ERC000047
ENA-CHECKLIST
2022-08-15T16:14:15Z
ENA-FIRST-PUBLIC
2022-08-15T16:14:15Z
ENA-LAST-UPDATE
SAMEA110651383
External Id
EMG
INSDC center name
2022-08-15T16:14:15Z
INSDC first public
2022-08-15T16:14:15Z
INSDC last update
public
INSDC status
ERS12748965
SRA accession
DRR089564_bin.1_metawrap_v1.3.0_MAG
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
metaSPAdes v3.15.3
assembly software
MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
binning parameters
metawrap v1.3.0
binning software
plant
broad-scale environmental context
EBI-EMG
broker name
2015-03-30
collection date
99.63
%
completeness score
CheckM
completeness software
0.3
%
contamination score
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run DRR089564 of study DRP003557.
description
rhizosphere
environmental medium
Japan
geographic location (country and/or sea)
38.25
DD
geographic location (latitude)
140.87
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
rhizosphere metagenome
isolation_source
soybeen
local environmental context
rhizosphere metagenome
metagenomic source
Bradyrhizobium diazoefficiens
organism
Recently, high-throughput sequencing technology is rapidly improving in quality, speed and cost. It is, therefore, becoming more widely used to study on whole bacterial communities. Rhizobial inoculation was often unsuccessful in legume fields, because soil native strains highly competed with the introduced inoculants. Conventional methods to monitor the behavior of inoculants are likely impractical and time-consuming in agricultural fields. Thus, We analyzed metagenome of the bacterial community associated with root nodules of soybean (Glycine max [L.] Merr., var. Tachinagaha) in order to descriminate the inoculant population from soil native population of soybean bradyrhizobia in an agricultural soil by mapping metagenome reads to the representative soybean bradyrhizobial genomes.
project name
SAMD00076775
sample derived from
Bradyrhizobium diazoefficiens
scientific_name
Illumina MiSeq
sequencing method
The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Bradyrhizobiaceae;g__Bradyrhizobium;s__Bradyrhizobium diazoefficiens
taxonomic classification
multi-marker approach
taxonomic identity marker
Metagenome-assembled genome: DRR089564_bin.1_metawrap_v1.3.0_MAG
title