{ "type": "genome", "identifier": "GCF_021166475.1", "organism": "Pelagibacterium xiamenense", "title": "Pelagibacterium xiamenense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Third Institute of Oceanography, Ministry of Natural Resources of PR China", "publication": [ {} ], "properties": { "assembly_accession": "GCF_021166475.1", "bioproject": "PRJNA224116", "biosample": "SAMN23672523", "wgs_master": "JAJOYS000000000.1", "refseq_category": "reference genome", "taxid": "2901140", "species_taxid": "2901140", "organism_name": "Pelagibacterium xiamenense", "infraspecific_name": "strain=HS1C4-1", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/12/12", "asm_name": "ASM2116647v1", "asm_submitter": "Third Institute of Oceanography, Ministry of Natural Resources of PR China", "gbrs_paired_asm": "GCA_021166475.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/166/475/GCF_021166475.1_ASM2116647v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3371788", "genome_size_ungapped": "3371788", "gc_percent": "63.000000", "replicon_count": "0", "scaffold_count": "8", "contig_count": "8", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_021166475.1-RS_2024_08_08", "annotation_date": "2024-08-08", "total_gene_count": "3289", "protein_coding_gene_count": "3220", "non_coding_gene_count": "54", "pubmed_id": "na" }, "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": [ "Pelagibacterium xiamenense" ], "sample_taxid": [ "2901140" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Haicang Coast, Xiamen, Fujian Province" ], "sample_host_location_id": [], "data_size": "0.940 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)": "3371788", "Number of Sequences": "8", "Longest Sequences (bp)": "1622505", "N50 (bp)": "991634", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.9", "Number of CDSs": "3268", "Average Protein Length": "311.6", "Coding Ratio (%)": "90.6", "Number of rRNAs": "0", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pelagibacterium xiamenense", "strain": "strain=HS1C4-1", "accession": "GCA_021166475.1", "taxid": 2901140, "species_taxid": 2901140, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1118, "total_fragments": 1119, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pelagibacterium lacus", "strain": "strain=XYN52", "accession": "GCA_003345525.1", "taxid": 2282655, "species_taxid": 2282655, "relation_to_type": "type", "validated": true, "ani": 79.2598, "matched_fragments": 442, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagibacterium sediminicola", "strain": "strain=IMCC34151", "accession": "GCA_003390885.1", "taxid": 2248761, "species_taxid": 2248761, "relation_to_type": "type", "validated": true, "ani": 79.1794, "matched_fragments": 426, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagibacterium halotolerans", "strain": "strain=B2", "accession": "GCA_000230555.1", "taxid": 531813, "species_taxid": 531813, "relation_to_type": "type", "validated": true, "ani": 79.0846, "matched_fragments": 456, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagibacterium montanilacus", "strain": "strain=CCL18", "accession": "GCA_003992665.1", "taxid": 2185280, "species_taxid": 2185280, "relation_to_type": "type", "validated": true, "ani": 78.8028, "matched_fragments": 412, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagibacterium limicola", "strain": "strain=NAJP-14", "accession": "GCA_015694405.1", "taxid": 2791022, "species_taxid": 2791022, "relation_to_type": "type", "validated": true, "ani": 78.5332, "matched_fragments": 411, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagibacterium luteolum", "strain": "strain=CGMCC 1.10267", "accession": "GCA_900100665.1", "taxid": 440168, "species_taxid": 440168, "relation_to_type": "type", "validated": true, "ani": 78.4241, "matched_fragments": 414, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia subaequoris", "strain": "strain=HST3-14", "accession": "GCA_024158985.1", "taxid": 395930, "species_taxid": 395930, "relation_to_type": "type", "validated": true, "ani": 77.5141, "matched_fragments": 227, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia oryziradicis", "strain": "strain=G19", "accession": "GCA_016698645.1", "taxid": 2801335, "species_taxid": 2801335, "relation_to_type": "type", "validated": true, "ani": 77.4644, "matched_fragments": 261, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia subaequoris", "strain": "strain=DSM 23447", "accession": "GCA_014197055.1", "taxid": 395930, "species_taxid": 395930, "relation_to_type": "type", "validated": true, "ani": 77.41, "matched_fragments": 230, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia ginsengisoli", "strain": "strain=Gsoil 520", "accession": "GCA_007859655.1", "taxid": 400770, "species_taxid": 400770, "relation_to_type": "type", "validated": true, "ani": 77.4008, "matched_fragments": 304, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Devosia rhizoryzae", "strain": "strain=LEGU1", "accession": "GCA_016698665.1", "taxid": 2774137, "species_taxid": 2774137, "relation_to_type": "type", "validated": true, "ani": 77.2518, "matched_fragments": 217, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitratireductor arenosus", "strain": "strain=CAU 1489", "accession": "GCA_009742725.1", "taxid": 2682096, "species_taxid": 2682096, "relation_to_type": "type", "validated": true, "ani": 76.7608, "matched_fragments": 134, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitratireductor alexandrii", "strain": "strain=Z3-1", "accession": "GCA_004000215.1", "taxid": 2448161, "species_taxid": 2448161, "relation_to_type": "type", "validated": true, "ani": 76.705, "matched_fragments": 145, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoligotrophos defluvii", "strain": "strain=lm1", "accession": "GCA_005281615.1", "taxid": 2561934, "species_taxid": 2561934, "relation_to_type": "type", "validated": true, "ani": 76.615, "matched_fragments": 97, "total_fragments": 1119, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003345525.1", "gtdb_species": "s__Pelagibacterium lacus", "ani": 79.2598, "matched_fragments": 442, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium", "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_003390885.1", "gtdb_species": "s__Pelagibacterium sp003390885", "ani": 79.1906, "matched_fragments": 425, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium", "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_000230555.1", "gtdb_species": "s__Pelagibacterium halotolerans", "ani": 79.0846, "matched_fragments": 456, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium", "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": 3, "status": "-" }, { "accession": "GCA_002337455.1", "gtdb_species": "s__Pelagibacterium sp002337455", "ani": 78.8788, "matched_fragments": 440, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.90", "min_intra_species_ani": "99.87", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003992665.1", "gtdb_species": "s__Pelagibacterium montanilacus", "ani": 78.7983, "matched_fragments": 413, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium", "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_002375765.1", "gtdb_species": "s__Pelagibacterium sp002375765", "ani": 78.7864, "matched_fragments": 433, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.84", "min_intra_species_ani": "99.84", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002723255.1", "gtdb_species": "s__Pelagibacterium sp002723255", "ani": 78.72, "matched_fragments": 379, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.69", "min_intra_species_ani": "98.23", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.73", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_015694405.1", "gtdb_species": "s__Pelagibacterium limicola", "ani": 78.5105, "matched_fragments": 414, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium", "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_900100665.1", "gtdb_species": "s__Pelagibacterium luteolum", "ani": 78.4241, "matched_fragments": 414, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium", "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_014837245.1", "gtdb_species": "s__Devosia sp014837245", "ani": 77.4859, "matched_fragments": 238, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_016698645.1", "gtdb_species": "s__Devosia sp016698645", "ani": 77.4563, "matched_fragments": 261, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_016698665.1", "gtdb_species": "s__Devosia sp016698665", "ani": 77.2651, "matched_fragments": 216, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_900470445.1", "gtdb_species": "s__Devosia sp900470445", "ani": 77.224, "matched_fragments": 254, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.41", "min_intra_species_ani": "95.41", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_015234425.1", "gtdb_species": "s__Devosia sp015234425", "ani": 77.1801, "matched_fragments": 232, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia", "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_002043005.1", "gtdb_species": "s__Martelella mediterranea", "ani": 76.8295, "matched_fragments": 187, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.32", "min_intra_species_ani": "95.96", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_003241695.1", "gtdb_species": "s__Hansschlegelia sp003241695", "ani": 76.2384, "matched_fragments": 136, "total_fragments": 1119, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia", "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": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": 4296818.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "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 }, "_genome_taxon": [ "Pelagibacterium", "xiamenense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }