Luteolibacter sp. strain Populi is bacterium from the phylum Verrucomicrobiota, isolated from the rhizosphere of a black cottonwood tree, Populus trichocarpa, from the Cascade mountains in Washington. Its 6.6 Mb chromosome was completely sequenced using Oxford Nanopore long-reads and is predicted to encode 5301 proteins and 60 RNAs.
The bacteria was isolated from the rhizosphere of a mature Populus trichocarpa from the Tieton riverwatershed of Washington state, USA (Lat: 46°42’9” N, Lon: 120°25 39’36” W). A rhizosphere sample (fine roots and adhering soil) was used to obtain a microbial fraction by centrifugation on Histodenz (12) and stained with 5µM Syto59 (Thermo Fisher Scientific Inc). A Cytopeia Influx cell sorter (BD, Franklin Lakes, NJ) was used to sort and array single cells (100 per plate) based on forward-side scatter and fluorescence intensity on asparagine-glucose nutrient agar (ATCC medium 184).
The Luteolibacter sp. Populi genome sequence has been deposited in GenBank under the accession number CP161812. A draft genome annotated with Prokka and DRAM is available in this Narrative as Luteolibacter_sp_Prokka.240711.
from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_batch(
[{
"app_id": "kb_uploadmethods/import_fastq_noninterleaved_as_reads_from_staging",
"tag": "release",
"version": "5b9346463df88a422ff5d4f4cba421679f63c73f",
"params": [{
"fastq_fwd_staging_file_name": "bc07.fastq.gz",
"fastq_rev_staging_file_name": None,
"name": "Reads"
}],
"shared_params": {
"sequencing_tech": "NanoPore",
"single_genome": 1,
"read_orientation_outward": 0,
"insert_size_std_dev": None,
"insert_size_mean": None
}
}],
cell_id="8aeeac6b-770a-439e-9707-65f702cb1c5e",
run_id="e5d964b1-293a-4171-a303-105164e7515f"
)
Created Object Name | Type | Description |
---|---|---|
Reads_filtlong.240702 | SingleEndLibrary | Filtered reads |
Reads_filtlong.240702 |
Created Object Name | Type | Description |
---|---|---|
Luteolibacter_sp_Flye.240702 | Assembly | Assembled contigs |
Luteolibacter_sp_Flye.240702 |
Luteolibacter.fasta_assembly |
Created Object Name | Type | Description |
---|---|---|
Luteolibacter_sp_Prokka.240711 | Genome | Annotated Genome |
Luteolibacter_sp_Flye.240702 |
Luteolibacter_ambystomatis.assembly |
Luteolibacter_arcticus.assembly |
Luteolibacter_flavescens.assembly |
Luteolibacter_marinus.assembly |
Luteolibacter_pohnpeiensis.assembly |
Luteolibacter_rhizosphaerae.assembly |
Luteolibacter_sp._G-1-1-1 |
Luteolibacter_yonseiensis.assembly |
Created Object Name | Type | Description |
---|---|---|
Luteolibacter_Genomeset | GenomeSet | KButil_Batch_Create_GenomeSet |
Created Object Name | Type | Description |
---|---|---|
Luteolibacter_ambystomatis | Genome | Taxonomy unchanged, taxon_assignment added GTDB |
Luteolibacter_arcticus | Genome | Taxonomy unchanged, taxon_assignment added GTDB |
Luteolibacter_yonseiensis | Genome | Taxonomy unchanged, taxon_assignment added GTDB |
Luteolibacter_sp_Prokka.240711 | Genome | Taxonomy and taxon_assignment updated with GTDB |
Akkermansia_muciniphila | Genome | Taxonomy unchanged, taxon_assignment added GTDB |
Haloferula_rosea | Genome | Taxonomy unchanged, taxon_assignment added GTDB |
Haloferula_luteola | Genome | Taxonomy unchanged, taxon_assignment added GTDB |
Luteolibacter_flavescens | Genome | Taxonomy unchanged, taxon_assignment added GTDB |
Luteolibacter_marinus | Genome | Taxonomy unchanged, taxon_assignment added GTDB |
Luteolibacter_pohnpeiensis | Genome | Taxonomy unchanged, taxon_assignment added GTDB |
Luteolibacter_rhizosphaerae | Genome | Taxonomy unchanged, taxon_assignment added GTDB |
Luteolibacter_sp._G-1-1-1 | Genome | Taxonomy unchanged, taxon_assignment added GTDB |
Luteolibacter_Genomeset | GenomeSet | Taxonomy and taxon_assignment updated with GTDB |
Created Object Name | Type | Description |
---|---|---|
Luteolibacter_flavescens | Genome | Imported Genome |
Created Object Name | Type | Description |
---|---|---|
Luteolibacter_arcticus | Genome | Imported Genome |
Created Object Name | Type | Description |
---|---|---|
Luteolibacter_marinus | Genome | Imported Genome |
Created Object Name | Type | Description |
---|---|---|
Luteolibacter_pohnpeiensis | Genome | Imported Genome |
Created Object Name | Type | Description |
---|---|---|
Luteolibacter_rhizosphaerae | Genome | Imported Genome |
Created Object Name | Type | Description |
---|---|---|
Luteolibacter_yonseiensis | Genome | Imported Genome |
Created Object Name | Type | Description |
---|---|---|
Luteolibacter_ambystomatis | Genome | Imported Genome |