………………………. 17 4.3 Terrestrial Wildlife………………..........…………………………………………………………. 19 4.3.1 Birds……………….………………………………………………………………………19 4.3.2 Terrestrial Invertebrates………………………………………………………………... 22 4.4 Marine Resources………………………………………………………………………...……… 23 4.4.1 Large Marine Vertebrates……………………………………………………………… 24 4.4.2 Fishes……………………………………………………………………………………..26
    [Show full text]
  • The Effects of Environmental Factors and Husbandry Techniques on Roe Enhancement of the New Zealand Sea Urchin, Evechinus Chloroticus
    The Effects of Environmental Factors and Husbandry Techniques on Roe Enhancement of the New Zealand Sea Urchin, Evechinus chloroticus By Philip James A thesis submitted to the Victoria University of Wellington in fulfilment of the requirements for the degree of Doctor of Philosophy in Marine Biology Victoria University of Wellington 2007 ABSTRACT The roe of sea urchins (Echinodermata: echinoidea) is a prized seafood in a number of countries around the world, including New Zealand. Increasing fishing pressure on world sea urchin stocks has failed to meet demand. This has led to increasing worldwide interest in roe enhancement of sea urchins. In New Zealand kina (Evechinus chloroticus) have also been heavily fished. However, there are large numbers of poor quality (low gonad index or GI) kina found in kina barrens which are uneconomic to harvest due to low returns. The primary aim of this research was to identify the key holding and environmental conditions for roe enhancement of E. chloroticus to assist in the development of a roe enhancement industry for E. chloroticus to utilise this resource. A series of experiments testing the optimal holding conditions for E. chloroticus in both land- and sea-based holding systems showed that culture depth (3 and 6 m) and removal of the urchins from the water three times per week had no significant effect on gonad growth or urchin mortality. However, exposing E. chloroticus to increased water movement resulted in significantly greater gonad growth in 12 weeks. Increasing water movement is believed to increase the available dissolved oxygen and facilitate the removal of metabolites from around the urchins.
    [Show full text]
  • Echinodermata Associated with Coral Reefs of Andaman and Nicobar Islands
    Rec. zoo!. Surv. India: 100 (Part 3-4) : 21-60, 2002 ECHINODERMATA ASSOCIATED WITH CORAL REEFS OF ANDAMAN AND NICOBAR ISLANDS D. R. K. SASTRY Zoological Survey of India, A & N Regional Station, Port Blair - 744 102 INTRODUCTION Coral reefs are an important ecosystem of the coastal environment. The reef ecosystem IS highly productive and provides substratum, shelter, food etc. to a variety of biota. Consequently a number of faunal and floral elements are attracted towards the reef ecosystem and are closely associated with each other to form a community. Thus the reefs are also rich in biodiversity. Among the coral reef associates echinoderms are a conspicuous element on account of their size, abundance and effect on the reef ecosystem including the corals. In spite of their importance in the coral reef ecosystem and its conservation, very few studies were made on the echinoderm associates of the coral reefs. Though there were some studies elsewhere, the information on reef­ associated echinoderms of Indian coast is meager and scattered (see Anon, 1995). Hence an attempt is made here to collate the scattered accounts and unpublished information available with Zoological Survey of India. Since the information is from several originals and quoted references and many are to be cited often, these are avoided in the text and a comprehensive bibliography is appended which served as source material and also provides additional references of details and further information. ECHINODERMS OF CORAL REEFS More than 200 species of echinoderms occur in the reef ecosystem of Andaman and Nicobar Islands. These belong to five extant classes with 30 to 60 species of each class.
    [Show full text]
  • The Echinoderm Newsletter
    ! ""'".--'"-,,A' THE ECHINODERM NEWSLETTER NUlIlber 24. 1999 Editor: Cynthia Ahearn Smithsonian Institution National Museum of Natural History Room W-31S, Mail Stop 163 Washington D.C. 20560-0163 U.S.A. [email protected] Distributed by: David Pawson Smithsonian Institution National Museum of Natural History Room W-323, Mail Stop 163 Washington D.C. 20560-0163 U.S.A. The newsletter contains information concerning meetings and conferences, publications of interest to echinoderm biologists, titles of theses on echinoderms, and research interests, and addresses of echinoderm biologists. Individuals who desire to receive the newsletter should send their name, address and research interests to the editor. scientific literature. and a published document. Koehler, 1899 '•.:.•/'i9 VIRTUAL ECHINODERM NEWSLETTER http://www.nmnh.si.edu/iz/echinoderm • TABLE OF CONTENTS Echinoderm Specialists Addresses; (p-); Fax (f-); e-mail numbers 1 Current Research 39 Papers Presented at Meetings (by country or region) Algeria 63 Australia 64 Europe. .................................................................64 Hong Kong 67 India 67 Jamaica ',' 67 Malaysia 68 Mexico 68 New Zealand 68 Pakistan 68 Russia 68 South America 69 United States 69 Papers Presented at Meetings (by conference) SYmposium on Cenozoic Paleobiology, Florida 71 Annual Meeting of Society for Integrative and Comparative Biology 71 Sixty-Ninth Annual Meeting of the Zoological Society of Japan 73 XIX Congreso de Ciencias del Mar, Chile 76 Evo 1uti on '99......................................................... 77 Fifth Florida Echinoderm Festival 78 10th International Echinoderm Conference 79 Theses and Dissertations 80 Announcements, Notices and Conference Announcements 86 Information Requests and Suggestions 88 Ailsa's Section Contribution by Lucia Campos-Creasey 90 Echinoderms in Literature 91 How I Began Studying Echinoderms - part 9 92 Obituaries Maria da Natividade Albuquerque 93 Alan S.
    [Show full text]
  • Sea Urchin Aquaculture
    American Fisheries Society Symposium 46:179–208, 2005 © 2005 by the American Fisheries Society Sea Urchin Aquaculture SUSAN C. MCBRIDE1 University of California Sea Grant Extension Program, 2 Commercial Street, Suite 4, Eureka, California 95501, USA Introduction and History South America. The correct color, texture, size, and taste are factors essential for successful sea The demand for fish and other aquatic prod- urchin aquaculture. There are many reasons to ucts has increased worldwide. In many cases, develop sea urchin aquaculture. Primary natural fisheries are overexploited and unable among these is broadening the base of aquac- to satisfy the expanding market. Considerable ulture, supplying new products to growing efforts to develop marine aquaculture, particu- markets, and providing employment opportu- larly for high value products, are encouraged nities. Development of sea urchin aquaculture and supported by many countries. Sea urchins, has been characterized by enhancement of wild found throughout all oceans and latitudes, are populations followed by research on their such a group. After World War II, the value of growth, nutrition, reproduction, and suitable sea urchin products increased in Japan. When culture systems. Japan’s sea urchin supply did not meet domes- Sea urchin aquaculture first began in Ja- tic needs, fisheries developed in North America, pan in 1968 and continues to be an important where sea urchins had previously been eradi- part of an integrated national program to de- cated to protect large kelp beds and lobster fish- velop food resources from the sea (Mottet 1980; eries (Kato and Schroeter 1985; Hart and Takagi 1986; Saito 1992b). Democratic, institu- Sheibling 1988).
    [Show full text]
  • SPC Beche-De-Mer Information Bulletin #35 – March 2015
    Secretariat of the Pacific Community ISSN 1025-4943 Issue 35 – March 2015 BECHE-DE-MER information bulletin Inside this issue Editorial Spatial sea cucumber management in th Vanuatu and New Caledonia The 35 issue of Beche-de-mer Information Bulletin has eight original M. Leopold et al. p. 3 articles, all very informative, as well as information about workshops and meetings that were held in 2014 and forthcoming 2015 conferences. The sea cucumbers (Echinodermata: Holothuroidea) of Tubbataha Reefs Natural Park, Philippines The first paper is by Marc Léopold, who presents a spatial management R.G. Dolorosa p. 10 strategy developed in Vanuatu and New Caledonia (p. 3). This study pro- vides interesting results on the type of approach to be developed to allow Species list of Indonesian trepang A. Setyastuti and P. Purwati p. 19 regeneration of sea cucumber resources and better management of small associated fisheries. Field observations of sea cucumbers in the north of Baa atoll, Maldives Species richness, size and density of sea cucumbers are investigated by F. Ducarme p. 26 Roger G. Dolorosa (p. 10) in the Tubbataha Reefs Natural Park, Philippines. Spawning induction and larval rearing The data complement the nationwide monitoring of wild populations. of the sea cucumber Holothuria scabra in Malaysia Ana Setyastuti and Pradina Purwati (p. 19) provide a list of all the species N. Mazlan and R. Hashim p. 32 included in the Indonesian trepang, which have ever been, and still are, Effect of nurseries and size of released being fished for trade. The result puts in evidence 54 species, of which 33 Holothuria scabra juveniles on their have been taxonomically confirmed.
    [Show full text]
  • A Literature Review on the Poor Knights Islands Marine Reserve
    A literature review on the Poor Knights Islands Marine Reserve Carina Sim-Smith Michelle Kelly 2009 Report prepared by the National Institute of Water & Atmospheric Research Ltd for: Department of Conservation Northland Conservancy PO Box 842 149-151 Bank Street Whangarei 0140 New Zealand Cover photo: Schooling pink maomao at Northern Arch Photo: Kent Ericksen Sim-Smith, Carina A literature review on the Poor Knights Islands Marine Reserve / Carina Sim-Smith, Michelle Kelly. Whangarei, N.Z: Dept. of Conservation, Northland Conservancy, 2009. 112 p. : col. ill., col. maps ; 30 cm. Print ISBN: 978-0-478-14686-8 Web ISBN: 978-0-478-14687-5 Report prepared by the National Institue of Water & Atmospheric Research Ltd for: Department of Conservation, Northland Conservancy. Includes bibliographical references (p. 67 -74). 1. Marine parks and reserves -- New Zealand -- Poor Knights Islands. 2. Poor Knights Islands Marine Reserve (N.Z.) -- Bibliography. I. Kelly, Michelle. II. National Institute of Water and Atmospheric Research (N.Z.) III. New Zealand. Dept. of Conservation. Northland Conservancy. IV. Title. C o n t e n t s Executive summary 1 Introduction 3 2. The physical environment 5 2.1 Seabed geology and bathymetry 5 2.2 Hydrology of the area 7 3. The biological marine environment 10 3.1 Intertidal zonation 10 3.2 Subtidal zonation 10 3.2.1 Subtidal habitats 10 3.2.2 Subtidal habitat mapping (by Jarrod Walker) 15 3.2.3 New habitat types 17 4. Marine flora 19 4.1 Intertidal macroalgae 19 4.2 Subtidal macroalgae 20 5. The Invertebrates 23 5.1 Protozoa 23 5.2 Zooplankton 23 5.3 Porifera 23 5.4 Cnidaria 24 5.5 Ectoprocta (Bryozoa) 25 5.6 Brachiopoda 26 5.7 Annelida 27 5.8.
    [Show full text]