{ "type": "genome", "identifier": "GCA_020692335.1", "organism": "Xanthomonas sp.", "title": "Xanthomonas sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University Duisburg-Essen", "publication": [ {} ], "properties": { "assembly_accession": "GCA_020692335.1", "bioproject": "PRJNA627655", "biosample": "SAMN20928806", "wgs_master": "JAIMKS000000000.1", "refseq_category": "na", "taxid": "29446", "species_taxid": "29446", "organism_name": "Xanthomonas sp.", "infraspecific_name": "", "isolate": "GA_180221_E-2-1-MAG-65_9", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/11/01", "asm_name": "ASM2069233v1", "submitter": "University Duisburg-Essen", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/692/335/GCA_020692335.1_ASM2069233v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-11-01", "dateModified": "2021-11-01", "datePublished": "2021-11-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Xanthomonas sp." ], "sample_taxid": [ "29446" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Volcanic Eifel, Andernach", "- on dry ice (field) or in 80 C fridge (lab)" ], "sample_host_location_id": [], "data_size": "1.238 MB", "sample_ph_range": { "min": 68.0, "max": 68.0 }, "sample_temperature_range": { "min": 18.0, "max": 80.0 }, "completeness": 87.5, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "4486174", "Number of Sequences": "275", "Longest Sequences (bp)": "84237", "N50 (bp)": "20173", "Gap Ratio (%)": "0.330460", "GCcontent (%)": "65.5", "Number of CDSs": "3677", "Average Protein Length": "333.3", "Coding Ratio (%)": "82.0", "Number of rRNAs": "0", "Number of tRNAs": "44", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Luteimonas lumbrici", "strain": "strain=1.1416", "accession": "GCA_006476065.1", "taxid": 2559601, "species_taxid": 2559601, "relation_to_type": "type", "validated": true, "ani": 77.3329, "matched_fragments": 211, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas aquatica", "strain": "strain=RIB1-20", "accession": "GCA_022662575.1", "taxid": 450364, "species_taxid": 450364, "relation_to_type": "type", "validated": true, "ani": 77.2593, "matched_fragments": 285, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteimonas cucumeris", "strain": "strain=CGMCC 1.10821", "accession": "GCA_007830035.1", "taxid": 985012, "species_taxid": 985012, "relation_to_type": "type", "validated": true, "ani": 77.2043, "matched_fragments": 232, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oleiagrimonas citrea", "strain": "strain=MEBiC09124", "accession": "GCA_012395255.1", "taxid": 1665687, "species_taxid": 1665687, "relation_to_type": "type", "validated": true, "ani": 77.1753, "matched_fragments": 190, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vulcaniibacterium tengchongense", "strain": "strain=YIM 77520", "accession": "GCA_008033455.1", "taxid": 1273429, "species_taxid": 1273429, "relation_to_type": "type", "validated": true, "ani": 77.158, "matched_fragments": 296, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oleiagrimonas soli", "strain": "strain=3.5X", "accession": "GCA_000761445.1", "taxid": 1543381, "species_taxid": 1543381, "relation_to_type": "type", "validated": true, "ani": 77.1271, "matched_fragments": 215, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoxanthomonas helianthi", "strain": "strain=110414", "accession": "GCA_017939625.1", "taxid": 1453541, "species_taxid": 1453541, "relation_to_type": "type", "validated": true, "ani": 77.1124, "matched_fragments": 225, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vulcaniibacterium tengchongense", "strain": "strain=DSM 25623", "accession": "GCA_003814555.1", "taxid": 1273429, "species_taxid": 1273429, "relation_to_type": "type", "validated": true, "ani": 77.0977, "matched_fragments": 302, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dokdonella koreensis", "strain": "strain=DS-123", "accession": "GCA_001632775.1", "taxid": 323415, "species_taxid": 323415, "relation_to_type": "type", "validated": true, "ani": 77.0959, "matched_fragments": 304, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oleiagrimonas soli", "strain": "strain=DSM 107085", "accession": "GCA_014201555.1", "taxid": 1543381, "species_taxid": 1543381, "relation_to_type": "type", "validated": true, "ani": 77.0705, "matched_fragments": 220, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodanobacter spathiphylli", "strain": "strain=B39", "accession": "GCA_000264295.1", "taxid": 347483, "species_taxid": 347483, "relation_to_type": "type", "validated": true, "ani": 77.0654, "matched_fragments": 235, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fulvimonas soli", "strain": "strain=DSM 14263", "accession": "GCA_003148905.1", "taxid": 155197, "species_taxid": 155197, "relation_to_type": "type", "validated": true, "ani": 76.9272, "matched_fragments": 288, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Fulvimonas soli", "strain": "strain=LMG 19981", "accession": "GCA_006352285.1", "taxid": 155197, "species_taxid": 155197, "relation_to_type": "type", "validated": true, "ani": 76.8704, "matched_fragments": 284, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Metallibacterium scheffleri", "strain": "strain=DSM 24874", "accession": "GCA_004798955.1", "taxid": 993689, "species_taxid": 993689, "relation_to_type": "type", "validated": true, "ani": 76.8235, "matched_fragments": 191, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas sacchari", "strain": "strain=CFBP4641", "accession": "GCA_002940085.1", "taxid": 56458, "species_taxid": 56458, "relation_to_type": "suspected-type", "validated": true, "ani": 76.8226, "matched_fragments": 285, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Metallibacterium scheffleri", "strain": "strain=DKE6", "accession": "GCA_002077135.1", "taxid": 993689, "species_taxid": 993689, "relation_to_type": "type", "validated": true, "ani": 76.7956, "matched_fragments": 195, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthomonas indica", "strain": "strain=PPL560", "accession": "GCA_022669045.1", "taxid": 2912242, "species_taxid": 2912242, "relation_to_type": "type", "validated": true, "ani": 76.7667, "matched_fragments": 287, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dyella acidiphila", "strain": "strain=7MK23", "accession": "GCA_014863405.1", "taxid": 2775866, "species_taxid": 2775866, "relation_to_type": "type", "validated": true, "ani": 76.7379, "matched_fragments": 192, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodanobacter fulvus", "strain": "strain=Jip2", "accession": "GCA_000264315.1", "taxid": 219571, "species_taxid": 219571, "relation_to_type": "type", "validated": true, "ani": 76.613, "matched_fragments": 204, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oxalicibacterium solurbis", "strain": "strain=CCM 7664", "accession": "GCA_014635845.1", "taxid": 69280, "species_taxid": 69280, "relation_to_type": "type", "validated": true, "ani": 75.7844, "matched_fragments": 51, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidiphilus thermophilus", "strain": "strain=JCM 19170", "accession": "GCA_001517365.1", "taxid": 876478, "species_taxid": 876478, "relation_to_type": "suspected-type", "validated": true, "ani": 75.6024, "matched_fragments": 69, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidiphilus thermophilus", "strain": "strain=JCM 19170", "accession": "GCA_001418245.1", "taxid": 876478, "species_taxid": 876478, "relation_to_type": "suspected-type", "validated": true, "ani": 75.5861, "matched_fragments": 70, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tepidiphilus margaritifer", "strain": "strain=DSM 15129", "accession": "GCA_000425565.1", "taxid": 203471, "species_taxid": 203471, "relation_to_type": "type", "validated": true, "ani": 75.3473, "matched_fragments": 53, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pandoraea commovens", "strain": "strain=LMG 31010", "accession": "GCA_902459615.1", "taxid": 2508289, "species_taxid": 2508289, "relation_to_type": "type", "validated": true, "ani": 75.2366, "matched_fragments": 79, "total_fragments": 1353, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 87.5, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_016717705.1", "gtdb_species": "s__JADKFD01 sp016717705", "ani": 83.1911, "matched_fragments": 868, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-5;g__JADKFD01", "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_016713135.1", "gtdb_species": "s__JADKFD01 sp016713135", "ani": 81.522, "matched_fragments": 810, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-5;g__JADKFD01", "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_019187485.1", "gtdb_species": "s__JADKFD01 sp019187485", "ani": 80.7659, "matched_fragments": 648, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__SZUA-5;g__JADKFD01", "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_000953855.2", "gtdb_species": "s__Mizugakiibacter sediminis", "ani": 77.3666, "matched_fragments": 304, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter", "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_016182785.1", "gtdb_species": "s__JADKHK01 sp016182785", "ani": 77.2725, "matched_fragments": 309, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__JADKHK01", "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_016889805.1", "gtdb_species": "s__Rhodanobacter sp001427365", "ani": 77.1327, "matched_fragments": 229, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter", "ani_circumscription_radius": 95.107, "mean_intra_species_ani": "97.01", "min_intra_species_ani": "96.97", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000761445.1", "gtdb_species": "s__Oleiagrimonas soli", "ani": 77.1271, "matched_fragments": 215, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Oleiagrimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003814555.1", "gtdb_species": "s__Lysobacter tengchongensis", "ani": 77.1051, "matched_fragments": 301, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_009996615.1", "gtdb_species": "s__Dokdonella_A sp009996615", "ani": 77.0974, "matched_fragments": 326, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A", "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_002483055.1", "gtdb_species": "s__Dokdonella sp002483055", "ani": 77.066, "matched_fragments": 280, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella", "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_000264295.1", "gtdb_species": "s__Rhodanobacter spathiphylli", "ani": 77.0655, "matched_fragments": 235, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter", "ani_circumscription_radius": 95.107, "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_003241385.1", "gtdb_species": "s__Dokdonella denitrificans_A", "ani": 76.9177, "matched_fragments": 338, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella", "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_002840015.1", "gtdb_species": "s__GCA-002840015 sp002840015", "ani": 76.7887, "matched_fragments": 126, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__GCA-002840015", "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_000425565.1", "gtdb_species": "s__Tepidiphilus margaritifer", "ani": 75.3473, "matched_fragments": 53, "total_fragments": 1353, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": 0.605, "growth_tmp": 27.096, "optimum_tmp": 27.699, "optimum_ph": null, "genome_size": 4930960.958, "gc_content": 64.384, "coding_genes": 4129.338, "rRNA16S_genes": 1.991, "tRNA_genes": 54.759, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Xanthomonadales", "f__SZUA-5", "g__JADKFD01", "s__JADKFD01 sp020693165" ], "_genome_taxon": [ "Xanthomonas", "sp.", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Xanthomonadales", "f__SZUA-5", "g__JADKFD01", "s__JADKFD01 sp020693165", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Xanthomonadales", "SZUA-5", "JADKFD01", "JADKFD01", "sp020693165" ], "_meo": [ { "id": "MEO_0000181", "label": "aquifer" }, { "id": "MEO_0001480", "label": "subsurface" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }