Mitochondrial genome diversity across the subphylum Saccharomycotina

Area of Science:

• * Mitochondrial genomics
• * Yeast evolutionary biology
• * Comparative genomics

Background:

• * Eukaryotic life relies on nuclear and organellar genomes, with mitochondrial genomes showing significant variation across species.
• * Previous studies had limited sampling of mitochondrial genomes in Saccharomycotina yeasts, despite available nuclear genome data.

Purpose of the Study:

• * To expand the sampling of yeast mitochondrial genomes by extracting data from existing short-read datasets.
• * To analyze the diversity in size, GC content, gene content, and intron distribution across Saccharomycotina mitochondrial genomes.
• * To investigate the evolutionary history of gene loss, particularly for Complex I genes, and assess evolutionary rates.

Main Methods:

• * Mitochondrial genome sequences were extracted from existing short-read genome datasets.
• * Comparative analysis of 353 yeast mitochondrial genomes was performed.
• * Phylogenetic analysis was used to trace gene loss events.

Main Results:

• * While mitochondrial genome size and GC content were generally consistent, Metschnikowia and Saccharomyces genera showed larger sizes, and Saccharomycetales species exhibited lower GC content.
• * A core set of protein-coding genes was conserved, but Complex I genes were variably present, with losses traced to a major event in Saccharomycetales/Saccharomycodales ancestors and independent losses in other orders.
• * Mitochondrial introns were widespread but enriched in certain groups, with evidence of horizontal gene transfer.

Conclusions:

• * The study provides a comprehensive analysis of yeast mitochondrial genome diversity, revealing significant variations in gene content and intron distribution.
• * The findings challenge previous hypotheses regarding evolutionary rates in relation to metabolic strategies.
• * The methods for retrieving mitochondrial genomes are valuable for future fungal genomics research, enabling studies to keep pace with nuclear genome advancements.