13 research outputs found
Evolutionary Trajectories are Contingent on Mitonuclear Interactions
Critical mitochondrial functions, including cellular respiration, rely on frequently interacting components expressed from both the mitochondrial and nuclear genomes. The fitness of eukaryotic organisms depends on a tight collaboration between both genomes. In the face of an elevated rate of evolution in mtDNA, current models predict that the maintenance of mitonuclear compatibility relies on compensatory evolution of the nuclear genome. Mitonuclear interactions would therefore exert an influence on evolutionary trajectories. One prediction from this model is that the same nuclear genome evolving with different mitochondrial haplotypes would follow distinct molecular paths toward higher fitness. To test this prediction, we submitted 1,344 populations derived from 7 mitonuclear genotypes of Saccharomyces cerevisiae to >300 generations of experimental evolution in conditions that either select for a mitochondrial function or do not strictly require respiration for survival. Performing high-throughput phenotyping and whole-genome sequencing on independently evolved individuals, we identified numerous examples of gene-level evolutionary convergence among populations with the same mitonuclear background. Phenotypic and genotypic data on strains derived from this evolution experiment identify the nuclear genome and the environment as the main determinants of evolutionary divergence, but also show a modulating role for the mitochondrial genome exerted both directly and via interactions with the two other components. We finally recapitulated a subset of prominent loss-of-function alleles in the ancestral backgrounds and confirmed a generalized pattern of mitonuclear-specific and highly epistatic fitness effects. Together, these results demonstrate how mitonuclear interactions can dictate evolutionary divergence of populations with identical starting nuclear genotypes
Genome shuffling improved acid-tolerance and succinic acid production of Actinobacillus succinogenes
Optimization of genome shuffling for high-yield production of the antitumor deacetylmycoepoxydiene in an endophytic fungus of mangrove plants
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Phylogeny of Clostridium spp. based on conservative genes and comparisons with other trees
The genus Clostridium includes a group of anaerobic bacteria, which have remarkable application prospects in cellulose degradation and industrial production or are important pathogens. In this study, the phylogeny of Clostridium spp., whose complete genomes were reported, was inferred based on concatenation of 49 conservative genes, including ribosomal protein genes. The results indicated that the topology of the genomic tree was consistent with the clusters of the species in the ribosomal protein tree and 16S rRNA trees. Based on the alignment and phylogenetic analysis of 49 conservative selected genes and 27218 final nucleotide characters, the genomic tree supported classification results and reassignments of some species in previous works, including other genomic trees. The phylogenetic deduction was not only the classification skeleton of the genus Clostridium, but also the relationship of those species in genes involved in basic cell cycles