{ "type": "genome", "identifier": "GCA_023934045.1", "organism": "Candidatus Phytoplasma vitis", "title": "Candidatus Phytoplasma vitis", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "Agroscope", "publication": [ {} ], "properties": { "assembly_accession": "GCA_023934045.1", "bioproject": "PRJNA838420", "biosample": "SAMN28422185", "wgs_master": "", "refseq_category": "na", "taxid": "131152", "species_taxid": "131152", "organism_name": "Candidatus Phytoplasma vitis", "infraspecific_name": "", "isolate": "CH", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/06/27", "asm_name": "ASM2393404v1", "submitter": "Agroscope", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/023/934/045/GCA_023934045.1_ASM2393404v1", "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": "2022-06-27", "dateModified": "2022-06-27", "datePublished": "2022-06-27", "_annotation": { "sample_count": 1, "sample_organism": [ "Candidatus Phytoplasma vitis" ], "sample_taxid": [ "131152" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Switzerland: Chardonne" ], "sample_host_location_id": [], "data_size": "0.168 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": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "654223", "Number of Sequences": "1", "Longest Sequences (bp)": "654223", "N50 (bp)": "654223", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "21.7", "Number of CDSs": "514", "Average Protein Length": "322.4", "Coding Ratio (%)": "76.0", "Number of rRNAs": "4", "Number of tRNAs": "32", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003640545.1", "gtdb_species": "s__Phytoplasma ziziphi", "ani": 90.8673, "matched_fragments": 171, "total_fragments": 218, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma", "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_018024475.1", "gtdb_species": "s__Phytoplasma luffae", "ani": 79.32, "matched_fragments": 113, "total_fragments": 218, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma", "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_005774685.2", "gtdb_species": "s__Phytoplasma sp005774685", "ani": 78.222, "matched_fragments": 94, "total_fragments": 218, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma", "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_007821455.1", "gtdb_species": "s__Phytoplasma pini", "ani": 77.5673, "matched_fragments": 87, "total_fragments": 218, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma", "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_003263355.1", "gtdb_species": "s__Phytoplasma oryzae", "ani": 77.4251, "matched_fragments": 96, "total_fragments": 218, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.65", "min_intra_species_ani": "99.65", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009268075.1", "gtdb_species": "s__Phytoplasma sp009268075", "ani": 77.371, "matched_fragments": 88, "total_fragments": 218, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma", "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_000026205.1", "gtdb_species": "s__Phytoplasma mali", "ani": 76.8331, "matched_fragments": 91, "total_fragments": 218, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma", "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_001307505.2", "gtdb_species": "s__Phytoplasma sp000364425", "ani": 76.6821, "matched_fragments": 79, "total_fragments": 218, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.91", "min_intra_species_ani": "98.40", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacillota_I", "c__Bacilli_A", "o__Acholeplasmatales", "f__Acholeplasmataceae", "g__Phytoplasma", "s__Phytoplasma rubi_A" ], "_genome_taxon": [ "Candidatus", "Phytoplasma", "vitis", "d__Bacteria", "p__Bacillota_I", "c__Bacilli_A", "o__Acholeplasmatales", "f__Acholeplasmataceae", "g__Phytoplasma", "s__Phytoplasma rubi_A", "Bacteria", "Bacillota", "I", "Bacilli", "A", "Acholeplasmatales", "Acholeplasmataceae", "Phytoplasma", "Phytoplasma", "rubi", "A" ], "_meo": [ { "id": "MEO_0000379", "label": "leaf" }, { "id": "MEO_0000419", "label": "plant body associated" } ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }