Published online 6 December 2007

Nucleic Acids Research, 2008, Vol. 36, Database issue D959D965

doi:10.1093/nar/gkm1041

PlantGDB: a resource for comparative

plant genomics
Jon Duvick1, Ann Fu1, Usha Muppirala1, Mukul Sabharwal1,
Matthew D. Wilkerson1, Carolyn J. Lawrence2, Carol Lushbough3 and Volker Brendel4,5,*
1

Department of Genetics, Development and Cell Biology, Iowa State University, 2USDA-ARS Corn Insects
and Crop Genetics Research Unit, Ames, IA 50011, 3Department of Computer Science, University of
South Dakota, Vermillion, SD 57069, 4Department of Genetics, Development and Cell Biology and 5Department of
Statistics, Iowa State University, Ames IA 50011, USA

Received September 12, 2007; Revised October 30, 2007; Accepted October 31, 2007

ABSTRACT
PlantGDB (http://www.plantgdb.org/) is a genomics
database encompassing sequence data for green
plants (Viridiplantae). PlantGDB provides annotated
transcript assemblies for `100 plant species, with
transcripts mapped to their cognate genomic context where available, integrated with a variety of
sequence analysis tools and web services. For 14
plant species with emerging or complete genome
sequence, PlantGDBs genome browsers (xGDB)
serve as a graphical interface for viewing, evaluating
and annotating transcript and protein alignments
to chromosome or bacterial artificial chromosome
(BAC)-based genome assemblies. Annotation is
facilitated by the integrated yrGATE module for
community curation of gene models. Novel web
services at PlantGDB include Tracembler, an iterative alignment tool that generates contigs from
GenBank trace file data and BioExtract Server, a
web-based server for executing custom sequence
analysis workflows. PlantGDB also hosts a plant
genomics research outreach portal (PGROP) that
facilitates access to a large number of resources for
research and training.
INTRODUCTION
PlantGDB serves the plant research community by
providing access to plant sequence data as well as a
variety of sequence and genome analysis tools in a single
online resource [(1,2); Table 1]. This update outlines recent
developments at PlantGDB that have expanded its
usefulness as a tool for comparative genomics. Key
features include: expanded EST assemblies; new genome
browsers for a larger number of species; overnight
annotation of emerging genome sequences; and novel

tools for sequence retrieval and analysis, including an

innovative system for the creation and management of
workows that integrates database queries, linked web
services, and local tools.

DATABASE FEATURES AND ADDITIONS

Plant sequence data and transcript assemblies
PlantGDB periodically uploads and parses all
Viridiplantae sequences from GenBank (3) and Uniprot
(4) into 70 000 individual data sets according to species
or subspecies origin (Figure 1). PlantGDBs sequence data
are refreshed approximately every 4 months, coinciding
with alternate bimonthly GenBank version releases.
GenBank and Uniprot sequences are uploaded, parsed
by (sub)species, indexed for BLAST (5) and GeneSeqer (6)
analysis, and loaded into MySQL tables. For all species
with 410 000 published transcripts, a non-redundant set
of PlantGDB-generated Unique Transcripts (PUTs) is
generated using a custom assembly pipeline (http://
www.plantgdb.org/prj/ESTCluster/PUT_procedure.php).
PUTs are aligned to UniProt entries using BLAST, and
the best matches (if any) and UniProt-associated Gene
Ontology (GO) annotations (7) are stored. Currently, 116
species have PUT assemblies at PlantGDB, spanning
diverse taxonomic groups (Figure 2). Users can track
assembly progress in PlantGDB at http://www.plantgdb.
org/prj/ESTCluster/progress.php. PlantGDB also provides genome survey sequence (GSS) assemblies for
maize and sorghum (http://www.plantgdb.org/prj/
GSSAssembly/). All PlantGDB sequence data (raw and
processed) are available for download in a variety of le
formats at http://www.plantgdb.org/download/download.php. In addition, all Zea mays sequence data at
PlantGDB are uploaded monthly to MaizeGDB, the
central repository for maize genetic information (http://
www.maizegdb.org) (8).

*To whom correspondence should be addressed. Tel: +1 515-294-9884; Fax: +1 515-294-6755; Email: [email protected]
2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

D960 Nucleic Acids Research, 2008, Vol. 36, Database issue

Table 1. Sequence resources and analytical tools available at PlantGDB

In this table, sequence resources are divided into four categories: Uploaded Sequence, Assembled Sequence, Genome Browsers, and Other Tools. For
each resource in column 1, the species available, source/version, current sequence count, update frequency, tool/services, download options, and
alignment to genome are shown in adjacent cells. Web links for both external and internal data/tool sources are indicated with superscript numbers
and are listed at the end of the table under Web Resources. Sequence counts displayed here are as of 30 October 2007.

Nucleic Acids Research, 2008, Vol. 36, Database issue D961

Figure 1. Database schema for PlantGDB, showing data sources, update frequency, computation and web services. PlantGDB is accessible at http://
www.plantgdb.org, and genome browsers are accessible at http://www.plantgdb.org/XxGDB, where Xx is the rst letter of the genus and species (e.g.
AtGDB = Arabidopsis thaliana genome database).

Query and analysis tools

Data housed at PlantGDB are stored in MySQL
tables and can be queried by accession number, GI
number or text search. TableMaker, a search module
for querying and retrieving PlantGDBs GenBank data
in tabular format, described previously (1), has been
expanded to include a new query wizard to simplify
the search process for users not familiar with GenBank

data models (http://www.bioextract.org/genbank/home/

index.jsp).
For sequence similarity searching, a batch NCBIBLAST tool is available for querying any combination
of plant species data sets against up to 100 query
sequences at a time (http://www.plantgdb.org/Plant
GDB-cgi/blast/PlantGDBblast). For specialized queries,
PatternSearch (http://www.plantgdb.org/PlantGDB-cgi/
vmatch/patternsearch.pl) interrogates the database for

D962 Nucleic Acids Research, 2008, Vol. 36, Database issue

Figure 2. Transcript assemblies (PUTs) at PlantGDB, grouped by taxonomic aliation. Sequence totals displayed here are as of 30 October 2007.
Parentheses indicate the number of species/subspecies per genus. Genera highlighted in yellow are associated with a genome browser at PlantGDB;
an underscore indicates chromosome-based genome browsers. An asterisk designates genera for which PlantGDB provides preprocessed GeneSeqer
indices for quick access to spliced alignments.

relatively short matches possibly interspersed with

mismatches and indels, and ProbeMatch (http://
www.plantdb.org/PlantGDB-cgi/prj/PLEXdb/
ProbeMatch.pl) allows users to match sequence to array
probes and link to array probe databases.
PlantGDB also provides online access to GeneSeqer
alignment software, allowing the user to calculate spliced
alignments of expressed transcripts to a target genomic
sequence, as described previously (1) (http://www.plantgd
b.org/PlantGDB-cgi/GeneSeqer/PlantGDBgs.cgi). Currently, transcript data sets (EST, cDNA, PUT) from 50
species are preprocessed at PlantGDB to allow rapid
online GeneSeqer analysis, and a range of splice site
models and alignment parameters can be specied at
runtime.
PlantGDB provides sequence analysis tools that automate processes that normally require iterative searching or
tedious parsing of information. Tracembler (http://
www.plantgdb.org/tool/tracembler/) allows the user to
do chromosome walks with pre-assembly trace data by
performing an iterated search of NCBIs trace archives
with a seed sequence (9). Tracembler invokes CAP3 (10)
to assemble a contig sequence from one or more
automated rounds of BLAST analysis and displays a
pairwise alignment between contig and seed sequence.
MuSeqBox (http://www.plantgdb.org/MuSeqBox/MuSeq
Box.html) is an online tool for generating tabular output
from multiple BLAST queries, based on user-specied
thresholds (11). The tool also contains algorithms for

detecting potential alternate splicing and full-length

transcripts. MuSeqBox provides pre-computed Uniprot
BLASTx data sets for maize, sorghum, barley, Arabidopsis
and rice PUTs, allowing the user to generate ltered,
tabulated output. Alternatively, the user can upload a
custom BLAST output le.
Bioinformatics workflow tools
A bioinformatics research project may utilize a variety of
query and computational tools, some web-based and
others local to the user, which may be carried out in serial
fashion along with parsing and formatting for input or
display. There is a growing need for systems that can
integrate disparate tools and workows in a way that
automates the process of input/output, computation and
documentation. The PlantGDB-associated BioExtract
Server
(http://www.bioextract.org/login/Login.html)
addresses this need by providing researchers with a web
interface that allows them to query sequence databases,
analyze data with web-based as well as local bioinformatics tools, save results and create and manage
workows using a directed acyclic graph (DAG)
model (Lushbough,C., Bergman,M.K., Lawrence,C.J.,
Jennewein,D. and Brendel,V. BioExtract server an
integrated system to access and analyze heterogeneous,
distributed biomolecular data. Submitted for publication.). As a simple example, a user could develop a
workow that performs a BLAST search, retrieves peptide
sequences from query results, eliminates redundant

Nucleic Acids Research, 2008, Vol. 36, Database issue D963

sequences and produces a multiple sequence alignment

output. BioExtract workows can be paused, modied,
saved, shared with an online workgroup or the world, and
documented electronically for future reference.
Genome browsers
PlantGDB provides genome browsers (xGDB) for 14
plant species whose genomes have been completely or
partially sequenced (12). AtGDB, OsGDB, MtGDB,
SbGDB, VvGDB and PtGDB are chromosome-based
genome browsers for Arabidopsis thaliana (thale cress),
Oryza sativa (rice), Medicago truncatula (barrel medic),
Sorghum bicolor (sorghum), Vitis vinifera (grapevine) and
Populus trichocarpa (western balsam poplar), respectively,
while ZmGDB, GmGDB, HvGDB, SlGDB, GhGDB,
TaGDB, BrGDB and LjGDB are BAC-based browsers
for Zea mays (corn or maize), Glycine max (soybean),
Hordeum vulgare (barley), Solanum lycopersicum
(tomato), Gossypium hirsutum (cotton), Triticum aestivum
(bread wheat), Brassica rapa (eld mustard) and Lotus
japonicus, respectively (http://www.plantgdb.org/prj/
Genome_browser.php).
The xGDB browser Context View (Figure 3B) displays
current gene model annotation together with high quality,
cognate and non-cognate GeneSeqer alignments of ESTs,
cDNAs, and PUTs to genomic sequence. Similarly, Oryza
sativa predicted polypeptides from TIGR (http://rice.tigr.
org/tdb/e2k1/osa1/) (13) and/or Arabidopsis thaliana
predicted polypeptides from TAIR (http://www.arabidop
sis.org/) (14) are splice-aligned to genomic sequence using
GenomeThreader (15) and displayed in the same window.
For species with microarray probe sequence, these
are downloaded from the microarray database at
PLEXdb (16), aligned relative to PUT assemblies and
displayed. Signicantly, users can view spliced alignments
in a genomic region at the nucleotide level and also
retrieve quality scores and provenance information for
any spliced alignment displayed at xGDB. Additional
sequence alignments, including GSS contigs and repeat
masked regions, are displayed for some genomes.
A subset of xGDB annotation data are accessible through
the Distributed Annotation System (DAS) (http://
www.biodas.org/). These data can be downloaded for
further analysis, or alternatively imported into
another genome browser capable of importing DAS
formatted data.
Key design features of the xGDB browsers are
modularity and expandability, such that a browser for a
newly emerging genome can be rapidly deployed and
populated with computed alignments. For the user, xGDB
provides a clean, easy to navigate interface with links to
internal and external data sources, zoomable and customizable views of transcript alignments, BLAST, search
tools and the ability to evaluate alignments and contribute
new annotations online (see next section). The browsers
are designed with Perl/PHP and MySQL database
management, and complete code is available from
SourceForge (http://xgdb.sourceforge.net/) for standalone
installations.

Community annotation
Although excellent tools are available for dening genic
regions and variant transcript forms from evidence-based
data as well as ab initio prediction, models can often
be improved further by human curated annotation.
PlantGDBs yrGATE (http://www.plantgdb.org/prj/
yrGATE/) is a recently developed tool for community
annotation of gene models that is integrated with
PlantGDBs xGDB genome browsers (17). From a single
browser window the user can rapidly evaluate a selected
region for intron/exon structures based on any combination of EST/cDNA evidence and ab initio prediction,
compare the model with known proteins via GenBank
BLAST, and submit the annotation for review and
publication on the genome browser. To assist in the
identication of gene models in need of annotation, the
Genome Annotation Evaluation (GAEVAL) module
generates quality scores for gene structure predictions
and classies cases of incongruence of the annotation
with experimental evidence (http://www.plantgdb.org/
AtGDB-chtml/gaeval/). The yrGATE tool is available
for both BAC and chromosome-based xGDB browsers
and is being used to communicate evidence-based gene
models to the A. thaliana genome database, TAIR (18).
Figure 1 shows an example of how yrGATE can be used,
together with xGDBs annotation tables and genome
browser, to identify and annotate potential splicing
variants for a gene of interest in maize.
Pipelines for genome annotation
Genome browsers at PlantGDB are refreshed on a
timetable that depends on the pace of accumulation of
new genomic or transcript sequence data or assemblies
for the respective species. New spliced alignments are
calculated for ESTs, cDNAs and PUTs as well as for
other sequence types (where available) and data are
uploaded. To match the rapid pace with which some
genomes are being sequenced, PlantGDB sta have
developed and implemented an automated genome data
pipeline for species with rapidly expanding sequence
data, using Zea mays as an initial example. In 2007, new
maize BAC sequences began to be deposited in GenBank
at the rate of over 60 BACs or 10 Mb of sequence
per day (http://www.maizesequence.org). In addition,
there is a growing catalog of transposable elementtagged maize genomic sequence in GenBank, facilitating
reverse genetics in maize (http://www.plantgdb.org/prj/
AcDsTagging/) (19) as well as a large repository of EST
sequence-derived PUTs. PlantGDBs daily Z. mays pipeline downloads and processes all new maize BACs with
transcript, protein, microarray probe, transposon insertion tag and other genomic alignments, and displays the
cumulative output for all BACs in ZmGDB (the xGDB
browser for Z. mays; http://www.plantgdb.org/ZmGDB/)
within 12 h. The pipeline also updates BLAST and
sequence download resources daily. Signicantly,
the pipeline also generates a browsable, searchable,
tabular output of rice gene models and putatively
transposon-tagged genes for the entire BAC data set
(http://www.plantgdb.org/ZmGDB/DisplayGeneAnn.php),

D964 Nucleic Acids Research, 2008, Vol. 36, Database issue

Figure 3. Screenshots from ZmGDB and yrGATE illustrate the use of online tools for gene discovery and community gene annotation. (A) A webaccessible table of Z. mays BACs (alternately shaded) displaying (left to right) the BAC GI, BAC clone name, followed by the ID, start/end
coordinates and functional annotation of splice-aligned TIGR-predicted proteins from O. sativa and nally the ZmGDB entry date. All elds are
searchable and each row is linked via column 1 to a genome browser view of the BAC region. This table is currently updated daily at ZmGDB
(http://www.plantgdb.org/ZmGDB/DisplayGeneAnn.php). (Similar tables are available for eight other BAC-based xGDB browsers.) Note that a
region of BAC GI 156523432 is aligned to three paralogous rice predicted polypeptides, annotated as autophagy-related protein 8 precursor.
Clicking on the BAC GI 156523432 in table column 1 (circled) brings up a BAC/Clone Context View of the specied region (B), showing spliced
alignments to the rice predicted polypeptides (black), along with other alignment data, in this case maize cDNAs (blue) and maize ESTs (red). Note
the evidence for alternative splicing among the maize ESTs (circles) suggesting at least two alternate transcripts (labeled 1 and 2). The user has the
option to explore and annotate this variation using yrGATE. (C) Launching the yrGATE annotation tool displays scrolling list of evidence scores
and supporting exons for all exon coordinates at a locus (alternative splice coordinates for 1 and 2 are circled). The user can build a complete gene
model on screen by selecting each desired exon and then compare the resulting open reading frame to known proteins using BLAST (data not
shown). (D) The chosen gene model is displayed graphically and will be published on the ZmGDB browser following curation by PlantGDB sta.
Shown here are yrGATE models for the two putative splice variants, with translation start/stop positions indicated by triangles. (E) Predicted protein
sequence for the two yrGATE gene models. This example illustrates how xGDB and yrGATE can be used to identify and publish gene model
predictions quickly and easily, enhancing the community genome knowledge base for maize as well as facilitating hypothesis-driven research.

providing a powerful and timely gene discovery tool for

researchers (Figure 3). This eort represents an early
implementation of a real-time, high-throughput, discovery-oriented annotation process using automated
workows.

the needs of a wide-ranging audience from high school

through postgraduate (20). Users can query for resources
or add a resource using simple online tools, and query
results are ranked via algorithms that highlight the most
popular resources.

Outreach

Future directions

The Plant Genome Outreach Portal (PGROP) at

PlantGDB provides a portal for plant genomics resources
online as well as a repository of outreach content, serving

PlantGDB will continue to provide comprehensive

and up-to-date plant sequence information online and
available for download. As additional genomes become

Nucleic Acids Research, 2008, Vol. 36, Database issue D965

available, xGDB browsers will be expanded, with additional annotations contemplated for certain species
[e.g. tracks for transcription factor binding sites and
conserved non-coding sequences (21)]. Also planned are
additional comparative genomics tools such as SynBrowse
(22), expanded DAS import and export, and the development of qualitative (e.g. quality score) and quantitative
(e.g. library) lters for spliced alignments. Expanded help
and tutorial sections are also under development.
CONCLUSIONS
PlantGDB has expanded greatly in scope since 2004,
providing today a wide range of data sets, query methods
and analysis tools for researchers interested in comparative plant genomics or gene discovery research. The site
aims to complement other, more specialized plant genome
sites by providing comprehensive plant sequence data as
well as a suite of tools and genome browsers that
emphasize spliced alignment of cognate and non-cognate
transcripts and similar protein sequences. PlantGDB also
addresses the need for timely access to, and processing of,
high-volume informatics data through use of automated
daily data pipelines (e.g. maize BAC pipeline) and online
workow tools (e.g. BioExtract Server and Tracembler).
With the yrGATE community annotation tool, PlantGDB
facilitates the sharing of user-generated gene annotation
information across the entire plant research community.
ACKNOWLEDGEMENTS
The authors would like to thank Dr. Q. Dong, Dr S.D.
Schlueter and Dr B.-B.Wang for their many contributions
to PlantGDB over the years, M. Brekke for system
support, and the many PlantGDB users who have helped
us to improve this resource by providing feedback and
suggestions. This work is supported in part by a grant from
the National Science Foundation Plant Genome Research
Program to V.B., C.J.L, and C.L. (DBI-0606909). Funding
to pay the Open Access publication charges for this article
was provided by the cited NSF grant.
Conict of interest statement. None declared.
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