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Eleanor
Smith
Life Sciences Librarian
919-513-3969
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Food Crops: legumes, Fruits, and Vegetables
Legumes | Fruits & Vegetables
Featured Articles:
Melon Fruits: Genetic Diversity, Physiology, and Biotechnology Features
Hector G, Nuñez-Palenius, Miguel G-L, Neftali O-A, et al.
CRITICAL REVIEWS IN BIOTECHNOLOGY 28(1): 13-55.
Structural and functional genomics of
tomato.
Barone A, Chiusano ML, Ercolano
MR, et al.
INT J PLANT GENOMICS Published online January 31, 2008.
Coffee and tomato share common gene repertoires as revealed by deep sequencing
of seed and cherry transcripts.
Lin C, Mueller LA, Mc Carthy J, et al.
THEOR APPL GENET 112(1):114-30, DEC 2005.
Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table
grape (Muscat Hamburg) and discovery of new candidate genes with potential
roles in berry development.
Peng FY, Reid KE, Liao N, Schlosser J, et al.
GENE 402(1-2):40-50, NOV 2007
Legumes
See also links for Medicago on
the Model Organisms pages.
BeanGenes --- A Phaseolus/Vigna sp. Database
http://ukcrop.net/perl/ace/search/BeanGenes (database)
http://beangenes.cws.ndsu.nodak.edu/ (about)
BeanGenes
contains information relevant to Phaseolus and Vigna species.
This includes all the published molecular maps of P. vulgaris (RFLP,
RFLP-RAPD) plus RFLP maps of mung bean (Vigna radiata) and cowpea
(V. unguiculata). In addition, all of the DNA and protein sequence
information for Phaseolus and Vigna species from Genbank
are part of the database along with links to Blast, EMBL, and Genbank. Pathology
information includes the type of pathogen, causal organism, host species, distribution,
symptoms, control, resistance alleles, and images of the disease.
Legume Information System (LIS)
http://www.comparative-legumes.org/
LIS integrates genetic and molecular data from multiple legume species: Arabidopsis
thaliana, Glycine max, Medicago truncatula, and Lotus
japonicus. Transcript libraries for different developmental stages
and plant organs and are accessible through images of plant organs and
stages. LIS uses the CMap system to enable comparisons of genetic and physical
maps from different species. Annotated genomic data is available and the
site makes it possible to navigate between transcript, genomic and map
data.
SoyBase
http://www.soybase.org/
An extensive
collection of information and references to information sources related to soybean.
Some of the information includes a composite genetic map, a classical genetic
map, almost 4,000 loci, data for 468 genes, QTL data, and germplasm sources.
Reaction or Pathway diagrams show >900 metabolic pathways
and include information about kinetics, enzymes (EC number, purification, clones,
physical properties), metabolites, and regulation. An extensive literature
database and many other resources are also available.
Fruits & Vegetables
Brassicaceae
Brassica Genome Gateway 2008
http://brassica.bbsrc.ac.uk/
Contains genome sequences, EST arrays, and a searchable database with
BACs, ESTs, and GSSs sequences. Includes links to other Brassica projects.
BrassicaDB
http://brassica.bbsrc.ac.uk/cgi-bin/ace/searches/browser/BrassicaDB
An
ACEDB database for Brassica species, developed and curated at the
John Innes Centre and funded by the BBSRC UK CropNet initiative. Contains data
from Brassica napus (oilseed rape or canola), Brassica oleracea (cabbage),
and Brassica rapa (turnip).
Shanghai RAPESEED Database (National Key Laboratory of Plant
Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy
of Sciences)
http://rapeseed.plantsignal.cn/welcome.do
A database created to provide a platform for functional genomics studies
of oilseed crops. Contains ESTs and SAGE tags related to seed development
and fatty acid metabolism in Brassica napus. Also contains sequence
data for EMS generated mutants. Is searchable by keywords, nucleotide or
protein sequences, and seed quality parameters.
Cucurbitaceae
Cucurbit Genomics Database (International Cucurbit Genomics
Initiative (ICuGI))
http://www.icugi.org/
Includes
Melon EST collection, Cucumber EST collection, and a Watermelon
EST collection, maps, and one array. http://www.icugi.org/cgi-bin/ICuGI/EST/index.cgi
The Spanish Melon Genomics Project (MELOGEN)
http://www.melogen.upv.es/genomica/melon/index.php
Includes an EST database. http://www.melogen.upv.es/genomica/melon/est_summary.php
Rosaceae
GDR (Genome Database for Rosaceae): Integrated Web-database for Rosaceae Genomics and Genetics Data
http://www.bioinfo.wsu.edu/gdr/ or http://www.rosaceae.org
GDR contains annotated databases of all publicly available Rosaceae ESTs,
the genetically anchored peach physical map, Rosaceae genetic
maps and comprehensively annotated markers and traits. The ESTs
are assembled to produce unigene sets of each genus and the entire
Rosaceae.
Includes updated species specific pages for apple, prunus (almond, apricot, cherry, peach), rose, and strawberry
with information for all GDR structural genomics, functional genomics,
funded projects, and other sites. GDR contains EST data from several
ongoing projects to develop extensive EST databases of Rosaceae family
plants. In addition to the EST data obtained from laboratories worldwide,
GDR contains all the Genbank Rosaceae ESTs downloaded daily.
ESTree, Version VI (The ESTree Interuniversitary Centre, Italy)
http://www.itb.cnr.it/estree/
ESTree is an Interuniversitary Centre of several research units in Italy focused
on functional genomics in the peach. The site includes a growing
EST database for peach (ESTree DB),
the analysis of several biochemical pathways based on oligonucleotide microarrays
derived from ESTs collection, and SNP-mapping of ESTs on available molecular
linkage maps.
ESTIMA: Apple EST Project
http://titan.biotec.uiuc.edu/cgi-bin/ESTWebsite/estima_start?seqSet=apple
The Apple EST project is focused on establishing tools for use in apple
functional genomics including flowering, fruiting, and pathogen response.
The first phase
of thes project involves construction of an expressed sequence tag (EST)
database of 120,000 sequences from flowering and fruiting tissues, and
from tissues responding to bacterial pathogen infection.
Solanaceae
Solanaceae Gene Indices (TIGR)
http://compbio.dfci.harvard.edu/tgi/plant.html
TIGR indexes integrate research data EST sequencing and gene research projects
for specific organisms. EST data are clustered and analyzed to form tentative
consensus sequences. Other information includes ORFs, clone and EST data, expression
information, SNPs, and GO annotation. Links are provided to the results of similarity
searches in databases such as UniProt and GenBank. Gene Indices of several members
of the Solanceae are available.
TIGR Tomato Gene Index http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=tomato
The SOL Genomics Network (SGN, Cornell University)
http://sgn.cornell.edu
SGN is designed to be a comprehensive, curated, resource for plants
in the Solanaceae family.
Contains genomic, genetic, and taxonomic information for tomato, potato,
eggplant, pepper, petunia (Solanaceae), and coffee (Rubiaceae).
Genomic information is displayed in a comparative format tied to the fully-sequenced Arabidopsis genome.
Available data include genomic maps and markers, phenotype information,
BACs, and ESTs. EST sequence data has been analyzed to identify unigenes.
Unigene builds are available for tomato, potato, pepper, eggplant, and
petunia. Links to other Solanaceae resources are included.
List of species currently in the database:
Solanaceae:
Solanum lycopersicum (formerly Lycopersicon
esculentum)
Solanum habrochaites (formerly Lycopersicon
hirsutum)
Solanum pennellii (formerly Lycopersicon
pennellii)
Solanum pimpinellifolium (formerly
Lycopersicon pimpinellifolium)
Solanum peruvianum
Solanum cheesmaniae
Solanum lycopersicoides
Solanum tuberosum
Solanum melongena
Capsicum annuum
Petunia hybrida
Nicotiana tabacum
Rubiaceae:
Coffea canephora var. robusta
Hedyotis centranthoides
Hedyotis terminalis
Plantaginaceae:
Antirrhinum majus
The US Tomato Sequencing Project (http://www.sgn.cornell.edu/about/us_tomato_sequencing.pl) is part of the larger International
Tomato Sequencing Project (http://www.sgn.cornell.edu/about/tomato_sequencing.pl),
which is in turn part of the broad International Solanaceae Genome
(SOL) Project (http://www.sgn.cornell.edu/solanaceae-project/index.pl).
Tomato Genome Browser (US Tomato Sequencing Project,
Cornell, NSF)
http://www.sgn.cornell.edu/gbrowse/index.pl
Browse by sequences on chromosomes, view physical maps, and download data.
Tomato Expression Database
http://ted.bti.cornell.edu/
Part of the Tomato Genome Project funded by the National Science Foundation (NSF).
It includes the tomato microarray data warehouse, tomato microarray expression
data, and tomato digital expression data.
- Tomato microarray data warehouse is for public
storage/retrieval of raw microarray data resulting from use of the publicly
available tomato arrays which currently include tomato TOM1, TOM2 and the Affy genome array. Tomato microarray data warehouse employs
the MIAME protocol for microarray experiment characterization.
- Tomato microarray expression data contains
basic information (e.g. probe sequence, the annotation information, the
link to SGN) and microarray data. Currently the database contains
normalized and processed microarray data for ten time points with nine
pair-wise comparisons during wild type and Nr mutant fruit development.
The database will continue to be updated with additional expression results.
- Tomato digital expression data presents
expression analysis resulting from sequence prevalence characterization
of over 150,000 tomato ESTs derived from 27 different non-normalized
EST libraries. More information about tomato ESTs can be found at the TIGR Tomato Gene Index and SGN websites.
TomatEST DB
http://biosrv.cab.unina.it/tomatestdb/index.php
This database is a collection of tomato EST sequences downloaded
from dbEST.
Includes Solanum lycopersicum, Solanum pennellii, Solanum habrochaites,
Solanum lycopersicum X Solanum pimpinellifolium. Data types include ESTs,
Gene Indices, Transcript Indices, Contigs, Singletons. The database is
searchable and browsable and includes BLAST functionality.
PoMaMo Database -Potato Maps and More
https://gabi.rzpd.de/projects/Pomamo/
Site contains molecular maps of all 12 potato chromosomes along with Solanaceae functional
maps. The GreenCards database contains sequence data, mapping data, gene functions,
SNPs, and publications. Tools are available for visualization of genetic and
physical maps.
NSF Potato Functional Genomics & Solonaceae Resources
(At TIGR)
http://www.tigr.org/tdb/potato/
TIGR hosts publicly available data from the NSF Potato Genome Project (http://www.potatogenome.org/nsf5/databases_resources/ ).
These resources include:
- Solanaceae Gene Expression Database (SGED) http://www.tigr.org/tdb/potato/SGED_index2.shtml
Gene expression data generated using the TIGR potato clone cDNA microarray
are accessible through the SGED. The high sequence conservation among Solanaceae species,
means that potato cDNA microarrays can be used for expression profiling of
a range of Solanaceae species, many of these are contained in the
database.
- Potato Simple Sequence Repeat (SSR) Database http://www.tigr.org/tdb/potato/SSR.shtml
Simple sequence repeats (SSR) have been identified using an in silico approach.
Data area available for the six Solanaceae gene indices: potato, tomato,
tobacco, pepper, petunia, and N. benthamiana.
- TIGR Solanaceae Disease Resistant Gene Database (SOLAR) http://www.tigr.org/tdb/potato/disease_db.shtml
Project data is being used to generate a comprehensive genomic resource of Solanaceae resistance
(R) gene sequences from wild potato, tomato, and pepper genomes. SOLAR is composed
of physical and genetic maps and genomic sequences of R gene hotspots.
http://www.coffeedna.net/
CoffeeDNA DB
CoffeeDNA is an Open Source Database on Coffee Genomics, includes comprehensive
information on the large coffee germplasm; Coffea specific Microsatellites;
Transposons; SNPs; Expressed Sequence Tags sequences; Gene profiling based
of ESTs; Web tools in bioinformatics and more
PART OF THE International Coffee
Genomic Network (ICGN). http://www.coffeegenome.org/ Vitaceae
VitisExpDB: A Database Resource for Grape Functional Genomics
http://cropdisease.ars.usda.gov/vitis_at/main-page.htm
This database stores ~320,000 EST sequences derived from 8 species/hybrids
with their annotation (BLAST top match) details and Gene Ontology based
vocabulary. Putative homologs for each EST in other species
and varieties along with information on their percent nucleotide identities,
phylogenetic relationship and common primers can be retrieved.
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