Available PLAZA versions (select the most appropriate)

Dicots PLAZA 4.0
Summary

Version 4.0 of the PLAZA platform. Focused on dicot species, but with the necessary outgroup organisms as reference species.

New release!
  • Actinidia chinensis (v1.0)
  • Amaranthus hypochondriacus (v2.1)
  • Amborella trichopoda (JGI v1.0)
  • Arabidopsis lyrata (v2.1)
  • Arabidopsis thaliana (Araport11)
  • Arachis ipaensis (1.0)
  • Beta vulgaris (v1.2)
  • Brassica oleracea (v2.1)
  • Brassica rapa (FPsc1.3)
  • Cajanus cajan (5.5)
  • Capsella rubella (1.0)
  • Capsicum annuum (2.0)
  • Carica papaya (ASGPB0.4)
  • Chenopodium quinoa (v1.0)
  • Chlamydomonas reinhardtii (JGI V5.5)
  • Cicer arietinum (1.0)
  • Citrullus lanatus (1.0)
  • Citrus clementina (v1.0)
  • Coffea canephora (1)
  • Corchorus olitorius (1.0)
  • Cucumis melo (3.5)
  • Cucumis sativus L. (v1.0)
  • Daucus carota (v2.0)
  • Erythranthe guttata (V2.0)
  • Eucalyptus grandis (v2.0)
  • Fragaria vesca (v1.1)
  • Glycine max (Wm82.a2.v1)
  • Gossypium raimondii (2.1)
  • Hevea brasiliensis (V?)
  • Malus domestica (2)
  • Manihot esculenta (v6.1)
  • Marchantia polymorpha (JGI v3.1)
  • Medicago truncatula (Mt4.0v1)
  • Micromonas commoda (JGI v3.0)
  • Nelumbo nucifera (1.1)
  • Oryza sativa ssp. japonica (v7.0)
  • Petunia axillaris (1.6.2)
  • Physcomitrella patens (JGI v3.3)
  • Picea abies (v1.0)
  • Populus trichocarpa (JGI v3.01)
  • Prunus persica (v2.1)
  • Pyrus bretschneideri (1.0)
  • Ricinus communis (1.0)
  • Schrenkiella parvula (2.0 (TpV84))
  • Selaginella moellendorffii (JGI v1.0)
  • Solanum lycopersicum (itag2.4)
  • Solanum tuberosum (v4.03)
  • Tarenaya hassleriana (1)
  • Theobroma cacao (1.1)
  • Trifolium pratense (v2)
  • Utricularia gibba (4)
  • Vigna radiata var. radiata (6?)
  • Vitis vinifera (12xMarch2010)
  • Zea mays (v4.0)
  • Ziziphus jujuba (1.1?)
Monocots PLAZA 4.0
Summary

Version 4.0 of the PLAZA platform. Focused on monocot species, but with the necessary outgroup organisms as reference species.

New release!
  • Amborella trichopoda (JGI v1.0)
  • Ananas comosus (v3.0)
  • Arabidopsis thaliana (Araport11)
  • Brachypodium distachyon (v3.1)
  • Chlamydomonas reinhardtii (JGI V5.5)
  • Elaeis guineensis (v1.0)
  • Hordeum vulgare (ASM32608v1)
  • Marchantia polymorpha (JGI v3.1)
  • Micromonas commoda (JGI v3.0)
  • Musa acuminata (v1.0)
  • Oropetium thomaeum (v1.0)
  • Oryza brachyantha (v1.4b)
  • Oryza sativa ssp. indica (v7.0)
  • Oryza sativa ssp. japonica (v7.0)
  • Phalaenopsis equestris (v1.0)
  • Phyllostachys edulis (v1.0)
  • Physcomitrella patens (JGI v3.3)
  • Picea abies (v1.0)
  • Populus trichocarpa (JGI v3.01)
  • Selaginella moellendorffii (JGI v1.0)
  • Setaria italica (v2.2)
  • Solanum lycopersicum (itag2.4)
  • Sorghum bicolor (v3.1)
  • Spirodela polyrhiza (v2.0)
  • Triticum aestivum (TGACv1)
  • Vitis vinifera (12xMarch2010)
  • Zea mays (v4.0)
  • Zostera marina (v2.2)
  • Zoysia japonica ssp. nagirizaki (v1.1)
pico-PLAZA 2.0
Summary

This PLAZA version focuses on marine eukaryotic micro-organisms. A wide selection of species was selected, from multiple branches of the tree of life; e.g. green algae, brown algae and diatoms. Some landplants were also added as reference.

pico-PLAZA, a genome database of microbial photosynthetic eukaryotes

  • Arabidopsis thaliana (TAIR10)
  • Aureococcus anophagefferens (JGI 1.0 )
  • Bathycoccus prasinos (UGent ORCAE)
  • Chlamydomonas reinhardtii (JGI 4.0)
  • Chlorella sp NC64A (JGI 1.0)
  • Coccomyxa sp. C169 (JGI 1.0)
  • Cyanidioschyzon merolae (Tokyo University)
  • Ectocarpus siliculosus (UGent ORCAE)
  • Fragilariopsis cylindrus (JGI 1.0)
  • Micromonas pusilla strain CCMP1545 (JGI 2.0)
  • Micromonas sp RCC299 (JGI 3.0)
  • Oryza sativa (TIGR6.1)
  • Ostreococcus lucimarinus (JGI 2.0)
  • Ostreococcus sp RCC809 (JGI 2.0)
  • Ostreococcus tauri (Ghent University)
  • Phaeodactylum tricornutum (JGI 2.0)
  • Physcomitrella patens (JGI 1.1 - cosmoss.org 1.2)
  • Thalassiosira pseudonana (JGI 3.0)
  • Volvox carteri (JGI 1.0)
Dicots PLAZA 3.0
Summary

Third iteration of the PLAZA platform. Focused on dicot species, but with some others as reference organisms.

PLAZA 3.0: an access point for plant comparative genomics

  • Amborella trichopoda (Amborella V1.0)
  • Arabidopsis lyrata (JGI v1.0)
  • Arabidopsis thaliana (TAIR10)
  • Beta vulgaris (RefBeet 1.1)
  • Brassica rapa (Annotation v1.2 on assembly v1.1 (Phytozome 9.1))
  • Capsella rubella (JGI annotation v1.0 on assembly v1)
  • Carica papaya (Hawaii Agriculture Research Center)
  • Chlamydomonas reinhardtii (JGI v5.0 assembly, annot v5.3.1 based on Augustus u11.6)
  • Citrullus lanatus (Cucurbit Genomics Database)
  • Citrus sinensis (JGI v1 assembly and v1.0 annotation)
  • Cucumis melo (Melonomics v3.5)
  • Eucalyptus grandis (JGI assembly v1.0, annotation v1.1)
  • Fragaria vesca (Strawberry Genome 1.0)
  • Glycine max (JGI Glyma1.1 annotation of the chromosome-based Glyma1 assembly)
  • Gossypium raimondii (JGI annotation v2.1 on assembly v2.0)
  • Lotus japonicus (Kazusa 2.5)
  • Malus domestica (IASMA)
  • Manihot esculenta (Cassava4)
  • Medicago truncatula (JCVI 4.0)
  • Oryza sativa ssp. japonica (MSU RGAP 7)
  • Ostreococcus lucimarinus (JGI v2.0 assembly and annotation)
  • Physcomitrella patens (JGI assembly release v1.1 and COSMOSS annotation v1.6)
  • Populus trichocarpa (JGI assembly release v3.0, annotation v3.0)
  • Prunus persica (JGI release v1.0)
  • Ricinus communis (JCVI 1.0)
  • Solanum lycopersicum (ITAG 2.3)
  • Solanum tuberosum (ITAG 001)
  • Thellungiella parvula (TpV84)
  • Theobroma cacao (D. Gilbert public gene set 8 Mar 2012 on assembly v1.1)
  • Vitis vinifera (genescope v1)
  • Zea mays (5b.60)
Monocots PLAZA 3.0
Summary

Third iteration of the PLAZA platform. Focused on monocot species, but with some others as reference organisms.

PLAZA 3.0: an access point for plant comparative genomics

  • Arabidopsis thaliana (TAIR10)
  • Brachypodium distachyon (MIPS 1.2)
  • Carica papaya (Hawaii Agriculture Research Center)
  • Chlamydomonas reinhardtii (JGI v5.0 assembly, annot v5.3.1 based on Augustus u11.6)
  • Hordeum vulgare (MIPS)
  • Musa acuminata (Genescope/Cirad)
  • Oryza sativa ssp. indica (9311_BGF_2005)
  • Oryza sativa ssp. japonica (MSU RGAP 7)
  • Ostreococcus lucimarinus (JGI 2.0)
  • Physcomitrella patens (JGI assembly release v1.1 and COSMOSS annotation v1.6)
  • Populus trichocarpa (JGI assembly release v3.0, annotation v3.0)
  • Setaria italica (JGI 8.3X chromosome-scale assembly release 2.0, annotation version 2.1)
  • Solanum lycopersicum (ITAG 2.3)
  • Sorghum bicolor (JGI 1.4)
  • Vitis vinifera (genescope v1)
  • Zea mays (5b.60)
Gymno PLAZA 1.0
Summary

Gymnosperms oriented PLAZA version.

  • Amborella trichopoda (Amborella V1.0)
  • Arabidopsis thaliana (TAIR10)
  • Cycas micholitzii (oneKP)
  • Ginkgo biloba (oneKP)
  • Gnetum montanum (oneKP)
  • Oryza sativa ssp. japonica (MSU RGAP 7)
  • Physcomitrella patens (JGI assembly release v1.1 and COSMOSS annotation v1.6)
  • Picea abies (Congenie)
  • Picea glauca (SMarTForests)
  • Picea sitchensis (ProCoGen)
  • Pinus pinaster (ProCoGen)
  • Pinus sylvestris (ProCoGen)
  • Pinus taeda (PineRefSeq)
  • Populus trichocarpa (JGI assembly release v3.0, annotation v3.0)
  • Pseudotsuga menziesii (PineRefSeq)
  • Taxus baccata (oneKP)
Summary

This update of PLAZA 2.0 contains a small number of updates/additions compared to the PLAZA 2.0 platform, most notably an update from the model organism Arabidopsis thaliana from TAIR9 to TAIR10.

Dissecting plant genomes with the PLAZA comparative genomics platform

  • Arabidopsis lyrata (JGI 1.0)
  • Arabidopsis thaliana (TAIR10)
  • Brachypodium distachyon (MIPS 1.2)
  • Carica papaya (Hawaii Agriculture Research Center)
  • Chlamydomonas reinhardtii (JGI 4.0)
  • Fragaria vesca (Strawberry Genome 1.0)
  • Glycine max (JGI 1.0)
  • Lotus japonicus (Kazusa 1.0)
  • Malus domestica (IASMA)
  • Manihot esculenta (Cassava4)
  • Medicago truncatula (Mt3.5)
  • Micromonas sp. RCC299 (JGI 3.0)
  • Oryza sativa ssp. indica (9311_BGF_2005)
  • Oryza sativa ssp. japonica (MSU RGAP 6.1)
  • Ostreococcus lucimarinus (JGI 2.0)
  • Ostreococcus tauri (Ghent University)
  • Physcomitrella patens (JGI 1.1 - cosmoss.org 1.2)
  • Populus trichocarpa (JGI 2.0)
  • Ricinus communis (JCVI 1.0)
  • Selaginella moellendorffii (JGI 1.0)
  • Sorghum bicolor (JGI 1.4)
  • Theobroma cacao (CocoaGen v1.0)
  • Vitis vinifera (Genoscope_v1)
  • Volvox carteri (JGI 1.0)
  • Zea mays (5b.60)
Summary

Second iteration of the PLAZA platform. This version was quickly discontinued with the release of the TAIR10 release of Arabidopsis thaliana. We strongly suggest using a next version of PLAZA (e.g. PLAZA v2.5) for any analyzes.

Not published

  • Arabidopsis lyrata (JGI 1.0)
  • Arabidopsis thaliana (TAIR9)
  • Brachypodium distachyon (JGI 8x)
  • Carica papaya (Hawaii Agriculture Research Center)
  • Chlamydomonas reinhardtii (JGI 4.0)
  • Glycine max (JGI 1.0)
  • Lotus japonicus (Kazusa 1.0)
  • Malus domestica (IASMA)
  • Manihot esculenta (JGI 1.1)
  • Medicago truncatula (Mt3.0)
  • Micromonas sp. RCC299 (JGI 3.0)
  • Oryza sativa ssp. indica (9311_BGF_2005)
  • Oryza sativa ssp. japonica (TIGR6.1)
  • Ostreococcus lucimarinus (JGI 2.0)
  • Ostreococcus tauri (Ghent University)
  • Physcomitrella patens (JGI 1.1 - cosmoss.org 1.2)
  • Populus trichocarpa (JGI 2.0)
  • Ricinus communis (JCVI 1.0)
  • Selaginella moellendorffii (JGI 1.0)
  • Sorghum bicolor (JGI 1.4)
  • Vitis vinifera (Genoscope_v1)
  • Volvox carteri (JGI 1.0)
  • Zea mays (Version 4.53)
Summary

PLAZA version 1.0 Released in 2009. Publication in plant cell.

PLAZA: a comparative genomics resource to study gene and genome evolution in plants.

  • Arabidopsis thaliana (TAIR8)
  • Carica papaya (Hawaii Agriculture Research Center)
  • Chlamydomonas reinhardtii (JGI 3.0)
  • Oryza sativa (TIGR5)
  • Ostreococcus lucimarinus (JGI 2.0)
  • Physcomitrella patens (JGI 1.1)
  • Populus trichocarpa (JGI 1.1)
  • Sorghum bicolor (JGI 1.4)
  • Vitis vinifera (Genoscope_v1)