{ "type": "genome", "identifier": "GCF_007000325.2", "organism": "Rhizobium rhododendri", "title": "Rhizobium rhododendri", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Julius Kuehn-Institut, Federal Research Centre for Cultivated Plants (JKI), EP", "publication": [ {} ], "properties": { "assembly_accession": "GCF_007000325.2", "bioproject": "PRJNA224116", "biosample": "SAMN10724087", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2506430", "species_taxid": "2506430", "organism_name": "Rhizobium rhododendri", "infraspecific_name": "strain=rho-6.2", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/04/19", "asm_name": "ASM700032v2", "asm_submitter": "Julius Kuehn-Institut, Federal Research Centre for Cultivated Plants (JKI), EP", "gbrs_paired_asm": "GCA_007000325.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/007/000/325/GCF_007000325.2_ASM700032v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5959131", "genome_size_ungapped": "5959131", "gc_percent": "60.000000", "replicon_count": "4", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_007000325.2-RS_2024_04_19", "annotation_date": "2024-04-19", "total_gene_count": "5668", "protein_coding_gene_count": "5404", "non_coding_gene_count": "71", "pubmed_id": "31294681" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-04-19", "dateModified": "2023-04-19", "datePublished": "2023-04-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhizobium rhododendri" ], "sample_taxid": [ "2506430" ], "sample_host_organism": [ "Rhododendron sp." ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany" ], "sample_host_location_id": [], "data_size": "1.671 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5959131", "Number of Sequences": "4", "Longest Sequences (bp)": "3709686", "N50 (bp)": "3709686", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.0", "Number of CDSs": "5697", "Average Protein Length": "298.2", "Coding Ratio (%)": "85.5", "Number of rRNAs": "12", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhizobium tumorigenes", "strain": "strain=1078", "accession": "GCA_003240565.1", "taxid": 2041385, "species_taxid": 2041385, "relation_to_type": "type", "validated": true, "ani": 93.7928, "matched_fragments": 1565, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium tubonense", "strain": "strain=CCBAU 85046", "accession": "GCA_003240585.1", "taxid": 484088, "species_taxid": 484088, "relation_to_type": "type", "validated": true, "ani": 80.1156, "matched_fragments": 870, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium rhizogenes", "strain": "strain=NBRC 13257", "accession": "GCA_000696095.1", "taxid": 359, "species_taxid": 359, "relation_to_type": "type", "validated": true, "ani": 80.0701, "matched_fragments": 855, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agrobacterium rhizogenes", "strain": "strain=LMG150", "accession": "GCA_007002985.1", "taxid": 359, "species_taxid": 359, "relation_to_type": "type", "validated": true, "ani": 79.9444, "matched_fragments": 875, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium sophorae", "strain": "strain=CCBAU 03386", "accession": "GCA_013087515.1", "taxid": 1535242, "species_taxid": 1535242, "relation_to_type": "type", "validated": true, "ani": 79.8269, "matched_fragments": 773, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium chutanense", "strain": "strain=C5", "accession": "GCA_002531935.1", "taxid": 2035448, "species_taxid": 2035448, "relation_to_type": "type", "validated": true, "ani": 79.7671, "matched_fragments": 781, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium leguminosarum", "strain": "strain=DSM 106839", "accession": "GCA_014202125.1", "taxid": 384, "species_taxid": 384, "relation_to_type": "suspected-type", "validated": true, "ani": 79.6014, "matched_fragments": 805, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium binae", "strain": "strain=BLR195", "accession": "GCA_019684455.1", "taxid": 1138190, "species_taxid": 1138190, "relation_to_type": "type", "validated": true, "ani": 79.5868, "matched_fragments": 749, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium leguminosarum", "strain": "strain=USDA 2370", "accession": "GCA_002008365.1", "taxid": 384, "species_taxid": 384, "relation_to_type": "suspected-type", "validated": true, "ani": 79.5752, "matched_fragments": 818, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium leguminosarum", "strain": "strain=USDA 2370", "accession": "GCA_003058385.1", "taxid": 384, "species_taxid": 384, "relation_to_type": "suspected-type", "validated": true, "ani": 79.5589, "matched_fragments": 816, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium binae", "strain": "strain=BLR195", "accession": "GCA_017357225.1", "taxid": 1138190, "species_taxid": 1138190, "relation_to_type": "type", "validated": true, "ani": 79.5568, "matched_fragments": 759, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium vallis", "strain": "strain=CCBAU 65647", "accession": "GCA_003985155.1", "taxid": 634290, "species_taxid": 634290, "relation_to_type": "type", "validated": true, "ani": 79.538, "matched_fragments": 772, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium leucaenae", "strain": "strain=CFN 299", "accession": "GCA_014727215.1", "taxid": 29450, "species_taxid": 29450, "relation_to_type": "type", "validated": true, "ani": 79.5166, "matched_fragments": 749, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium hainanense", "strain": "strain=CCBAU 57015", "accession": "GCA_900094555.1", "taxid": 52131, "species_taxid": 52131, "relation_to_type": "type", "validated": true, "ani": 79.5041, "matched_fragments": 811, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium leucaenae", "strain": "strain=USDA 9039", "accession": "GCA_000426285.1", "taxid": 29450, "species_taxid": 29450, "relation_to_type": "type", "validated": true, "ani": 79.4997, "matched_fragments": 756, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium multihospitium", "strain": "strain=HAMBI 2975", "accession": "GCA_900094585.1", "taxid": 410764, "species_taxid": 410764, "relation_to_type": "type", "validated": true, "ani": 79.4845, "matched_fragments": 809, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium jaguaris", "strain": "strain=CCGE525", "accession": "GCA_003627755.1", "taxid": 1312183, "species_taxid": 1312183, "relation_to_type": "type", "validated": true, "ani": 79.4431, "matched_fragments": 803, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium miluonense", "strain": "strain=HAMBI 2971", "accession": "GCA_900094545.1", "taxid": 411945, "species_taxid": 411945, "relation_to_type": "type", "validated": true, "ani": 79.3601, "matched_fragments": 753, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella pollutisoli", "strain": "strain=KCTC 52677", "accession": "GCA_024609765.1", "taxid": 2250594, "species_taxid": 2250594, "relation_to_type": "type", "validated": true, "ani": 79.0123, "matched_fragments": 571, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pararhizobium antarcticum", "strain": "strain=NAQVI 59", "accession": "GCA_001885585.1", "taxid": 1798805, "species_taxid": 1798805, "relation_to_type": "type", "validated": true, "ani": 78.9922, "matched_fragments": 564, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella fusca", "strain": "strain=DSM 21319", "accession": "GCA_014203155.1", "taxid": 544480, "species_taxid": 544480, "relation_to_type": "type", "validated": true, "ani": 78.9522, "matched_fragments": 619, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium altiplani", "strain": "strain=BR 10423", "accession": "GCA_001542405.1", "taxid": 1864509, "species_taxid": 1864509, "relation_to_type": "type", "validated": true, "ani": 78.894, "matched_fragments": 619, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium grahamii", "strain": "strain=CCGE 502", "accession": "GCA_000298315.2", "taxid": 1120045, "species_taxid": 1120045, "relation_to_type": "type", "validated": true, "ani": 78.8821, "matched_fragments": 603, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella sumterensis", "strain": "strain=MEC087", "accession": "GCA_004514425.2", "taxid": 1967501, "species_taxid": 1967501, "relation_to_type": "type", "validated": true, "ani": 78.8717, "matched_fragments": 569, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella yambaruensis", "strain": "strain=DSM 18801", "accession": "GCA_022899355.1", "taxid": 415996, "species_taxid": 415996, "relation_to_type": "type", "validated": true, "ani": 78.8662, "matched_fragments": 651, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium populisoli", "strain": "strain=XQZ8", "accession": "GCA_019430945.1", "taxid": 2859785, "species_taxid": 2859785, "relation_to_type": "type", "validated": true, "ani": 78.7809, "matched_fragments": 579, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shinella curvata", "strain": "strain=C3", "accession": "GCA_022899935.1", "taxid": 1817964, "species_taxid": 1817964, "relation_to_type": "type", "validated": true, "ani": 78.7595, "matched_fragments": 578, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ciceribacter ferrooxidans", "strain": "strain=F8825", "accession": "GCA_004137355.1", "taxid": 2509717, "species_taxid": 2509717, "relation_to_type": "type", "validated": true, "ani": 78.4825, "matched_fragments": 513, "total_fragments": 1985, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_007000325.1", "gtdb_species": "s__Rhizobium sp007000325", "ani": 99.9719, "matched_fragments": 1894, "total_fragments": 1985, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.07", "min_intra_species_ani": "97.10", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 7, "status": "conclusive" }, { "accession": "GCF_003240565.1", "gtdb_species": "s__Rhizobium tumorigenes", "ani": 93.7803, "matched_fragments": 1566, "total_fragments": 1985, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.15", "min_intra_species_ani": "97.15", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003240585.1", "gtdb_species": "s__Rhizobium tubonense", "ani": 80.1274, "matched_fragments": 869, "total_fragments": 1985, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_014195095.1", "gtdb_species": "s__Rhizobium sp014195095", "ani": 80.1141, "matched_fragments": 885, "total_fragments": 1985, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_014189535.1", "gtdb_species": "s__Rhizobium lusitanum_C", "ani": 79.8904, "matched_fragments": 856, "total_fragments": 1985, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_004341625.1", "gtdb_species": "s__Rhizobium sp004341625", "ani": 79.8815, "matched_fragments": 823, "total_fragments": 1985, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.83", "min_intra_species_ani": "97.83", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002211285.1", "gtdb_species": "s__Rhizobium sp002211285", "ani": 79.8643, "matched_fragments": 750, "total_fragments": 1985, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_900470805.1", "gtdb_species": "s__Rhizobium sp900470805", "ani": 79.8188, "matched_fragments": 755, "total_fragments": 1985, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_002531755.2", "gtdb_species": "s__Rhizobium acidisoli", "ani": 79.768, "matched_fragments": 818, "total_fragments": 1985, "gtdb_taxonomy": 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