Table Of ContentMethods in
Molecular Biology 1236
Ichiro Uyeda
Chikara Masuta Editors
Plant Virology
Protocols
New Approaches to Detect
Viruses and Host Responses
Third Edition
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
http://www.springer.com/series/7651
Plant Virology Protocols
New Approaches to Detect Viruses
and Host Responses
Third Edition
Edited by
Ichiro Uyeda and Chikara Masuta
Hokkaido University, Sapporo, Japan
Editors
Ichiro U yeda Chikara Masuta
Hokkaido University Hokkaido University
Sapporo, Japan Sapporo, J apan
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-4939-1742-6 ISBN 978-1-4939-1743-3 (eBook)
DOI 10.1007/978-1-4939-1743-3
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Prefa ce
Recent developments in genome analyses and cytological technologies have made noble
approaches to solving many problems in plant virology. The techniques have been applied
to not only diagnostic studies of virus diseases but also ecology and pathogenicity of viruses
and host responses to viral infection.
The fi rst six chapters describe techniques relevant to the detection of unknown viruses
and disease diagnosis. Shimura et al. describe a simple and practical diagnostic method of
macroarray. Diagnostic methods using PCR are presented by MacKenzie et al. for P otato
virus X , Gabino for grapevine viruses, Sasaya for rice viruses, and Noris and Miozzi for
Tomato yellow leaf curl Sardinia virus . Atsumi et al. describe the dsRNA extraction method
for isolating viruses of unknown sequences.
The next nine chapters deal with utilization of meta-genome sequencing and global
gene expression analyses for the search and identifi cation of viruses, as well as the elucida-
tion of host responses to viral infection. They also describe analyses of huge sequence data.
The methods have potential to detect undescribed viruses and network of host responses
not yet known. Kondo et al. look for non-retroviral RNA viruslike sequence in plant
genome. Nagano et al. describe sequencing of RNAs by next-generation sequencers to
detect viruses in wild plants. Wang et al. describe the cloning and profi le analysis of satsiR-
NAs from satRNAs of C ucumber mosaic virus . Miozzi and Pantaleo describe analyses of the
huge amount of data collected from viral short interfering RNA sequencing. Motooka et
al. detected many viral sequences of plant and algal and protozoal viruses in addition to
bacteriophage, mammal, and insect-derived viruses in fecal samples from cows by high-
throughput sequencing. Adkar-Purushothama et al. describe a deep sequencing of viroid-
infected plants and analyses of viroid-specifi c small RNAs. Ezawa et al. describe extraction
of total dsRNAs from fungi, and their cDNAs are sequenced and searched for viral sequence.
Matsuura et al. describe the high-throughput SuperSAGE for host and viral gene expres-
sion. Ishihara et al. describe the use of global gene expression analyses for elucidating the
complex network for resistance to viruses.
The next three chapters describe construction methods of infectious cDNAs. The use
of infectious cDNA clones of RNA viruses provides a homogenous viral genome popula-
tion and makes it possible to examine critical single-point mutations involved in pathoge-
nicity and breaking resistance of host plants. It is also used as a vector for expressing foreign
gene genes. Nakahara et al. describe construction of infectious cDNA to B ean yellow mosaic
virus and Clover yellow vein virus , legume-infecting potyviruses. Li and Yoshikawa describe
construction of infectious Apple latent spherical virus cDNA vectors and its use for virus-
induced gene silencing. Nagata et al. describe simplifi ed methods for the construction of
Pepper mild mottle virus and Begomovirus .
The last two chapters contain methods relevant to plant virus control. Voloudakis et al.
describe production of dsRNA of a target RNA virus and its use for inducing RNA silenc-
ing. Mochizuki and Ohki detect and examine virus localization in the shoot apical meristem
tissue in order to obtain virus-free meristem tips.
v
vi Preface
We would like to thank professor emeritus John M. Walker for his patient guidance and
suggestions to complete the book. Lastly, we would like to thank Dr. Kenji Nakahara for
helping us edit the manuscripts and all of the authors for their excellent contributions.
Sapporo, Japan Chikara M asuta
Ichiro U yeda
Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 Detection of Plant Viruses in Mixed Infection
by a Macroarray-Assisted Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Hanako Shimura, Kazuyoshi Furuta, and Chikara Masuta
2 RT-PCR and Real-Time RT-PCR Methods for the Detection
of Potato Virus Y in Potato Leaves and Tubers. . . . . . . . . . . . . . . . . . . . . . . . . 13
Tyler D.B. MacKenzie, Xianzhou Nie, and Mathuresh Singh
3 A New Method to Isolate Total dsRNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Go Atsumi, Ken-Taro Sekine, and Kappei Kobayashi
4 Multiplex RT-PCR Method for the Simultaneous Detection
of Nine Grapevine Viruses. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Giorgio Gambino
5 Detection Methods for Rice Viruses by a Reverse-T ranscription
Loop-Mediated Isothermal Amplification (RT-LAMP) . . . . . . . . . . . . . . . . . . 49
Takahide Sasaya
6 Real-Time PCR Protocols for the Quantification
of the Begomovirus Tomato Yellow Leaf Curl Sardinia Virus
in Tomato Plants and in Its Insect Vector . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Emanuela Noris and Laura Miozzi
7 Detection and Analysis of Non-retroviral RNA Virus-Like Elements
in Plant, Fungal, and Insect Genomes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Hideki Kondo, Sotaro Chiba, and Nobuhiro Suzuki
8 Detection of Plant Viruses in Natural Environments by Using RNA-Seq. . . . . 89
Atsushi J. Nagano, Mie N. Honjo, Motohiro Mihara, Masanao Sato,
and Hiroshi Kudoh
9 Cloning and Profiling of Small RNAs from Cucumber
Mosaic Virus Satellite RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Yuan-Yuan Fang, Neil A. Smith, Jian-Hua Zhao, Joanne R.M. Lee,
Hui- Shan Guo, and Ming-Bo Wang
10 Drawing siRNAs of Viral Origin Out from Plant siRNAs Libraries. . . . . . . . . . 111
Laura Miozzi and Vitantonio Pantaleo
11 Viral Detection by High-Throughput Sequencing. . . . . . . . . . . . . . . . . . . . . . 125
Daisuke Motooka, Shota Nakamura, Katsuro Hagiwara,
and Takaaki Nakaya
vii
viii Contents
12 Analysis and Application of Viroid-Specific Small RNAs
Generated by Viroid-Inducing RNA Silencing. . . . . . . . . . . . . . . . . . . . . . . . . 135
Charith Raj Adkar-Purushothama, Zhixiang Zhang,
Shifang Li, and Teruo Sano
13 Detection and Characterization of Mycoviruses
in Arbuscular Mycorrhizal Fungi by Deep-Sequencing . . . . . . . . . . . . . . . . . . 171
Tatsuhiro Ezawa, Yoji Ikeda, Hanako Shimura, and Chikara Masuta
14 SuperSAGE as an Analytical Tool for Host and Viral Gene Expression. . . . . . . 181
Hideo Matsumura, Detlev H. Krüger, Günter Kahl,
and Ryohei Terauchi
15 Microarray Analysis of R-Gene-Mediated Resistance to Viruses. . . . . . . . . . . . 197
Takeaki Ishihara, Yukiyo Sato, and Hideki Takahashi
16 Construction of Infectious cDNA Clones Derived
from the Potyviruses Clover Yellow Vein Virus
and Bean Yellow Mosaic Virus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
Kenji S. Nakahara, Kei Nishino, and Ichiro Uyeda
17 Virus-Induced Gene Silencing of N Gene in Tobacco
by Apple Latent Spherical Virus Vectors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
Chunjiang Li and Nobuyuki Yoshikawa
18 Simplified Methods for the Construction of RNA
and DNA Virus Infectious Clones. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
Tatsuya Nagata and Alice Kazuko Inoue-Nagata
19 Efficient Double-Stranded RNA Production Methods
for Utilization in Plant Virus Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Andreas E. Voloudakis, Maria C. Holeva, L. Peter Sarin,
Dennis H. Bamford, Marisol Vargas, Minna M. Poranen,
and Francisco Tenllado
20 Detection of Plant Virus in Meristem by Immunohistochemistry
and In Situ Hybridization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
Tomofumi Mochizuki and Satoshi T. Ohki
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289
Contributors
CHARITH R AJ A DKAR-PURUSHOTHAMA • RNA Group, Département de Biochimie, Pavillon
de Recherche Appliquée sur le, Université de Sherbrooke, Sherbrooke, Q C , C anada
GO A TSUMI • Iwate Biotechnology Research Center, K itakami, Iwate, J apan
DENNIS H . BAMFORD • Department of Biosciences and Institute of Biotechnology, University
of Helsinki, H elsinki, F inland
SOTARO CHIBA • Institute of Plant Science and Resources (IPSR), O kayama University,
Kurashiki, J apan
TATSUHIRO EZAWA • Graduate School of Agriculture, Hokkaido University, Sapporo,
Hokkaido, J apan
YUAN-YUAN F ANG • State Key Laboratory of Plant Genomics and National Center for
Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, B eijing,
China
KAZUYOSHI F URUTA • Hokusan Co. Ltd., Kitahiroshima , J apan
GIORGIO GAMBINO • Institute for Sustainable Plant Protection , N ational Research Council
(IPSP-CNR), Grugliasco Unit, Grugliasco, T O , I taly
HUI-SHAN GUO • State Key Laboratory of Plant Genomics and National Center for Plant
Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
KATSURO H AGIWARA • School of Veterinary Medicine, R akuno Gakuen University , E betsu ,
Japan
MARIA C . HOLEVA • Department of Phytopathology, Laboratory of Bacteriology , Benaki
Phytopathological Institute, Kifi ssia , G reece
MIE N . HONJO • Center for Ecological Research, K yoto University, O tsu , S higa, J apan
YOJI I KEDA • Graduate School of Agriculture, Hokkaido University, Sapporo, H okkaido,
Japan
ALICE KAZUKO I NOUE-NAGATA • Laboratory of Virology and Molecular Biology, Embrapa
Vegetables, Brazilian Agricultural Research Corporation, B rasilia, DF, B razil
TAKEAKI ISHIHARA • National Agricultural Research Center, N ational Agriculture and
Food Research Organization , T sukuba, Ibaraki , J apan
GÜNTER K AHL • Biocenter, University of Frankfurt am Main, F rankfurt, G ermany
KAPPEI KOBAYASHI • Faculty of Agriculture, Ehime University, Matsuyama, E hime , J apan
HIDEKI KONDO • Institute of Plant Science and Resources (IPSR), O kayama University,
Kurashiki, J apan
DETLEV H. KRÜGER • Institute of Medical Virology, C harité Universitätsmedizin Berlin,
Berlin , G ermany
HIROSHI KUDOH • Center for Ecological Research, K yoto University, O tsu , S higa, Japan
JOANNE R . M. L EE • CSIRO Plant Industry , C anberra, A CT , A ustralia
CHUNJIANG LI • F aculty of Agriculture, I wate University, M orioka , J apan
SHIFANG LI • State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of
Plant Protection , C hinese Academy of Agricultural Sciences, B eijing, C hina
TYLER D. B . M ACKENZIE • Agricultural Certifi cation Services, F redericton, NB, C anada
CHIKARA MASUTA • R esearch Faculty of Agriculture, Hokkaido University, S apporo, J apan
ix
