{ "type": "genome", "identifier": "GCF_017676385.1", "organism": "Streptomyces spirodelae", "title": "Streptomyces spirodelae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "KASETSART UNIVERSITY", "publication": [ {} ], "properties": { "assembly_accession": "GCF_017676385.1", "bioproject": "PRJNA224116", "biosample": "SAMN17934891", "wgs_master": "JAFFZN000000000.1", "refseq_category": "reference genome", "taxid": "2812904", "species_taxid": "2812904", "organism_name": "Streptomyces spirodelae", "infraspecific_name": "strain=DW4-2", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/04/02", "asm_name": "ASM1767638v1", "asm_submitter": "KASETSART UNIVERSITY", "gbrs_paired_asm": "GCA_017676385.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/676/385/GCF_017676385.1_ASM1767638v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7310765", "genome_size_ungapped": "7310765", "gc_percent": "71.000000", "replicon_count": "0", "scaffold_count": "72", "contig_count": "72", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_017676385.1-RS_2024_08_29", "annotation_date": "2024-08-29", "total_gene_count": "6538", "protein_coding_gene_count": "6324", "non_coding_gene_count": "65", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-04-02", "dateModified": "2021-04-02", "datePublished": "2021-04-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptomyces spirodelae" ], "sample_taxid": [ "2812904" ], "sample_host_organism": [ "duckweed" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Thailand" ], "sample_host_location_id": [], "data_size": "1.979 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "7310765", "Number of Sequences": "72", "Longest Sequences (bp)": "494977", "N50 (bp)": "191641", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.0", "Number of CDSs": "6568", "Average Protein Length": "325.4", "Coding Ratio (%)": "87.7", "Number of rRNAs": "2", "Number of tRNAs": "66", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptomyces spirodelae", "strain": "strain=DW4-2", "accession": "GCA_017676385.1", "taxid": 2812904, "species_taxid": 2812904, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2396, "total_fragments": 2401, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptomyces smyrnaeus", "strain": "strain=DSM 42105", "accession": "GCA_017676345.1", "taxid": 1387713, "species_taxid": 1387713, "relation_to_type": "type", "validated": true, "ani": 89.1891, "matched_fragments": 1912, "total_fragments": 2401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces oryzae", "strain": "strain=S16-07", "accession": "GCA_017676365.1", "taxid": 1434886, "species_taxid": 1434886, "relation_to_type": "type", "validated": true, "ani": 88.9375, "matched_fragments": 1718, "total_fragments": 2401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces qinglanensis", "strain": "strain=172205", "accession": "GCA_003265665.1", "taxid": 943816, "species_taxid": 943816, "relation_to_type": "type", "validated": true, "ani": 86.9853, "matched_fragments": 1739, "total_fragments": 2401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces qinglanensis", "strain": "strain=CGMCC 4.6825", "accession": "GCA_900111245.1", "taxid": 943816, "species_taxid": 943816, "relation_to_type": "type", "validated": true, "ani": 86.9817, "matched_fragments": 1744, "total_fragments": 2401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces albus subsp. albus", "strain": "strain=NRRL B-1811", "accession": "GCA_000725885.1", "taxid": 67257, "species_taxid": 1888, "relation_to_type": "suspected-type", "validated": true, "ani": 85.122, "matched_fragments": 1579, "total_fragments": 2401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces albus", "strain": "strain=NBRC 13014", "accession": "GCA_000813365.1", "taxid": 1888, "species_taxid": 1888, "relation_to_type": "suspected-type", "validated": true, "ani": 85.0787, "matched_fragments": 1566, "total_fragments": 2401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces boncukensis", "strain": "strain=SB3404", "accession": "GCA_011045075.1", "taxid": 2711219, "species_taxid": 2711219, "relation_to_type": "type", "validated": true, "ani": 82.6587, "matched_fragments": 1174, "total_fragments": 2401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces paromomycinus", "strain": "strain=NBRC 15454", "accession": "GCA_003865155.1", "taxid": 92743, "species_taxid": 92743, "relation_to_type": "type", "validated": true, "ani": 80.3923, "matched_fragments": 1188, "total_fragments": 2401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces gobiensis", "strain": "strain=1_25", "accession": "GCA_021216675.1", "taxid": 2875706, "species_taxid": 2875706, "relation_to_type": "type", "validated": true, "ani": 80.3737, "matched_fragments": 899, "total_fragments": 2401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces monomycini", "strain": "strain=NRRL B-24309", "accession": "GCA_022271435.1", "taxid": 371720, "species_taxid": 371720, "relation_to_type": "type", "validated": true, "ani": 80.2494, "matched_fragments": 1161, "total_fragments": 2401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces rimosus subsp. rimosus", "strain": "strain=R7", "accession": "GCA_022760195.1", "taxid": 132474, "species_taxid": 1927, "relation_to_type": "type", "validated": true, "ani": 80.2327, "matched_fragments": 1206, "total_fragments": 2401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces spinosus", "strain": "strain=SBTS01", "accession": "GCA_020400655.1", "taxid": 2872623, "species_taxid": 2872623, "relation_to_type": "type", "validated": true, "ani": 79.9133, "matched_fragments": 1090, "total_fragments": 2401, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinacidiphila alni", "strain": "strain=CGMCC 4.3510", "accession": "GCA_900112845.1", "taxid": 380248, "species_taxid": 380248, "relation_to_type": "type", "validated": true, "ani": 79.6827, "matched_fragments": 979, "total_fragments": 2401, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 1.04, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_017676385.1", "gtdb_species": "s__Streptomyces sp017676385", "ani": 100.0, "matched_fragments": 2396, "total_fragments": 2401, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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": "conclusive" }, { "accession": "GCF_017676345.1", "gtdb_species": "s__Streptomyces smyrnaeus", "ani": 89.1866, "matched_fragments": 1912, "total_fragments": 2401, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.11", "min_intra_species_ani": "97.08", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_017676365.1", "gtdb_species": "s__Streptomyces oryzae", "ani": 88.9658, "matched_fragments": 1714, "total_fragments": 2401, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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_900111245.1", "gtdb_species": "s__Streptomyces qinglanensis", "ani": 86.9713, "matched_fragments": 1744, "total_fragments": 2401, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000424765.1", "gtdb_species": "s__Streptomyces sp000424765", "ani": 86.9296, "matched_fragments": 1710, "total_fragments": 2401, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.13", "min_intra_species_ani": "98.98", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000725885.1", "gtdb_species": "s__Streptomyces albus", "ani": 85.1051, "matched_fragments": 1581, "total_fragments": 2401, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.54", "min_intra_species_ani": "97.77", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.92", "num_clustered_genomes": 14, "status": "-" }, { "accession": "GCF_003323735.1", "gtdb_species": "s__Streptomyces reniochalinae", "ani": 85.0847, "matched_fragments": 1575, "total_fragments": 2401, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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_014083985.1", "gtdb_species": "s__SCUT-3 sp014083985", "ani": 79.939, "matched_fragments": 907, "total_fragments": 2401, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__SCUT-3", "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": -0.201, "cell_length": -0.05, "doubling_h": 0.103, "growth_tmp": 27.757, "optimum_tmp": 29.036, "optimum_ph": 7.341, "genome_size": 8292419.302, "gc_content": 71.543, "coding_genes": 7141.289, "rRNA16S_genes": 6.155, "tRNA_genes": 67.804, "gram_stain": 0.998, "sporulation": 0.958, "motility": 0.049, "range_salinity": 0.666, "facultative_respiration": 0.0, "anaerobic_respiration": 0.005, "aerobic_respiration": 0.994, "mesophilic_range_tmp": 0.98, "thermophilic_range_tmp": 0.019, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.208, "coccus_cell_shape": 0.032, "filament_cell_shape": 0.582, "coccobacillus_cell_shape": 0.098, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.076 }, "_genome_taxon": [ "Streptomyces", "spirodelae" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }