Plant Genomics Databases: Methods and Protocols

337 Pages·2017·22.017 MB·English

by  Aalt D.J van Dijk (eds.)

Methods in
Molecular Biology 1533
Aalt D.J. van Dijk Editor
Plant
Genomics
Databases
Methods and Protocols
M M B
ethods in olecular iology
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes:
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Plant Genomics Databases
Methods and Protocols
Edited by
Aalt D.J. van Dijk
PRI Bioscience, Biometris, and Bioinformatics, Wageningen University & Research,
Wageningen, The Netherlands
Editor
Aalt D.J. van Dijk
PRI Bioscience, Biometris and Bioinformatics
Wageningen University & Research Wageningen
The Netherlands
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-6656-1 ISBN 978-1-4939-6658-5 (eBook)
DOI 10.1007/978-1-4939-6658-5
Library of Congress Control Number: 2016958617
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Preface
Plant genomics has witnessed a dramatic increase in data production, in particular due to
the revolution in sequencing technologies. This volume of Methods in Molecular Biology
introduces databases containing the results of this data explosion. Chapters describe data-
base contents as well as typical use cases, written in the spirit of the Series which aims to
provide practical guidance and troubleshooting advice. Clearly, an assembled genome
sequence is simply a foundation. The challenge for any researcher interested in the biology
of a particular plant is to identify the features of the genome that describe this biology.
Chapters 1–10 describe databases that primarily present genome sequences, integrated with
various features relevant for biology. This includes large databases including data from vari-
ous species, as well as databases focusing on one or a few related species. Expression and
co-expression are in particular useful in order to add biological value to genomes. Databases
presenting these data are described in Chapters 11–13. Finally, Chapters 14–19 present
more specific and focused databases.
This volume focuses on “databases” as distinct from “analysis tools.” Hence, several
tools are not included, because they do not present data but aim to analyze data provided
by users. Other inclusion criteria were that the resource should be up to date and of mini-
mal sufficient size. Small databases obviously can be extremely relevant but would not make
for a useful chapter in this volume. However, a use case is included in Chapter 9 in which
various small species-specific databases are compared. It should also be noted that this vol-
ume focuses on plant-specific resources. For that reason, various more general resources
have not been included. Finally, the focus of this volume on genomics databases means that
databases presenting purely other types of omics data, e.g., purely metabolomics data, are
not included.
The data explosion mentioned above is ongoing. Much more data—de novo genome
sequencing, resequencing of individuals, transcriptomics, epigenomics, etc—will be added
to the databases described in this volume in the near future. That notwithstanding, the
chapters presented here provide clear guidance in accessing an important collection of plant
databases which can be used to add biological value to genomics data.
Wageningen, The Netherlands Aalt-Jan van Dijk
v
Contents
Preface.......................................................... v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
1 Ensembl Plants: Integrating Tools for Visualizing, Mining,
and Analyzing Plant Genomic Data................................. 1
Dan M. Bolser, Daniel M. Staines, Emily Perry, and Paul J. Kersey
2 PGSB/MIPS PlantsDB Database Framework for the Integration
and Analysis of Plant Genome Data................................. 33
Manuel Spannagl, Thomas Nussbaumer, Kai Bader, Heidrun Gundlach,
and Klaus F.X. Mayer
3 Plant Genome DataBase Japan (PGDBj)............................. 45
Akihiro Nakaya, Hisako Ichihara, Erika Asamizu, Sachiko Shirasawa,
Yasukazu Nakamura, Satoshi Tabata, and Hideki Hirakawa
4 FLAGdb++: A Bioinformatic Environment to Study and Compare
Plant Genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Jean Philippe Tamby and Véronique Brunaud
5 Mining Plant Genomic and Genetic Data Using the GnpIS
Information System............................................. 103
A.-F. Adam-Blondon, M. Alaux, S. Durand, T. Letellier, G. Merceron,
N. Mohellibi, C. Pommier, D. Steinbach, F. Alfama, J. Amselem,
D. Charruaud, N. Choisne, R. Flores, C. Guerche, V. Jamilloux,
E. Kimmel, N. Lapalu, M. Loaec, C. Michotey, and H. Quesneville
6 The Bio-Analytic Resource for Plant Biology.......................... 119
Jamie Waese and Nicholas J. Provart
7 The Evolution of Soybean Knowledge Base (SoyKB).................... 149
Trupti Joshi, Jiaojiao Wang, Hongxin Zhang, Shiyuan Chen,
Shuai Zeng, Bowei Xu, and Dong Xu
8 Using TropGeneDB: A Database Containing Data on Molecular Markers,
QTLs, Maps, Genotypes, and Phenotypes for Tropical Crops ............. 161
Manuel Ruiz, Guilhem Sempéré, and Chantal Hamelin
9 Species-Specific Genome Sequence Databases: A Practical Review.......... 173
Aalt D.J. van Dijk
10 A Guide to the PLAZA 3.0 Plant Comparative Genomic Database ......... 183
Klaas Vandepoele
11 Exploring Plant Co-Expression and Gene-Gene Interactions
with CORNET 3.0............................................. 201
Michiel Van Bel and Frederik Coppens
12 PlaNet: Comparative Co-Expression Network Analyses for Plants .......... 213
Sebastian Proost and Marek Mutwil
vii
viii Contents
13 Practical Utilization of OryzaExpress and Plant Omics Data Center
Databases to Explore Gene Expression Networks in Oryza Sativa
and Other Plant Species ......................................... 229
Toru Kudo, Shin Terashima, Yuno Takaki, Yukino Nakamura,
Masaaki Kobayashi, and Kentaro Yano
14 Pathway Analysis and Omics Data Visualization using Pathway
Genome Databases: FragariaCyc, A Case Study........................ 241
Sushma Naithani and Pankaj Jaiswal
15 CSGRqtl: A Comparative Quantitative Trait Locus Database
for Saccharinae Grasses .......................................... 257
Dong Zhang and Andrew H. Paterson
16 Plant Genome Duplication Database................................ 267
Tae-Ho Lee, Junah Kim, Jon S. Robertson, and Andrew H. Paterson
17 Variant Effect Prediction Analysis Using Resources Available
at Gramene Database ........................................... 279
Sushma Naithani, Matthew Geniza, and Pankaj Jaiswal
18 Plant Promoter Database (PPDB).................................. 299
Kazutaka Kusunoki and Yoshiharu Y. Yamamoto
19 Construction of the Leaf Senescence Database and Functional
Assessment of Senescence-Associated Genes .......................... 315
Zhonghai Li, Yi Zhao, Xiaochuan Liu, Zhiqiang Jiang, Jinying Peng,
Jinpu Jin, Hongwei Guo, and Jingchu Luo
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
Contributors
A.-F. AdAm-Blondon • Research Unit in Genomics-Info UR1164, INRA, Université
Paris-Saclay, Versailles, Versailles Cedex, France
m. AlAux • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
F. AlFAmA • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
J. Amselem • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
erikA AsAmizu • Department of Plant Life Sciences, Faculty of Agriculture, Ryukoku
University, Otsu, Shiga, Japan
kAi BAder • Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg,
Germany
michiel VAn Bel • Department of Plant Systems Biology, VIB, Ghent, Belgium;
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent,
Belgium
dAn m. Bolser • European Molecular Biology Laboratory, European Bioinformatics
Institute, Hinxton, Cambridge, UK
Véronique BrunAud • Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA,
University Paris-Sud, University Evry, Univ Paris-Saclay, Orsay, France; Institute of
Plant Sciences Paris-Saclay IPS2, Univ Paris-Diderot, Sorbonne Paris Cité, Orsay, France
d. chArruAud • Research Unit in Genomics-Info UR1164, INRA, Université Paris-
Saclay, Versailles, Versailles Cedex, France; ADRINORD Espace Recherche Innovation,
Lille, France
shiyuAn chen • Department of Computer Science, Christopher S . Bond Life Science Center,
University of Missouri, Columbia, MO, USA
n. choisne • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
Frederik coppens • Department of Plant Systems Biology, VIB, Ghent, Belgium;
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent,
Belgium
AAlt d.J. VAn diJk • Applied Bioinformatics, Plant Sciences Group, Wageningen
University & Research Centre (WUR), Wageningen, The Netherlands; Laboratory of
Bioinformatics, Plant Sciences Group, Wageningen University & Research Centre
(WUR), Wageningen, The Netherlands; Biometris, Plant Sciences group, Wageningen
University & Research Centre (WUR), Wageningen, The Netherlands
s. durAnd • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
r. Flores • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
mAtthew GenizA • Department of Botany and Plant Pathology, Oregon State University,
Corvallis, OR, USA; Molecular and Cellular Biology Graduate Program, Oregon State
University, Corvallis, OR, USA
ix
x Contributors
c. Guerche • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
heidrun GundlAch • Plant Genome and Systems Biology, Helmholtz Center Munich,
Neuherberg, Germany
honGwei Guo • State Key Laboratory of Protein and Plant Gene Research, College of Life
Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
chAntAl hAmelin • UMR Amélioration Génétique et Adaptation des Plantes
Méditerranéennes et Tropicales (AGAP), CIRAD, Montpellier, France
hideki hirAkAwA • Department of Technology Development, Kazusa DNA Research
Institute, Kisarazu, Chiba, Japan
hisAko ichihArA • Department of Technology Development, Kazusa DNA Research
Institute, Kisarazu, Chiba, Japan
pAnkAJ JAiswAl • Department of Botany and Plant Pathology, Oregon State University,
Corvallis, OR, USA
V. JAmilloux • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
zhiqiAnG JiAnG • Channing Division of Network Medicine, Brigham and Women’s
Hospital and Harvard Medical School, Boston, MA, USA; State Key Laboratory of
Protein and Plant Gene Research, College of Life Sciences and Center for Bioinformatics,
Peking University, Beijing, China
Jinpu Jin • State Key Laboratory of Protein and Plant Gene Research, College of Life
Sciences and Center for Bioinformatics, Peking University, Beijing, China
trupti Joshi • Department of Molecular Microbiology and Immunology, Medical Research
Office School of Medicine, Informatics Institute, University of Missouri, Columbia, MO,
USA; Department of Computer Science, Christopher S . Bond Life Science Center,
University of Missouri, Columbia, MO, USA
pAul J. kersey • European Molecular Biology Laboratory, European Bioinformatics
Institute, Hinxton, Cambridge, UK
JunAh kim • Genomics Division, Department of Agricultural Bio-resource, National
Academy of Agricultural Science, Rural Development Administration (RDA), Jeonju,
South Korea
e. kimmel • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
mAsAAki koBAyAshi • Bioinformatics Laboratory, School of Agriculture, Meiji University,
Kawasaki, Kanagawa, Japan
toru kudo • Bioinformatics Laboratory, School of Agriculture, Meiji University,
Kawasaki, Kanagawa, Japan
kAzutAkA kusunoki • United Graduate School of Agricultural Science, Gifu University,
Gifu City, Gifu, Japan
n. lApAlu • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versaille, Versailles Cedex, France; UMR BIOGER, UMR1290, INRA, AgroParisTech,
Thiverval-Grignon, France
tAe-ho lee • Genomics Division, Department of Agricultural Bio-Resource, National
Academy of Agricultural Science, Rural Development Administration (RDA), Jeonju,
South Korea; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA,
USA
Contributors xi
t. letellier • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
zhonGhAi li • State Key Laboratory of Protein and Plant Gene Research, College of Life
Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
xiAochuAn liu • State Key Laboratory of Protein and Plant Gene Research, College of Life
Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing,
China; Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers
University, New Brunswick, NJ, USA
m. loAec • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
JinGchu luo • State Key Laboratory of Protein and Plant Gene Research, College of Life
Sciences and Center for Bioinformatics, Peking University, Beijing, China
klAus F.x. mAyer • Plant Genome and Systems Biology, Helmholtz Center Munich,
Neuherberg, Germany
G. merceron • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
c. michotey • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
n. mohelliBi • Research Unit in Genomics-Info UR1164, INRA, Université
Paris-Saclay, Versailles, Versailles Cedex, France
mArek mutwil • Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm,
Germany
sushmA nAithAni • Department of Botany and Plant Pathology, Oregon State University,
Corvallis, OR, USA
yAsukAzu nAkAmurA • Department of Technology Development, Kazusa DNA Research
Institute, Kisarazu, Chiba, Japan
yukino nAkAmurA • Bioinformatics Laboratory, School of Agriculture, Meiji University,
Kawasaki, Kanagawa, Japan
Akihiro nAkAyA • Department of Genome Informatics, Graduate School of Medicine,
Osaka University, Suita, Osaka, Japan
thomAs nussBAumer • Plant Genome and Systems Biology, Helmholtz Center Munich,
Neuherberg, Germany
Andrew h. pAterson • Plant Genome Mapping Laboratory (Dept #398), University of
Georgia, Athens, GA, USA
JinyinG penG • State Key Laboratory of Protein and Plant Gene Research, College of Life
Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
emily perry • European Molecular Biology Laboratory, European Bioinformatics Institute,
Hinxton, Cambridge, UK
c. pommier • Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay,
Versailles, Versailles Cedex, France
seBAstiAn proost • Max Planck Institute of Molecular Plant Physiology, Potsdam-G olm,
Germany
nicholAs J. proVArt • Department of Cell and Systems Biology, Centre for the Analysis of
Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
h. quesneVille • Research Unit in Genomics-Info UR1164, INRA, Université
Paris-Saclay, Versailles, Versailles Cedex, France