118 new plant reference genomes and transcriptomes added to Galaxy Europe!

By erxleben

January 5, 2020

List of plant reference genomes

In cooperation with our ELIXIR partner in Belgium, the VIB, we have recently added more than 100 new plant reference genomes and transcriptomes to the European Galaxy server. These reference datasets are obtained from PLAZA, a platform for comparative plant genomics, with the help of the Belgian Galaxy team led by Frederik Coppens. The PLAZA Data Warehouse provides access to the parsed and curated data, through an FTP-server and API, which is leveraged to provide, and in the future keep up-to-date, the plant genomes for the Galaxy Community.

A list of all the newly added plant reference genomes can be found below: the genomic sequence, an annotation file (GTF), and kallisto and salmon indices are provided in the European Galaxy server. We also have developed scripts and documentation to add these genomes to your own instance.

We hope that those reference datasets will make plant research even easier in Galaxy and will support the awesome work of the COST action INDEPTH and the ELIXIR plant science community.

All together, Galaxy now provides you with access to more than 1700 different reference genomes and we hope we can support your work with it!

New plant genomes

List of plant reference genomes

Actinidia_chinensis_FEI_Lab_v1.0
Amborella_trichopoda_Amborella_V1.0
Amborella_trichopoda_JGI_v1.0
Ananas_comosus_JGI_v3.0
Apostasia_shenzhenica_v1.0
Arabidopsis_lyrata_JGI_v1.0
Arabidopsis_lyrata_JGI_v2.1
Arabidopsis_thaliana_COL-0_Araport11
Arabidopsis_thaliana_COL-0_TAIR10
Arachis_ipaensis_Peanut_Base_v1.0
Asparagus_officinalis_v1.1
Beta_vulgaris_RefBeet_1.1
Beta_vulgaris_RefBeet_v1.2
Brachypodium_distachyon_JGI_v3.1
Brachypodium_distachyon_MIPS_1.2
Brassica_oleracea_Ensembl_Genomes_v2.1
Brassica_rapa_Annotation_v1.2_on_assembly_v1.1_Phytozome_9.1
Brassica_rapa_JGI_FPsc1.3
Cajanus_cajan_Penguin_Genomics_v5.0
Capsella_rubella_JGI_annotation_v1.0_on_assembly_v1
Capsella_rubella_JGI_v1.0
Capsicum_annuum_Pepper_Genome_v2.0
Carica_papaya_Hawaii_Agriculture_Research_Center
Carica_papaya_JGI_ASGPB0.4
Cenchrus_americanus_v1.0
Chenopodium_quinoa_JGI_v1.0
Chlamydomonas_reinhardtii_JGI_v5.0_assembly_annot_v5.3.1
_based_on_Augustus_u11.6
Chlamydomonas_reinhardtii_JGI_v5.5
Cicer_arietinum_LIS_v1.0
Citrullus_lanatus_Cucurbit_Genomics_Database
Citrullus_lanatus_Cucurbit_Genomics_Database_v1.0
Citrus_clementina_JGI_v1.0
Citrus_sinensis_JGI_v1_assembly_and_v1.0_annotation
Coffea_canephora_Coffee_Genome_Hub_v1
Corchorus_olitorius_GenBank_v1.0
Cucumis_melo_Melonomics_v3.5
Cucumis_sativus_L._JGI_v1.0
Daucus_carota_JGI_v2.0
Elaeis_guineensis_EG5.1
Elaeis_guineensis_NCBI_Genome_v1.0
Erythranthe_guttata_JGI_v2.0
Eucalyptus_grandis_JGI_assembly_v1.0_annotation_v1.1
Eucalyptus_grandis_JGI_v2.0
Fragaria_vesca_JGI_v1.1
Fragaria_vesca_Strawberry_Genome_1.0
Glycine_max_JGI_Glyma1.1_annotation_of_the_chromosome-
based_Glyma1_assembly
Glycine_max_JGI_Wm82.a2.v1
Gossypium_raimondii_JGI_annotation_v2.1_on_assembly_v2.0
Gossypium_raimondii_JGI_v2.1
Hevea_brasiliensis_NCBI_Genomes_v1
Hordeum_vulgare_Ensembl_Genomes_ASM32608v1
Hordeum_vulgare_IBC_PGSB_v2
Hordeum_vulgare_MIPS
Lotus_japonicus_Kazusa_2.5
Malus_domestica_IASMA
Malus_domestica_Penguin_Genomics_v2
Manihot_esculenta_Cassava4
Manihot_esculenta_JGI_v6.1
Marchantia_polymorpha_JGI_v3.1
Medicago_truncatula_JCVI_4.0
Medicago_truncatula_JGI_Mt4.0v1
Micromonas_commoda_JGI_v3.0
Musa_acuminata_Banana_Genome_v1.0
Musa_acuminata_Banana_Genome_v2.0
Musa_acuminata_Genescope-Cirad
Nelumbo_nucifera_LOTUS-DB_v1.1
Oropetium_thomaeum_JGI_v1.0
Oryza_brachyantha_Ensembl_Plants_v1.4b
Oryza_sativa_ssp._indica_9311_BGF_2005
Oryza_sativa_ssp._indica_MBKBASE_v1.0
Oryza_sativa_ssp._japonica_JGI_v7.0
Oryza_sativa_ssp._japonica_MSU_RGAP_7
Ostreococcus_lucimarinus_JGI_2.0
Ostreococcus_lucimarinus_JGI_v2.0_assembly_and_annotation
Petunia_axillaris_Sol_Genomics_v1.6.2
Phalaenopsis_equestris_Genomics_v1.0
Phyllostachys_edulis_NCGR_v1.0
Physcomitrella_patens_JGI_assembly_release_v1.1_and_COS
MOSS_annotation_v1.6
Physcomitrella_patens_JGI_v3.3
Picea_abies_ConGenIE_v1.0
Populus_trichocarpa_JGI_assembly_release_v3.0_annotation_v3.0
Populus_trichocarpa_JGI_v3.1
Prunus_persica_JGI_release_v1.0
Prunus_persica_JGI_v2.1
Pyrus_bretschneideri_Pear_Genome_Project_v1.0
Ricinus_communis_JCVI_1.0
Ricinus_communis_JGI_v0.1
Saccharum_spontaneum_v20190103
Schrenkiella_parvula_Thellungiella_v2.0_TpV84
Selaginella_moellendorffii_JGI_v1.0
Selaginella_moellendorffii_NCBIr100
Setaria_italica_JGI_8.3X_chromosome-
scale_assembly_release_2.0_annotation_version_2.1
Setaria_italica_JGI_v2.2
Solanum_lycopersicum_ITAG_2.3
Solanum_lycopersicum_Sol_Genomics_itag2.4
Solanum_tuberosum_ITAG_001
Solanum_tuberosum_JGI_v4.03
Sorghum_bicolor_JGI_1.4
Sorghum_bicolor_JGI_v3.1
Spirodela_polyrhiza_JGI_v2.0
Tarenaya_hassleriana_RefSeq_v1
Thellungiella_parvula_TpV84
Theobroma_cacao_D._Gilbert_public_gene_set_8_Mar_2012_on_assembly_v1.1
Theobroma_cacao_RefSeq_v1.1
Trifolium_pratense_JGI_v2
Triticum_aestivum_Ensembl_Plants_TGACv1
Triticum_aestivum_IWGSC1.1
Triticum_turgidum_Svevo_v1.0
Utricularia_gibba_CoGe_v4
Vigna_radiata_var._radiata_LIS_v6
Vitis_vinifera_JGI_12xMarch2010
Vitis_vinifera_genescope_v1
Zea_mays_B73_5b.60
Zea_mays_B73_AGP_v4.0
Zea_mays_PH207_v1.0
Ziziphus_jujuba_RefSeq_v1.1
Zostera_marina_JGI_v2.2
Zoysia_japonica_ssp._nagirizaki_Zoysia_Genome_Database_v1.1