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We controlled for this by inspecting manually every duplication case to discard dubious cases.
Moreover, even when species-specific duplications in which duplicates had more than 95% identity at the nucleotide level or all duplications from the recently assembled genomes were not taken into account, the fraction of OXPHOS families with a duplication event remained high (71% and 74%, respectively).
For instance, the evolutionary analysis of Complex I across a set of eighteen eukaryotes, lead to the prediction that the so-far uncharacterised human protein B17L was involved in Complex I function .
Indeed, the adaptation to oxygen-limited conditions or to high levels of oxidative stress during certain phases of their life cycle may have been crucial in the emergence of fermentative or pathogenic lifestyles.
To identify the main mechanisms behind the evolution of respiratory pathways, we conducted a phylogenomics survey of oxidative phosphorylation components in the genomes of sixty fungal species.
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For instance, we found duplications in 60% of the genes involved in ], in a comprehensive study that catalogues duplicated regions where the gene order is conserved.
Processes of gene loss and gene duplication followed by functional divergence have been rampant in the evolution of fungal respiration.
Overall, the core proteins of the respiratory pathways are conserved in most lineages, with major changes affecting the lineages of microsporidia, ].
A recent comparative genomics study  has provided a comprehensive view of the patterns of presence and absence of OXPHOS components in 27 fungal species.
Here we extend the analyses to 60 fully-sequenced fungal genomes and use a phylogenetics approach that enables us not only to obtain reliable orthology relationships but also to trace the history of duplications of OXPHOS components and related pathways during fungal evolution.
Molecular phylogenies of eukaryotic OXPHOS components indicate that the core subunits of the complexes were inherited from the alpha-proteobacterial ancestor of mitochondria .
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