植物基因数据库汇总plant genomics resources

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.

• 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

• TheVirtual 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) is a unified public resource for gene expression for plants and plant pathogens.http://www.plexdb.org

• ArrayExpress is a public repository for transcriptomics and related data at EBI.http://www.ebi.ac.uk/arrayexpress/

• http://signal.salk.edu

• MPSS (Massively Parallel Signature Sequencing) datasets for Arabidopsis, rice, and grape, at U Delaware:http://mpss.udel.edu

• Botany Array Resources (BAR).http://www.bar.utoronto.ca

• GeneVestigator is 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.https://www.genevestigator.ethz.ch/

Gene Indices and EST resources

• The Gene Index project (formerly, TIGR gene indices)http://compbio.dfci.harvard.edu/tgi/

• PlantTA: Plant Transcript Assemblieshttp://plantta.tigr.org

• HarvEST: EST analysis resources for barley, Brachypodium, Citrus, Coffea, cowpea, soybean, rice, and wheat.http://harvest.ucr.edu/

Arabidopsis resources

• TAIR (The Arabidopsis Information Resource) http://www.arabidopsis.org; http://www.tair.org)

• Salk Institute Genome Analysis Laboratory.http://signal.salk.edu/

• AtGenExpress, a multinational effort to uncover the transcriptome of A. thaliana.http://www.arabidopsis.org/info/expression/ATGenExpress.jsp

• Botany Array Resources (BAR).http://www.bar.utoronto.ca

• Arabidopsis small RNA projecthttp://asrp.cgrb.oregonstate.edu/

• Arabidopsis MPSS data at U Delaware.http://mpss.udel.edu/at/

Grasses and cereals: rice, maize, sorghum, wheat, barley, Brachypodium, et al.

• Gramene: A Resource for Comparative Grass Genomicshttp://www.gramene.org

• Grain Genes 2.0: A Database for Triticeae and Avena.http://wheat.pw.usda.gov

• Sorghum genome sequence at Phytozome:www.phytozome.net/sorghum

• MaizeDB (www.maizedb.org)

• Maize genome sequence at CSHL (www.maizesequence.org)

• Oryza map; maize FPC map. Arizona Genome Institute.http://www.genome.arizona.edu/

• Maize and sorghum assembled gene islands (Methyl-filtration)http://magi.plantgenomics.iastate.edu/

• Brachpodium genome databasewww.brachybase.org

• www.modelcrop.org

• Brachypodium genome database at Phytozome:www.phytozome.net/brachypodium

• Marker Assisted Selection for wheat.http://maswheat.ucdavis.edu

• PanZea: Molecular and Functional Diversity of the Maize Genomewww.panzea.org

• Maize Oligonucleotide Array Projecthttp://www.maizearray.org/

• Beijing Genome Institute Rice Information System (RISE):http://rise.genomics.org.cn/rice

• Rice Annotation Project Database (RAP-DB)http://rapdb.dna.affrc.go.jp/

• TIGR rice genome annotation and resources.www.tigr.org/tdb/rice

• International Rice Research Institutehttp://www.irri.org/

• Rice MPSS data at U. Delawarehttp://mpss.udel.edu/rice/

Legumes: Soybean, Medicago, Lotus, et al.

• Soybean genome sequence at Phytozome:www.phytozome.net/soybean

• Medicago truncatula: a model for legume research (www.medicago.org). Links to genome sequencing, functional genomics, comparative genomics

• Legume Information Systemhttp://www.comparative-legumes.org

• Soybase and the soybean breeders toolbox.http://soybase.agron.iastate.edu/

• Lotus japonicus genome project at Kazusahttp://www.kazusa.or.jp/lotus/

• BeanGenes: a Phaseolus/Vigra database, including links to other useful sites.http://beangenes.cws.ndsu.nodak.edu/

• SoyMap: An integrated map of soybean for resolution and dissection of multiple genome duplication events.http://www.soymap.org/

• Soybean genome map at Southern Illinois Universityhttp://soybeangenome.siu.edu/

Forest tree genomics

• Populus trichocarpa genome at Phytozome.http://www.phytozome.net/poplar

• Dendrome is 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.http://dendrome.ucdavis.eduEucalyptus

• TreeGenes EST database:http://treegenes.ucdavis.edu

• PopulusDB expression database at Umea Sweden. http://www.populus.db.umu.se/

• Genomic tool development for the chestnut tree and other Fagaceaehttp://www.fagaceae.org/

Other plant species

• International Grape Genome Projecthttp://www.vitaceae.org

• Grape genome sequence at Genoscope:http://www.genoscope.cns.fr/externe/English/Projets/Projet_ML/index.html

• Grape genome at Phytozome:www.phytozome.net/grape

• Grape MPSS data at U Delawarehttp://mpss.udel.edu/grape/

• Genome Database of Rosaceae (www.bioinfo.wsu.edu/gdr)

• Tomato genome project

• SOL Genomics Network is 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.www.sgn.cornell.edu

• Compositae genomics projecthttp://compgenomics.ucdavis.edu/

• Mimulus, columbine

• The Physcomitrella patens computational biology resourceshttp://www.cosmoss.org/

• Physcomitrella patens genome at Phytozome:www.phytozome.net/physcomitrella

• Selaginella moellendorfii genome sequence at Phytozome:www.phytozome.net/selaginella

• Castor Bean Genome Database at TIGR.http://castorbean.tigr.org/

• Papaya Genome Project at University of Hawaiihttp://cgpbr.hawaii.edu/papaya/

• Brassica rapa genome

• Cotton genome database contains genomic, genetic and taxonomic information for cotton at USDA-ARS College Station TX.http://cottondb.org/

• Cotton Genome Database at the Plant Genome Mapping Laboratory, University of Georgiahttp://www.plantgenome.uga.edu/cotton/StartFrame.htm

• International Cotton Genome Initiativehttp://icgi.tamu.edu/

Plant pathogen genomics

• Pseudomonas syringae comparative genomicswww.pseudomonas-syringae.org

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