Plant Genome Databases and Websites
General plant genomics resources
- Phytozome: comparative genomics of plants.
- PlantGDB: plant genome database
- NCBI Plant Genomes Central: Links to NCBI resources for plant genomics.
- Munich Information System for Protein Sequences.
- PLAZA: Green plant comparative genomics
- Arizona Genome Institute
- Clemson University Genomics Institute
- ChromatinDB
- Carbohydrate active enzymes
- Cell Wall Genomics
- Primer3 primer design tool
- Gene Ontology
- Plant Ontology
- MicroRNAs
- GRIN: Germplasm Resources Information Network
- The Virtual Plant at NYU.
- Agricola, a Bibliographic database of citations to the agricultural literature
- Phytome supports phylogenetic and functional analyses of predicted protein sequences across plants.
- OrthologID provide phylogenetic analysis of Arabidopsis, rice, Populus, and Chlamydomonas genes
- PlantTribes provides OrthoMCL clustering of plant proteins, developed as part of the Floral Genome Project.
Gene expression
- PLEXdb (Plant Expression Database): a unified public resource for gene expression for plants and plant pathogens.
- ArrayExpress: a public repository for transcriptomics and related data at EBI.
- SIGnAL: Salk Institute Genomic Analysis Laboratory
- MPSS (Massively Parallel Signature Sequencing): datasets for Arabidopsis, rice, and grape, at U Delaware
- Botany Array Resources (BAR)
- GeneVestigator: a reference expression database and meta-analysis system for studying the expression and regulation of genes by summarizing information from hundreds of microarray experiments into easily interpretable results.
Gene Indices and EST resources
- The Gene Index project (formerly TIGR gene indices)
- PlantTA: Plant Transcript Assemblies
- HarvEST: EST analysis resources for barley, Brachypodium, Citrus, Coffea, cowpea, soybean, rice, and wheat.
Arabidopsis resources
- TAIR: The Arabidopsis Information Resource
- SIGnAL: Salk Institute Genomic Analysis Laboratory
- AtGenExpress: a multinational effort to uncover the transcriptome of A. thaliana.
- Botany Array Resources (BAR)
- ASRP: Arabidopsis small RNA project
- Arabidopsis MPSS data at U Delaware
Grasses and cereals: rice, maize, sorghum, wheat, barley, Brachypodium, et al.
- Gramene: a Resource for Comparative Grass Genomics
- Grain Genes 2.0: a Database for Triticeae and Avena.
- Sorghum genome sequence at Phytozome
- MaizeDB
- Maize genome sequence at CSHL
- Arizona Genome Institute Oryza map; maize FPC map.
- Maize and sorghum assembled gene islands (Methyl-filtration)
- Brachpodium genome database
- www.modelcrop.org: comparative genomics using the model grass Brachypodium distachyon
- Brachypodium genome database at Phytozome
- Marker Assisted Selection for wheat
- PanZea: Molecular and Functional Diversity of the Maize Genome
- Maize Oligonucleotide Array Project
- Beijing Genome Institute Rice Information System (RISE)
- Rice Annotation Project Database (RAP-DB)
- TIGR rice genome annotation and resources
- International Rice Research Institute
- Rice MPSS data at U. Delaware
Legumes: Soybean, Medicago, Lotus, et al.
- Soybean genome sequence at Phytozome
- Medicago truncatula: a model for legume research: links to genome sequencing, functional genomics, comparative genomics
- Legume Information System
- Soybase and the soybean breeders toolbox
- Lotus japonicus genome project at Kazusa
- BeanGenes: a Phaseolus/Vigra database, including links to other useful sites.
- SoyMap: An integrated map of soybean for resolution and dissection of multiple genome duplication events.
- Soybean genome map at Southern Illinois University
Forest tree genomics
- Populus trichocarpa genome at Phytozome
- Dendrome: a collection of forest tree genome databases and other forest genetic information resources for the international forest genetics community. Dendrome is part of a larger collaborative effort to construct genome databases for major crop and forest species.
- TreeGenes EST database
- PopulusDB expression database at Umea Sweden
- Populus Genome Integrative Explorer also at Umea Sweden
- Genomic tool development for the chestnut tree and other Fagaceae
Other plant species
- International Grape Genome Project
- Grape genome sequence at Genoscope
- Grape genome at Phytozome
- Grape MPSS data at U Delaware
- Genome Database of Rosaceae
- Tomato genome project
- SOL Genomics Network: a clade-oriented database containing genomic, genetic and taxonomic information for species in the families Solanaceae (e.g., tomato, potato, eggplant, pepper, petunia) and Rubiaceae (coffee). Genomic information is presented in a comparative format and tied to the Arabidopsis genome.
- Compositae genomics project
- Mimulus, columbine
- Cosmoss: the Physcomitrella patens computational biology resource
- Physcomitrella patens genome at Phytozome
- Selaginella moellendorffii genome sequence at Phytozome
- Castor Bean Genome Database at TIGR
- Papaya Genome Project at University of Hawaii
- Brassica rapa genome
- Cotton genome database: contains genomic, genetic and taxonomic information for cotton at USDA-ARS College Station TX.
- Cotton Genome Database at the Plant Genome Mapping Laboratory, University of Georgia
- International Cotton Genome Initiative