2024-09-19
ENA first public
ERC000047
ENA-CHECKLIST
Spribille Lab
INSDC center name
public
INSDC status
ERS20915163
SRA accession
public_SRR5808930_metawrap_bin.1
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
metaSPAdes_v3.13
assembly software
default
binning parameters
metaWRAP_v.1.2
binning software
Thallus of Evernia prunastri lichen
broad-scale environmental context
not provided
collection date
88.16
%
completeness score
CheckM_v1.1.3
completeness software
1.17
%
contamination score
This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic run SRR5808930 of study SRP111200.
description
lichen thallus
environmental medium
Norway
geographic location (country and/or sea)
59.42553000
DD
geographic location (latitude)
10.60794000
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
lichen metagenome
isolation_source
lichen thallus
local environmental context
lichen metagenome
metagenomic source
uncultured Acetobacteraceae bacterium
organism
The metagenome skimming approach, i.e. low coverage shotgun sequencing of multi-species assemblages and subsequent reconstruction of individual genomes is increasingly used for in-depth genomic characterization of eukaryotic communities. This approach is a promising tool for reconstructing genomes of facultative symbionts, such as lichen-forming fungi, from metagenomic reads. However, no study has so far tested accuracy and completeness of assemblies based on metagenomic sequences compared to assemblies based on pure culture strains of lichenized fungi. Here we assembled the genomes of Evernia prunastri and Pseudevernia furfuracea based on metagenomic sequences derived from whole lichen thalli. We extracted fungal contigs using two different taxonomic binning methods, and performed gene prediction on the fungal contig subsets. We then assessed quality and completeness of the metagenome-based assemblies using as reference genome assemblies which are based on pure culture strains of the two fungal species. Our comparison showed that we were able to reconstruct fungal genomes from uncultured lichen thalli, and also cover most of the gene space. Metagenome skimming is a viable tool to reconstruct fungal genomes from uncultured lichen thalli. It will facilitate genome mining, comparative (phylo)genomics, and populations genetics of lichen-forming fungi by circumventing the time-consuming, sometimes unfeasible, step of aposymbiotic cultivation.
project name
SAMN07327787
sample derived from
uncultured Acetobacteraceae bacterium
scientific_name
Illumina MiSeq
sequencing method
multi-marker approach
taxonomic identity marker
Metagenome-assembled genome: public_SRR5808930_metawrap_bin.1
title