De novo assemblies for the mitochondria reveal its expansion in all subpopulations and high level of reorganization for the teq/EtOH strains. (A) De novo assembly size difference. All subpopulations increased their mitochondrial genome compared to the reference genome (accession number GQ354526.1), from 75.3 to 88–90 kb. The teq/EtOH subpopulation stands out with de novo assembly sizes >100 kb. Red dotted line denotes the mitochondrial size of the reference genome. (B) Mitochondrial synteny. Synteny is conserved among subpopulations (compared to the reference), with the exception for the teq/EtOH subpopulation. Additionally, synteny within teq/EtOH was not congruent among strains. Here, the strain I_H06_YJS7889 harbors a large inversion. (C) Intron content contributes to genome expansion of teq/EtOH subpopulation. For teq/EtOH strains, the two protein-coding genes COB and COX1 have increased in intron content, whereas other subpopulations have the expected intron sizes compared to the reference genome (accession number GQ354526.1).
