{ "type": "genome", "identifier": "GCF_021166635.1", "organism": "Pseudomonas petroselini", "title": "Pseudomonas petroselini", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Agriculture and Food Research Organization (NARO)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_021166635.1", "bioproject": "PRJNA224116", "biosample": "SAMN23560408", "wgs_master": "JAJOZG000000000.1", "refseq_category": "na", "taxid": "2899822", "species_taxid": "2899822", "organism_name": "Pseudomonas petroselini", "infraspecific_name": "strain=MAFF 311094", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/12/12", "asm_name": "ASM2116663v1", "asm_submitter": "National Agriculture and Food Research Organization (NARO)", "gbrs_paired_asm": "GCA_021166635.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/166/635/GCF_021166635.1_ASM2116663v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6944956", "genome_size_ungapped": "6944956", "gc_percent": "60.000000", "replicon_count": "0", "scaffold_count": "332", "contig_count": "332", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_021166635.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "6477", "protein_coding_gene_count": "6151", "non_coding_gene_count": "64", "pubmed_id": "35695838" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-12-12", "dateModified": "2021-12-12", "datePublished": "2021-12-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudomonas petroselini" ], "sample_taxid": [ "2899822" ], "sample_host_organism": [ "Parsley" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Miyagi" ], "sample_host_location_id": [], "data_size": "1.966 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)": "6944956", "Number of Sequences": "332", "Longest Sequences (bp)": "121937", "N50 (bp)": "37395", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "60.1", "Number of CDSs": "6375", "Average Protein Length": "319.3", "Coding Ratio (%)": "87.9", "Number of rRNAs": "4", "Number of tRNAs": "58", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudomonas marginalis", "strain": "strain=ICMP 3553", "accession": "GCA_001645105.1", "taxid": 298, "species_taxid": 298, "relation_to_type": "suspected-type", "validated": true, "ani": 98.7945, "matched_fragments": 1872, "total_fragments": 2155, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas marginalis", "strain": "strain=ICMP 3553", "accession": "GCA_003700725.1", "taxid": 298, "species_taxid": 298, "relation_to_type": "suspected-type", "validated": true, "ani": 98.7285, "matched_fragments": 1775, "total_fragments": 2155, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas pergaminensis", "strain": "strain=1008", "accession": "GCA_024112395.1", "taxid": 2853159, "species_taxid": 2853159, "relation_to_type": "type", "validated": true, "ani": 91.1759, "matched_fragments": 1631, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lurida", "strain": "strain=LMG 21995", "accession": "GCA_002563895.1", "taxid": 244566, "species_taxid": 244566, "relation_to_type": "type", "validated": true, "ani": 90.974, "matched_fragments": 1615, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas extremorientalis", "strain": "", "accession": "GCA_900625005.1", "taxid": 169669, "species_taxid": 169669, "relation_to_type": "type", "validated": true, "ani": 90.4971, "matched_fragments": 1586, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas azotoformans", "strain": "strain=LMG 21611", "accession": "GCA_900103345.1", "taxid": 47878, "species_taxid": 47878, "relation_to_type": "suspected-type", "validated": true, "ani": 90.4763, "matched_fragments": 1635, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas azotoformans", "strain": "", "accession": "GCA_900624915.1", "taxid": 47878, "species_taxid": 47878, "relation_to_type": "suspected-type", "validated": true, "ani": 90.4375, "matched_fragments": 1651, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas azotoformans", "strain": "strain=NBRC 12693", "accession": "GCA_002091515.1", "taxid": 47878, "species_taxid": 47878, "relation_to_type": "suspected-type", "validated": true, "ani": 90.4288, "matched_fragments": 1635, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas simiae", "strain": "strain=CCUG 50988", "accession": "GCA_001730615.1", "taxid": 321846, "species_taxid": 321846, "relation_to_type": "type", "validated": true, "ani": 90.2999, "matched_fragments": 1574, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas simiae", "strain": "strain=CCUG 50988", "accession": "GCA_900111895.1", "taxid": 321846, "species_taxid": 321846, "relation_to_type": "type", "validated": true, "ani": 90.2832, "matched_fragments": 1568, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas marginalis", "strain": "strain=DSM 13124", "accession": "GCA_007858155.1", "taxid": 298, "species_taxid": 298, "relation_to_type": "suspected-type", "validated": true, "ani": 89.4267, "matched_fragments": 1687, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas asgharzadehiana", "strain": "strain=SWRI132", "accession": "GCA_019139815.1", "taxid": 2842349, "species_taxid": 2842349, "relation_to_type": "type", "validated": true, "ani": 88.3497, "matched_fragments": 1541, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas antarctica", "strain": "strain=CMS 35", "accession": "GCA_010634845.1", "taxid": 219572, "species_taxid": 219572, "relation_to_type": "type", "validated": true, "ani": 88.0283, "matched_fragments": 1478, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas salmasensis", "strain": "strain=SWRI126", "accession": "GCA_014268375.2", "taxid": 2745514, "species_taxid": 2745514, "relation_to_type": "type", "validated": true, "ani": 87.6746, "matched_fragments": 1484, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas spelaei", "strain": "strain=CCM 7893", "accession": "GCA_009724245.1", "taxid": 1055469, "species_taxid": 1055469, "relation_to_type": "type", "validated": true, "ani": 85.8492, "matched_fragments": 1405, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas karstica", "strain": "strain=CCM 7891", "accession": "GCA_009707515.1", "taxid": 1055468, "species_taxid": 1055468, "relation_to_type": "type", "validated": true, "ani": 85.1728, "matched_fragments": 1254, "total_fragments": 2155, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001645105.1", "gtdb_species": "s__Pseudomonas_E marginalis_B", "ani": 98.7945, "matched_fragments": 1872, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.70", "min_intra_species_ani": "98.28", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 10, "status": "conclusive" }, { "accession": "GCF_000612585.1", "gtdb_species": "s__Pseudomonas_E sp000612585", "ani": 91.3858, "matched_fragments": 1531, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_002007785.1", "gtdb_species": "s__Pseudomonas_E azotoformans_B", "ani": 91.1206, "matched_fragments": 1628, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "98.86", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_002563895.1", "gtdb_species": "s__Pseudomonas_E lurida", "ani": 90.9761, "matched_fragments": 1615, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.19", "min_intra_species_ani": "99.03", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 25, "status": "-" }, { "accession": "GCF_900103345.1", "gtdb_species": "s__Pseudomonas_E azotoformans", "ani": 90.4933, "matched_fragments": 1633, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.97", "min_intra_species_ani": "95.87", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.87", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_001870465.1", "gtdb_species": "s__Pseudomonas_E extremorientalis", "ani": 90.4107, "matched_fragments": 1594, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.37", "min_intra_species_ani": "98.13", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 29, "status": "-" }, { "accession": "GCF_001579805.1", "gtdb_species": "s__Pseudomonas_E azotoformans_A", "ani": 90.3427, "matched_fragments": 1627, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.75", "min_intra_species_ani": "96.24", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_001186335.1", "gtdb_species": "s__Pseudomonas_E trivialis_B", "ani": 90.3083, "matched_fragments": 1636, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.34", "min_intra_species_ani": "95.31", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_900111895.1", "gtdb_species": "s__Pseudomonas_E simiae", "ani": 90.2832, "matched_fragments": 1568, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.45", "min_intra_species_ani": "99.32", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 20, "status": "-" }, { "accession": "GCF_003097075.1", "gtdb_species": "s__Pseudomonas_E sp003097075", "ani": 89.4713, "matched_fragments": 1572, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.77", "min_intra_species_ani": "98.77", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014207255.1", "gtdb_species": "s__Pseudomonas_E sp014207255", "ani": 89.4292, "matched_fragments": 1660, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.31", "min_intra_species_ani": "98.90", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_012844475.1", "gtdb_species": "s__Pseudomonas_E sp012844475", "ani": 89.2891, "matched_fragments": 1449, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_016937595.1", "gtdb_species": "s__Pseudomonas_E fulgida", "ani": 88.9475, "matched_fragments": 1073, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_001050345.1", "gtdb_species": "s__Pseudomonas_E fildesensis", "ani": 88.7533, "matched_fragments": 1570, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_013386585.1", "gtdb_species": "s__Pseudomonas_E sp013386585", "ani": 88.6087, "matched_fragments": 1526, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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_009834565.1", "gtdb_species": "s__Pseudomonas_E sp009834565", "ani": 88.5864, "matched_fragments": 1551, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.71", "min_intra_species_ani": "97.35", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001439695.1", "gtdb_species": "s__Pseudomonas_E veronii", "ani": 88.4448, "matched_fragments": 1514, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "98.13", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.82", "num_clustered_genomes": 43, "status": "-" }, { "accession": "GCF_900583165.1", "gtdb_species": "s__Pseudomonas_E sp900583165", "ani": 88.1657, "matched_fragments": 1455, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "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": "0.99", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_001902145.1", "gtdb_species": "s__Pseudomonas_E fluorescens_BV", "ani": 87.6482, "matched_fragments": 1440, "total_fragments": 2155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.76", "min_intra_species_ani": "95.23", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 22, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.248, "cell_length": 0.186, "doubling_h": -0.025, "growth_tmp": 28.767, "optimum_tmp": 27.972, "optimum_ph": 7.258, "genome_size": 5663774.24, "gc_content": 60.938, "coding_genes": 5204.79, "rRNA16S_genes": 5.319, "tRNA_genes": 67.35, "gram_stain": 0.0, "sporulation": 0.013, "motility": 0.975, "range_salinity": 0.666, "facultative_respiration": 0.021, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.978, "mesophilic_range_tmp": 0.926, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.073, "bacillus_cell_shape": 0.988, "coccus_cell_shape": 0.011, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pseudomonas", "petroselini" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }