Project Coordination

Arabidopsis Genome Initiative

Ancestral Angiosperm Genome Project

BarleyWorld

BBSRC {United Kingdom}

The Compositae Genome Project {CGP}

Cacao Genome Database

Deep Gene

The Floral Genome Project

Genomanalyse im biologischen system Pflanze {GABI}

Green Plant BAC Library Project

Global Musa Genomics Consortium

International Cotton Genome Initiative

International Cucurbit Genomics Initiative {ICuGI}

International Grape Genome Project {IGGP}

International Rice Genome Sequencing Project {IRGSP}

International Triticeae Consortium

ITEC - International Triticeae EST Cooperative

International Triticeae Mapping Initiative

IWGSC - International Wheat Genome Sequencing Consortium

Maize Gene Discovery Project

Medicago truncatula Consortium

Maize Mapping Project

Mimulus Project

North American Barley Genome Mapping Project

Plant Genome Resource Center {Germany}

Rice Genome Research Project {Japan}

Scottish Crop Research Institute Hordeum vulgare {Scotland}

U.S. Wheat Genome Project

Sequencing Centers

• Library preparation

• Library preparation

  Amplicon Express

  custom and premade libraries

  Arizona Genomics Institute and Computational Laboratory

  Projects: The Green Plant BAC Library Project, Oryza BAC library project

  Centre National de Ressources Genomiques Vegetales

  Libraries available: Aphanomyces, Arabidopsis thaliana, barley, grapevine, Medicago truncatula, melon, pepper, radish, rapeseed, rye, sunflower, tobacco, tomato, wheat

  Clemson University Genomics Institute

  Libraries available: Arabidopsis thaliana, barley, bean, cassava, citrus, cocoa, corn, cotton, Cucumis melo, fern, Medicago truncatula, Mimulus, peach, rice, sorghum, soybean, tomato, tulip poplar and wheat

  Plant Genome Mapping Laboratory

  Libraries available: Arachis hypogaea, Brassica oleracea, Carica papaya, Cynodon dactylon, Cynodon tranvaalensis, Gossypium barbadense, Gossypium arboreum, Gossypioides kirkii, Gossypium longicalyx, Gossypium raimondii, Opuntia cochinellifera, Saccharum spp, Sorghum bicolor, Sorghum halepense, Sorghum propinquum

  Laboratory for Plant Genomics, Texas A&M University

  Libraries available: apple, Aegilops tauschii, Arabidopsis thaliana, banana, brassicas, chickpea, cotton, cucumber, loblolly pine, maize, melon, orange, peach, poplar, potato, rice, sorghum, soybean, tomato, wheat

  Scottish Crop Research Institute

  Projects: barley, blackberry/raspberry and potato

  The Samuel Roberts Noble Foundation

  Project: Medicago truncatula

• Sequencing

• Sequencing

  Amplicon Express

  Arizona Genomics Institute and Computational Laboratory

  EST projects: barley, cotton, rice

  Genomic projects: rice, maize, tomato, sorghum, cotton

  Clemson University Genomics Institute

  EST projects: almond, barley, cotton, peach

  Genomic projects: cotton, rice, tomato, maize, cassava, grape

  Delaware Biotech Institute; University of Delaware

  Project: plant small RNAs

  Lita Annenberg Hazen Genome Sequencing Center at Cold Spring Harbor

  EST project: maize

  Genomic projects: rice, maize and Arabidopsis thaliana

  Genoscope

  Plant EST project: Medicago truncatula

  Plant genomic project: rice, wheat, tropical plants

  Malaysian Genomics Resource Centre

  NCGR Sequencing Center

  The Samuel Roberts Noble Foundation

  Project: Medicago truncatula

  University of Oklahoma
  

  EST project: Plumbago zeylanica

  Genomic project: Medicago truncatula

  Plant Genome Resource Center {Germany}

  Project: barley

  Scottish Crop Research Institute

  Projects: barley and potato

  Stanford Genome Technology Center; Stanford University; Stanford, CA

  Plant EST project: maize

  Plant genomic project: Arabidopsis thaliana,and maize

  SucEST

  Project: sugarcane

  Washington University; St. Louis, MO

  EST projects

  Plant genomic projects: Arabidopsis thaliana, maize

  University of Trieste

  Project: coffee

Sequence Analysis

• EST analysis

• EST analysis

  Cold Spring Harbor Laboratory

  Project: maize

  The Computational Biology and Functional Genomics Laboratory

  Project: The Gene Index Project

  National Institute of Fruit Tree Science {Japan}

  Projects: citrus, Japanese pear, peach

  National Center for Genome Resources

  The Samuel Roberts Noble Foundation

  Project: Medicago truncatula

  SucEST

  Project: sugarcane

  Plant Genome Resource Center {Germany}

  Project: barley

  University of Trieste

  Project: coffee

• Genomic analysis

• Genomic analysis

  Arizona Genomics Institute and Computational Laboratory

  Project: rice

  Cold Spring Harbor Laboratory

  Projects: Arabidopsis thaliana, rice, maize

  Delaware Biotech Institute; University of Delaware

  Project: plant small RNAs

  Genoscope

  Plant projects: wheat microsatellite sequences, tropical plant microsatellite sequences, Arabidopsis thaliana, rice,

  PABS - Platform Assisted BAC-by-BAC Sequencing

  PABS-Select

  PABS-Validate

  Plant Genome Resource Center {Germany}

  Project: synteny of rice and barley

  RNA target detection

  microCosm - at EBI

  MapMi - at EBI

  TargetScan

  Pictar - at Max Delbruck Centrum, Berlin

• Genome Annotation

• Genome Annotation

  Delaware Biotech Institute; University of Delaware

  Project: plant small RNAs

  GNPAnnot

  International Medicago Genome Annotation Group

  Maizesequence.org

  RNA target detection

  microCosm - at EBI

  TargetScan

  Pictar - at Max Delbruck Centrum, Berlin

  Superfamily

• Comparative genomics

• Comparative genomics

  Delaware Biotech Institute; University of Delaware

  Project: plant small RNAs

  EnsemblPlants EBI-EMBL

  modelcrop.org Comparative genomics relative to Brachypodium distachyon

  Oryza Map Alignment Project

  Phytozome

Germplasm Centers

Arabidopsis Biological Resources Center

Barley Germplasm Database

Center for Genetic Resources - The Netherlands

C.M. Rick Tomato Genetics Resource Center

Genetic Stocks - Oryza Collection - Dale Bumpers National Rice Research Center

ECP/GR - lettuce {Netherlands}

International Cocoa Germplasm Database - United Kingdom

International Rice Research Institute - Philipines

Maize Genetics Cooperative Stock Center

National Plant Germplasm System - a cooperative effort in the United States

Ornamental Plant Germplasm Center

Oryzabase {Japan; rice}

POOL {Agriculture and Agri-Food Canada; oat}

Scottish Crop Research Institute {Commonwealth Potato Collection}

SoyBase and The Soybean Breeder's Toolbox {supported by USDA}

SPARC {USDA; cotton, pecan}

Tomato Genetics Cooperative

University of Kentucky Clover Germplasm Center

Database Centers

• Bioinformatic software

• Bioinformatic software

  ACEDB

  AceBrowser

  AcePerl

  BioConductor

  BioJava

  BioPerl

  BioPython

  BioRuby

  Cytoscape

  DAS

  GMOD

  Open Bioinformatics Foundation

  Osprey

  Phylip

  POSsum initiative

  Savant a desktop genome browser

  Structure 2.2

• General genomic

• General genomic

  GOLD - complilation of databases for organisms with genomic projects

  Plant DNA C-values - database of DNA C-values for greater than 3800 Embryophyte plants

  DOGS - Database of Genome Sizes

  KEGG - Kyoto Encyclopedia of Genes and Genomes

• Metabolic pathway

• Metabolic pathway

  BBID - Biological Biochemical Image Database

  BpC - BioPathways Consortium

  Boehringer Mannheim wall chart courtesy of ExPASy

  EcoCyc - Encyclopedia of Escherichia coli K12 Genes and Metabolism

  KEGG - Kyoto Encyclopedia of Genes and Genomes

  IUBMB - Nicholson Minimaps

  Brenda - The Comprehensive Enzyme Information System

  Reactome - a curated knowledgebase of biological pathways

• Nomenclature for genetics, genomics and proteomics

• Nomenclature for genetics, genomics and proteomics

  Enzyme Commission

  IUPAC names/rules

  ExPASy - Enzyme

  GO, Gene Ontology

  Gene Ontology Consortium - eukaryote wide

  AmiGO

  genomic standards consortium

  Hordeum vulgare - barley

  Barley Nomenclature Workshop

  HUPO Proteomics Standards Initiative

  Medicago truncatula

  Clemson University

  Phaseolus vulgaris - bean

  bean cooperative - at North Dakota State University

  RNA genomics

  miRBase - at University of Manchester, UK

  Solanum lycopersicum - tomato

  tomato genetics coop - at U. Florida

  Gene Names- at UC Davis

  Triticum aestivum - bread wheat

  1998 Catalog of Gene Symbols

  2003 Catalog of Gene Symbols

  1999 Supplement

  2000 Supplement

  2001 Supplement

  2002 Supplement

  2003 Supplement

  2004 Supplement

  2005 Supplement

  2006 Supplement

  UniProt

  guidelines for naming proteins

  publication list for protein nomenclature

  Zea mays - maize

  maize genetics cooperative

  1996 Updates

• Plant-specific

• Plant-specific

  The Arabidopsis Information Resource - TAIR

  AtGDB {supported by NSF}

  Bean Genes - Vigna and Phaseolus {North Dakota State University}

  BrassicaDB {at John Innes Centre}

  CHARGE {supported by NSF}

  ChromDB - The Plant Chromatin Database {supported by NSF}

  Clover GARDEN - clover {Kazusa DNA Research Institute, Japan}

  Cacao Genome Database

  COMPOSITdb - lettuce, sunflower {UC Davis, CA}

  CottonDB {supported by USDA}

  Cucurbit Genomics Database {supported by BARD grants}

  Cucumber Genome Database

  Dendrome - forest tree genome databases {supported by USDA}

  DragonDB- snapdragon

  GDR | genome database for rosaceae - rosaceae {supported by NSF}

  GENica - wheat, barley {Australia}

  GLIP {European Union}

  Genoscope- Arabidopsis thaliana, Medicago truncatula {Centre Nationale de Sequencage, France}

  GrainGenes 2.0 - wheat, barley, oats, rye, sugarcane {supported by USDA}

  GrainGenes - query and table dump

  Gramene - mapping resource for grains {supported by NSF and USDA}

  INRA Genome Databases mirror

  Kazusa - Arabidopsis thaliana {Japan}

  KOMUGI {Japan}

  The Korea Rice Genome Database

  Legume Base NBRP {Japan}

  LegumeDB {Australia}

  Legume Information System {supported by USDA}

  Maize Assembled Genomic Island - {hosted at Iowa State University, supported by NSF}

  MaizeGDB - the data in MaizeDB and ZMDB have been moved to here {supported by NSF and USDA}

  NIBLRRS {supported by NSF}

  OatGenes {Canada}

  Oryzabase {Japan}

  OryGenesDB {France}

  Phytome {supported by NSF}

  PhytoPath {supported by BBSRC}

  PlantGDB {supported by NSF}

  Plant Genome Network {supported by NSF}

  PLEXdb {supported by USDA}

  Rice GD

  Rice Annotation Program, mirrored at NIAS

  Japanese Rice Genome Research Program

  Safflower {Washington State University}

  Scarlet Runner Bean Embryo EST Project {UCLA}

  Solanaceae Genomics Network {hosted at Boyce Thompson Institute, supported by NSF, USDA}

  SorghumDb {supported by USDA}

  SoyBase and The Soybean Breeder's Toolbox {supported by USDA}

  Sunflower {Steve Knapp lab}

  Tomato Functional Genomics Database {supported by NSF}

  TropGENE DB

  Organisms: banana, cocoa, coconut, coffee, cotton, oilpalm, rice, rubbertree, sugarcane,

  UK CropNet

  In addition to being a site for BarleyDB, BrassicaDB, CropSeqDB, FoggDB {forage grasses}, MilletGenes, AlfaGenes, BeanGenes, CassavaDB, CompositDB, CoolGenes, CottonDB, DictyDB, RiceGenes, SolGenes, and SorghumDB; this site provides a mirror for SoyBase.

  VegMarks {National Institute of Vegetable and Tea Science, Japan}

  Organisms: Chinese cabbage, bunching onion, cucumber, eggplant, melon and tomato