Aquatic Genomics: Steps Toward a Great Future

448 Pages·2003·13.14 MB·English

by  Melody S. Clark (auth.)

Springer Japan KK
N. Shimizu · T. Aoki
I. Hirono · F. Takashima
(Eds.)
Aquatic Genomics
Steps Toward a Great Future
With 120 Figures, Including 12 in Color
, Springer
ISBN 978-4-431-65940-2
Library of Congress Cataloging-in-Publication Data
Aquatic genomics : steps toward a great future / N. Shimizu ... ret al.l (eds.).
p.cm.
Includes bibliographical references (p. ).
ISBN 978-4-431-65940-2 ISBN 978-4-431-65938-9 (eBook)
DOI 10.1007/978-4-431-65938-9
I. Fishes--Genome mapping. 2. Shellfish--Genome mapping. 3. Fishes--Genetics. 4.
Shellfish--Genetics. I. Shimizu, Nobuyoshi, 1941-
QL638.99.A672002
572.8'63317--dc21 2002030465
Printed on acid-free paper
© Springer Japan 2003
Originally published by Springer-Verlag Tokyo Heidelberg New York in 2003
Softcove:r reprint of the hardcover 1st edition 2003
This work is subject to copyright. All rights are reserved, whether the whole or part of the material is
concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting,
reproduction on microfilms or in other ways, and storage in data banks.
The use of registered names, trademarks, etc. in this publication does not imply, even in the absence of a
specific statement, that such names are exempt from the relevant protective laws and regulations and
therefore free for general use.
Typesetting: Authors
SPIN: 10832954
Preface
In a scientific pursuit there is continual food for discovery and wonder.
M. Shelley (1818)
Genomic analysis of aquatic species has long been overshadowed by the superb
activity of the human genome project. However, aquatic genomics is now in the
limelight as evidenced by the recent accomplishment of fugu genome sequencing,
which provided a significant foundation for comparative fish genomics. Undoubt
edly, such progress will provide an exciting and unparalleled boost to our knowl
edge of the genetics of aquatic species. Thus, aquatic genomics research has become
a promising new research field with an impact on the fishery industry. It is notewor
thy that the Food and Agriculture Organization (FAO) of the United Nations has
projected that current global fisheries production will soon become insufficient to
supply the increasing world population and that aquaculture has a great potential to
fulfill that demand.
This book, Aquatic Genomic.~: Steps Toward a Great Future, was designed as a
collection of advanced knowledge in aquatic genomics and biological sciences. It
covers a variety of aquatic organisms including fish, crustaceans, and shellfish, and
describes various advanced methodologies, including genome analysis, gene map
ping, DNA markers, and EST analysis. Also included are discussions of many sub
jects such as regulation of gene expression, stress and immune responses, sex differ
entiation, hormonal control, and transgenic fishes. This book therefore establishes a
foundation to unify our current understanding of the genomic nature of the aquatic
species, which we believe is essential for taking steps toward a great future of aquatic
genomics.
This volume was conceived following the first Aquatic Genomics Symposium,
held at the Tokyo University of Fishcries in November 2000. The editors (also as
symposium organizers) gratefully acknowledge the generous financial support pro
vided by the Ministry of Education, Sports and Culture of Japan, the Japanese Soci
ety for the Promotion of Science, Tokyo University of Fisheries, Keio University,
Mitsubishi Chemical Corporation, Vic Bang Co. Ltd., and the Mie Union of Fisher
ies Co-operative Association. We also thank the many people who participated in
the symposium.
v
VI Preface
We believe that Aquatic Genomics will become a bible for all scientists who are
interested in aquatic creatures and are fascinated with the as-yet-unrevealed nature
oftheir genomics.
EDITORS
Nobuyoshi Shimizu
Takashi Aoki
Ikuo Hirono
Fumio Takashima
Contents
Preface......................................................... V
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . X
Fugu: a comparative perspective
M.S. Clark ................................................... .
Duplication Of a portion of human chromosome 20q containing
Topoisomerase (TopJ) and Snail genes provides evidence on
genome expansion and the radiation of teleost fish
IH. Postlethwait, A. Amores, Y-L. Yan, and C. Austin ............. 20
The genetic basis of biodiversity: genomic studies of cichlid fishes
T.D. Kocher, R.C. Albertson, K.L. Carleton, and IT. Streelman . . . . . 35
Gene mapping, isolation and genetic improvement in catfish
R.A. Dunham and Z. Liu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Shrimp genomics: development of a genetic map to identify QTLs
responsible for economically important traits in Litopenaeus vannamei
A. Alcivar-Warren, Z. Xu, D. Meehan, Y. Fan, and L. Song. . . . . . . . . 61
Genomic approaches to understanding heterosis and improving
yield of Pacific oysters
D. Hedgecock . . . . . . . . . . . . . . . . . . . . . ... . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Genomic approaches to marker development and mapping in
the eastern oyster, Crassostrea virginica
P. Gaffney .................................................... 84
The impact of aquatic genomics on fish immunology
G. Warr ...................................................... 92
Expressed sequence tag analyses of the Japanese flounder,
Paralichthys olivaceus
T. Aoki, C. Tucker, and I. Hirono .......... . . . . . . . . . . . . . . . . . . . . . . 102
Expressed sequence tags - a snapshot of the fish genome
S.E. Douglas, S.C.M. Tsoi, S. Penny, K. Melville, M.E. Reith, and
K.V. Ewart ................................................... 115
VII
VIII Contents
Genomics of the Pacific oyster Crassostrea gigas
N. Shimizu, J -Y. Lee, Y. Shimizu, H. Ohtake, Y. Sato, and
S. Asakawa ................................................... 128
Survey of Hox genes in the skate, Raja egalanteria
c.B. Kim, D. Weiss, and F. Ruddle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Toward genetic dissection of motor neuron differentiation
H. Okamoto, H. Segawa, and S. Higashijima . . . . . . . . . . . . . . . . . . . . . . 139
Genes regulating the growth of myotomal muscle in teleost fish
LA. Johnston, T.E. Hall, and D.A. Fernandez. . . . . . . . . . . . . . . . . . . . . 153
Temporal and spatial expression patterns of mRNAs encoding myosin
heavy chain isoforms in association with those of related transcription
factors during temperature acclimation of carp
A. Kobiyama, Y. Nihei, and S. Watabe.. . ... ..... .. . .. . . .. ...... .. 167
Genome fluidity in the fish Xiphophorus
J-N. Volff, A. Froschauer, C. Korting, W. Bernhardt, 1. Nanda,
C. Schultheis, M. Schmid, and M. Schartl . . . . . . . . . . . . . . . . . . . . . . . . . 185
Stress response and apoptosis in zebrafish embryos
M. Yamashita, K. Uchino, Y. Taguchi, S. Imamura, D. Uchida,
T. Yabu, M. Hojo, and N. Ojima . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
Taurine transporter: hyperosmotic stress-responsive gene
K. Takeuchi and H. Toyohara . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Molecular evolution of proopiomelanocortin in fish
A. Takahashi, Y. Amemiya, M. Nozaki, S.A. Sower, and
H. Kawauchi. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
Quantitative analyses of the levels of hormonal mRNAs in the salmon
neuroendocrine system
A. Urano and H. Ando . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
Positional cloning of the sex-determining region of medaka using a
Y congenic strain
M. Matsuda and Y. Nagahama . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
The GnRH system in teleosts
K. Okubo, Y. Yoshiura, M. Amano, H. Suetake, and K. Aida. . . . . . . . 244
Gene expression and structure of globin genes of carp
S. Minagawa, M. Miyata, 1. Hirono, and T. Aoki .................. 263
Induction and molecular regulation of host cell apoptosis by
infectious pancreatic necrosis virus infection
J-R. Hong and J-L. Wu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
Contents IX
Fish cytokine genes
C.1. Secombes, 1. Zou, and B. Collet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Immune-related genes of the Japanese flounder, Paralichthys olivaceus
I. Hirono and T. Aoki . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286
The lysozyme gene in fish
1. Hikima, I. Hirono, and T. Aoki .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301
Visualization and isolation of live primordial germ cells aimed at
cell-mediated gene transfer in rainbow trout
Y. Takeuchi, G. Yoshizaki, H. Tominaga, T. Kobayashi, and
T. Takeuchi..... ..... . .. ... . .. .... .. ...... .. .. .... .. . . .. ...... 310
Transgenic medaka as a model for fish biology and aquaculture
M. Kinoshita and M. Tanaka ................................... 320
Generation of living color transgenic zebrafish
Z. Gong, H. Wan, B. Ju, 1. He, X. Wang, and T. Yan . . . . . . . . . . . . . . . . 329
Identification of virulence genes in bacterial fish pathogens:
a genomic and proteomic approach
y'p. Tan, P.S.S. Rao, Y.L. Zhang, C.L. Hew, and K.Y. Leung 340
Identification of minimal promoter required for retinal-specific
expression of carp rhodopsin gene by transgenic fish
C-Y. Su, T-M. Wang, and H-1. Tsai. . ..... .. ........ . . ..... .... ... 352
Exploiting transgenic tilapia and the tilapia genome
N. Maclean, G-L. Hwang, and H. Farahmand T. .................. 365
Recent advances in transgenic fish technology
T.T. Chen, A. Sarmasik, C.Z. Chun, 1.K. Lu. and P. Chiou .......... 382
Genetic analysis of complex traits using clonal rainbow trout lines
G.H. Thorgaard, P.A. Wheeler, WP. Young, B.D. Robison, and
S.S. Ristow ................................................... 395
The contribution of quantitative genetics to fish breeding
A. Ozaki, T. Sakamoto, and N. Okamoto .. . . . . . . . . . . . . . . . . . . . . . . . 399
Production of cloned fish by chromosome manipulation and
confirmation by DNA markers
K. Kato ...................................................... 410
DNA markers as a tool for genetic management of brood stock
for aquaculture
N. Taniguchi, R. Perez-Enriquez, and N. Estu . . . . . . . . . . . . . . . . . . . . . 417
Key-word Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 430
Contributors
Asakawa, S., Department of Molecular Biology, Keio University School of
Medicine, Japan
Aida, K., Department of Aquatic Bioscience, Graduate School of Agricultural
and Life Sciences, University of Tokyo, Japan
Albertson, R.C., Hubbard Center for Genome Studies, University of New
Hampshire, USA
Alcivar-Warren, A., Aquatics Program, Department of Environmental and
Population Health, Tufts University School of Veterinary Medicine, USA
Amano, M., School of Fisheries Sciences, Kitasato University, Japan
Amemiya, Y., Laboratory of Molecular Endocrinology, Kitasato University,
Japan
Amores, A., Institute of Neuroscience, University of Oregon, USA
Ando, H., Division of Biological Sciences, Hokkaido University Graduate
School of Science, Japan
Aoki, T., Laboratory of Genetics and Biochemistry, Department of Aquatic
Biosciences, Graduate School of Fisheries Science, Tokyo University of
Fisheries, Japan
Austin, C., School of Biochemistry and Genetics, The Medical School, Univer
sity of Newcastle, UK
Bernhardt, W., Physiologische Chemie I, University of Wiirzburg, Germany
Carleton, K.L., Hubbard Center for Genome Studies, University of New
Hampshire, USA
Chen, T.T., Biotechnology Center and Department of Molecular and Cell
Biology, University of Connecticut, USA
Chiou, P., Biotechnology Center and Department of Molecular and Cell
Biology, University of Connecticut, USA
Chun, C.Z., Biotechnology Center and Department of Molecular and Cell
Biology, University of Connecticut, USA
Clark, M.S., Fugu Genomics, UK MRC HGMP Resource Centre, UK
x