Metagenome Assembly

Microorganisms comprise the majority of the planet's biological diversity, however, due to the varied environments and conditions in which these organisms reside, many of these cannot be cultured. By standard genome analysis methods requiring isolation and laboratory cultivation, limited knowledge was gained regarding these uncultured microorganisms. Metagenomics is a culture-independent genomic analysis method which surveys genomes of uncultured microorganisms and has brought new discoveries about the genetic diversity, population structure and ecological roles of these uncultured microorganisms.

Metagenome projects may include raw sequence reads collected from an ecological or organismal source (submitted to the DDBJ Sequence Read Archive), assembled contigs derived from the raw sequence data, binned metagenome assemblies derived from a subset of the raw sequence data, and metagenomic assemblies (Metagenomic Assembly, MAG) from taxonomically defined organisms.

This guide explains how to submit these metagenomic sequencing data to the BioProject/BioSample/DRA/DDBJ. Raw sequencing data deposition to DRA is not required but highly recommended.

Submission of metagenome assembly data

Submission of metagenome assembly data
Submission of metagenome assembly data

1) Raw reads (Run)

Unassembled raw sequence data should be submitted to DRA Run.

BioProject

Register your BioProject as a metagenome/environmental project. For the organism name, choose the most appropriate "xyz metagenome" (e.g., soil metagenome) from this list of metagenome organism names in the taxonomy database. Please include information about the project, including a detailed description of the isolation source, and the scope of the project.

BioSample

Register your BioSample by using the "Genome, metagenome or marker sequences (MIxS compliant) - Environmental/Metagenome Genomic Sequences (MIMS)" package. For the organism name, choose the most appropriate "xyz metagenome" (e.g., soil metagenome) from this list of metagenome organism names in the taxonomy database. Please provide as much metadata and information as possible about the samples in order to provide context for the experimental data.

DRA

Submit unassembled raw sequence data to DRA Run.

2) Primary metagenome

Assembled contigs derived from the raw sequence data should be submitted to DDBJ or DRA.

BioProject

Same as 1) Raw reads (Run).

BioSample

Same as 1) Raw reads (Run).

DDBJ

Submit assembled contigs as WGS entries of ENV division through the Mass Submission System (MSS).

DRA

Submit assembled contigs derived from the raw sequence data in fasta/bam files to the DRA Analysis (Analysis type = 'De Novo Assembly'). Submit the Analysis along with the Run registered in 1). Please note that Analysis data are not shared with NCBI/ENA.

3) Binned metagenome

Binned metagenome assemblies derived from a subset of the raw sequence data should be submitted to DDBJ or DRA. Example cases are when there are only a few short contigs for each organism, or when the organisms were binned based only on BLAST similarity.

BioProject

Same as 1) Raw reads (Run).

BioSample

Same as 1) Raw reads (Run).

DDBJ

Submit binned metagenome assemblies as WGS entries of ENV division through the Mass Submission System (MSS).

DRA

Submit binned metagenome assemblies derived from the raw sequence data in fasta/bam files to the DRA Analysis (Analysis type = 'De Novo Assembly'). Include information of analysis software used and organism bin in the description. Submit the Analysis along with the Run registered in 1). Please note that Analysis data are not shared with NCBI/ENA.

4) MAG (DDBJ)

Metagenomic assemblies (Metagenomic Assembly, MAG) predicted to be derived from taxonomically defined organisms should be submitted to DDBJ as genome entries of ENV division.

BioProject

Register your BioProject as a metagenome/environmental project. If you have already registered a BioProject for submission of the corresponding raw reads to DRA, then, in general, you would use the BioProject when you submit the MAG to DDBJ.

BioSample

Register a virtual BioSample by using the "Other samples" package. Describe an organism name without 'uncultured' (e.g., Methanosarcina thermophila) in the taxonomy database from which the MAG was derived. Please note that a virtual BioSample derived from the MIMS metagenomic sample used in 1) is required for a MAG submission.

Following sample attributes other than the organism are necessary. Example BioSample

Fixed terms

  • sample_type: metagenomic assembly

Sample isolation

  • metagenome_source: xyz metagenome
  • isolate
  • isolation_source

Sample collection

  • collection_date
  • env_biome
  • env_feature
  • env_material
  • geo_loc_name
  • lat_lon

Derived BioSample

  • note: This biosample is a metagenomic assembly obtained from the xyz metagenome BioSample: SAMDxxxxxxxx.
  • derived_from: SAMDxxxxxxxx

DRA

The raw sequence data used for the MAG assembly should be submitted to the DRA Run.

DDBJ

Submit the MAG as a genome entry of ENV division through the Mass Submission System (MSS). Following information is necessary.

Required for the MAG entry.

  • Add /metagenome_source = 'xyz metagenome' ('xyz metagenome' should be from this list of metagenome organism names in the taxonomy database) to the source feature.

Required for the ENV division entry.

Required for the genome entry.

  • Include Assembly Method, Genome Coverage and Sequencing Technology in the ST_COMMENT
  • Include Assembly Name in the ST_COMMENT for eukaryotes.

In the MAG (ENV division) entry, /strain can not be used. Please describe natural host of the organism from which sequenced molecule was obtained in /host.