{ "type": "genome", "identifier": "GCF_900380235.1", "organism": "Xanthomonas fragariae", "title": "Xanthomonas fragariae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Zurich University of Applied Sciences (ZHAW), School of Life Sciences and Facility Management, Institute of Natural Resource Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900380235.1", "bioproject": "PRJNA224116", "biosample": "SAMEA4590007", "wgs_master": "ORZX00000000.1", "refseq_category": "na", "taxid": "48664", "species_taxid": "48664", "organism_name": "Xanthomonas fragariae", "infraspecific_name": "strain=PD 885", "isolate": "PD 885", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/05/02", "asm_name": "PD_885", "asm_submitter": "Zurich University of Applied Sciences (ZHAW), School of Life Sciences and Facility Management, Institute of Natural Resource Sciences", "gbrs_paired_asm": "GCA_900380235.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/380/235/GCF_900380235.1_PD_885", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3967798", "genome_size_ungapped": "3967291", "gc_percent": "62.000000", "replicon_count": "0", "scaffold_count": "315", "contig_count": "315", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900380235.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "3867", "protein_coding_gene_count": "3181", "non_coding_gene_count": "138", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-05-02", "dateModified": "2018-05-02", "datePublished": "2018-05-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Xanthomonas fragariae" ], "sample_taxid": [ "48664" ], "sample_host_organism": [ "Fragaria chiloensis var. ananassa" ], "sample_host_organism_id": [], "sample_host_disease": [ "diseased" ], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "1.115 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)": "3967798", "Number of Sequences": "315", "Longest Sequences (bp)": "77575", "N50 (bp)": "25808", "Gap Ratio (%)": "0.013862", "GCcontent (%)": "62.1", "Number of CDSs": "3447", "Average Protein Length": "307.8", "Coding Ratio (%)": "80.2", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Xanthomonas fragariae", "strain": "strain=PD 885", "accession": "GCA_900380235.1", "taxid": 48664, "species_taxid": 48664, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1167, "total_fragments": 1176, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Xanthomonas fragariae", "strain": "strain=PD885", "accession": "GCA_900183975.1", "taxid": 48664, "species_taxid": 48664, "relation_to_type": "type", "validated": true, "ani": 99.9815, "matched_fragments": 1171, "total_fragments": 1176, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Xanthomonas hortorum", "strain": "strain=WHRI 7744", "accession": "GCA_003064105.1", "taxid": 56454, "species_taxid": 56454, "relation_to_type": "suspected-type", "validated": true, "ani": 87.3776, "matched_fragments": 989, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas hydrangeae", "strain": "strain=LMG 31884", "accession": "GCA_905142475.1", "taxid": 2775159, "species_taxid": 2775159, "relation_to_type": "type", "validated": true, "ani": 87.3027, "matched_fragments": 1005, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas hortorum", "strain": "strain=CFBP2533", "accession": "GCA_012922215.1", "taxid": 56454, "species_taxid": 56454, "relation_to_type": "pathovar", "validated": true, "ani": 87.2417, "matched_fragments": 994, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas hortorum", "strain": "strain=CFBP 2533", "accession": "GCA_021353095.1", "taxid": 56454, "species_taxid": 56454, "relation_to_type": "pathovar", "validated": true, "ani": 87.2274, "matched_fragments": 990, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas arboricola", "strain": "strain=CFBP 2528", "accession": "GCA_001013475.1", "taxid": 56448, "species_taxid": 56448, "relation_to_type": "type", "validated": true, "ani": 87.1907, "matched_fragments": 984, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas euroxanthea", "strain": "strain=CPBF 424", "accession": "GCA_900476395.1", "taxid": 2259622, "species_taxid": 2259622, "relation_to_type": "type", "validated": true, "ani": 86.9312, "matched_fragments": 987, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas nasturtii", "strain": "strain=WHRI 8853", "accession": "GCA_001660815.1", "taxid": 1843581, "species_taxid": 1843581, "relation_to_type": "type", "validated": true, "ani": 86.5863, "matched_fragments": 985, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas oryzae", "strain": "strain=WHRI 5234", "accession": "GCA_003064145.1", "taxid": 347, "species_taxid": 347, "relation_to_type": "pathovar", "validated": true, "ani": 85.8872, "matched_fragments": 911, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas vasicola", "strain": "strain=CFBP2543", "accession": "GCA_002939925.1", "taxid": 56459, "species_taxid": 56459, "relation_to_type": "type", "validated": true, "ani": 85.8116, "matched_fragments": 958, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas bromi", "strain": "", "accession": "GCA_900092025.1", "taxid": 56449, "species_taxid": 56449, "relation_to_type": "type", "validated": true, "ani": 85.7885, "matched_fragments": 966, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas bromi", "strain": "strain=CFBP1976", "accession": "GCA_002939755.1", "taxid": 56449, "species_taxid": 56449, "relation_to_type": "type", "validated": true, "ani": 85.7716, "matched_fragments": 968, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900183975.1", "gtdb_species": "s__Xanthomonas fragariae", "ani": 99.9815, "matched_fragments": 1171, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.74", "min_intra_species_ani": "99.53", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.96", "num_clustered_genomes": 62, "status": "inconclusive" }, { "accession": "GCF_017603965.1", "gtdb_species": "s__Xanthomonas fragariae_A", "ani": 95.1192, "matched_fragments": 1038, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "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": "inconclusive" }, { "accession": "GCF_003064105.1", "gtdb_species": "s__Xanthomonas hortorum", "ani": 87.3669, "matched_fragments": 990, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 96.0883, "mean_intra_species_ani": "96.84", "min_intra_species_ani": "96.16", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.83", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_002939945.1", "gtdb_species": "s__Xanthomonas arboricola_A", "ani": 87.2264, "matched_fragments": 951, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.91", "min_intra_species_ani": "95.91", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001013475.1", "gtdb_species": "s__Xanthomonas arboricola", "ani": 87.1907, "matched_fragments": 984, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.94", "min_intra_species_ani": "96.17", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.85", "num_clustered_genomes": 117, "status": "-" }, { "accession": "GCF_002939985.1", "gtdb_species": "s__Xanthomonas hortorum_A", "ani": 87.1663, "matched_fragments": 985, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 96.0883, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "97.51", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 28, "status": "-" }, { "accession": "GCF_905142465.1", "gtdb_species": "s__Xanthomonas sp905142465", "ani": 87.1508, "matched_fragments": 986, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.1927, "mean_intra_species_ani": "99.49", "min_intra_species_ani": "99.23", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001423495.1", "gtdb_species": "s__Xanthomonas sp001423495", "ani": 87.0103, "matched_fragments": 962, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "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_900476395.1", "gtdb_species": "s__Xanthomonas euroxanthea", "ani": 86.9195, "matched_fragments": 989, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "97.74", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 25, "status": "-" }, { "accession": "GCF_014197275.1", "gtdb_species": "s__Xanthomonas campestris_B", "ani": 86.6321, "matched_fragments": 937, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.71", "min_intra_species_ani": "98.71", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001660815.1", "gtdb_species": "s__Xanthomonas nasturtii", "ani": 86.5863, "matched_fragments": 985, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.97", "min_intra_species_ani": "98.97", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900092025.1", "gtdb_species": "s__Xanthomonas bromi", "ani": 85.7949, "matched_fragments": 964, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000772705.2", "gtdb_species": "s__Xanthomonas vasicola", "ani": 85.7152, "matched_fragments": 966, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "98.20", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 113, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": 0.605, "growth_tmp": 28.0, "optimum_tmp": 27.699, "optimum_ph": null, "genome_size": 4273011.857, "gc_content": 62.262, "coding_genes": 3287.714, "rRNA16S_genes": 2.0, "tRNA_genes": 52.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Xanthomonas", "fragariae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }