2024-09-19
ENA first public
ERC000047
ENA-CHECKLIST
Spribille Lab
INSDC center name
public
INSDC status
ERS20918161
SRA accession
private_X12_concoct_bin.4
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 Alectoria sarmentosa lichen
broad-scale environmental context
not provided
collection date
84.59
%
completeness score
EukCC_v2
completeness software
0.0
%
contamination score
This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic run ERR4586588 of study ERP123954.
description
lichen thallus
environmental medium
USA
geographic location (country and/or sea)
46.56742000
DD
geographic location (latitude)
-114.63975000
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
lichen metagenome
isolation_source
lichen thallus
local environmental context
lichen metagenome
metagenomic source
Alectoria sarmentosa
organism
Basidiomycete yeasts have recently been reported as stably associated secondary fungal symbionts (SFS) of many lichens, but their role in the symbiosis remains unknown. Attempts to sequence their genomes have been hampered both by the inability to culture them and their low abundance in the lichen thallus alongside two dominant eukaryotes (an ascomycete fungus and chlorophyte alga). Using the lichen Alectoria sarmentosa, we selectively dissolved the cortex layer in which SFS are embedded to enrich yeast cell abundance and sequenced DNA from the resulting slurries as well as bulk, pulverized lichen thallus. In addition to yielding a near-complete genome of the filamentous ascomycete using both methods, metagenomes from cortex slurries yielded a 36- to 84-fold increase in coverage and near-complete genomes for two basidiomycete species, members of Cystobasidiomycetes and Tremellomycetes. The ascomycete possesses the largest gene inventory of the three. It is enriched in proteases often associated with pathogenicity and harbours the majority of predicted secondary metabolite clusters. The basidiomycete genomes possess ~35% fewer predicted genes than the ascomycete and have reduced secretomes even compared to close relatives, while exhibiting signs of nutrient limitation and scavenging. Furthermore, both basidiomycetes are enriched in genes coding for secreted acidic polysaccharides, representing a potential contribution to the shared extracellular matrix. All three fungi appear to retain genes involved in dimorphic switching, despite the ascomycete not being known to possess an anamorphic state. The basidiomycete genomes are an important new resource for exploration of lifestyle and function in fungal-fungal interactions in lichen symbioses.
project name
SAMEA7305566
sample derived from
Alectoria sarmentosa
scientific_name
Illumina HiSeq 2500
sequencing method
multi-marker approach
taxonomic identity marker
Metagenome-assembled genome: private_X12_concoct_bin.4
title