ENA-FIRST-PUBLIC
2023-01-03
ENA-LAST-UPDATE
2023-01-03
External Id
SAMEA14035955
INSDC center alias
EBI
INSDC center name
European Bioinformatics Institute
INSDC first public
2023-01-03T00:32:06Z
INSDC last update
2023-01-03T00:32:06Z
INSDC status
public
Submitter Id
SRR13685171_bin.7_CONCOCT_v1.1_MAG
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
metaspades_v3.13.0
binning parameters
Default
binning software
CONCOCT v1.1
broker name
EMG broker account, EMBL-EBI
collection date
2016-12-29
completeness score
79.63
completeness software
CheckM
contamination score
1.85
environment (biome)
Algae
environment (feature)
Green algae
environment (material)
Ectosymbionts
geographic location (country and/or sea)
USA
geographic location (latitude)
not provided
geographic location (longitude)
not provided
investigation type
metagenome-assembled genome
isolation_source
lichen metagenome
metagenomic source
lichen metagenome
project name
Reductions in genome size and complexity are a hallmark of obligate symbioses. The mitochondrial genome displays clear examples of these reductions, with the ancestral alpha-proteobacterial genome size and gene number having been reduced by orders of magnitude in most descendent modern mitochondrial genomes. Here, we examine patterns of mitochondrial evolution specifically looking at intron size, number, and position across 58 species from 21 genera of lichenized Ascomycete fungi, representing a broad range of fungal diversity and niches. Our results show that the cox1 gene always contained the highest number of introns out of all the mitochondrial protein-coding genes, that high intron sequence similarity can be maintained between different genera, and that lichens have undergone at least two instances of complete, genome-wide intron loss consistent with evidence for genome streamlining via loss of parasitic, noncoding DNA, in Phlyctis boliviensis and Graphis lineola. Notably, however, lichenized fungi have not only undergone intron loss but in some instances have expanded considerably in size due to intron proliferation (e.g., Alectoria fallacina and Parmotrema neotropicum), even between closely related sister species (e.g., Cladonia). These results shed light on the highly dynamic mitochondrial evolution that is occurring in lichens and suggest that these obligate symbiotic organisms are in some cases undergoing recent, broad-scale genome streamlining via loss of protein-coding genes as well as noncoding, parasitic DNA elements.
sample derived from
SAMN17834492
sample name
SRR13685171_bin.7_CONCOCT_v1.1_MAG
scientific_name
uncultured candidate division WPS-2 bacterium
sequencing method
NextSeq 550
taxonomic identity marker
multi-marker approach