Comparative Mitochondrial Genomics within and among Yeast Species of the Lachancea Genus

Abstract

Yeasts are leading model organisms for mitochondrial genome studies. The explosion of complete sequence of yeast mitochondrial (mt) genomes revealed a wide diversity of organization and structure between species. Recently, genome-wide polymorphism survey on the mt genome of isolates of a single species, Lachancea kluyveri, was also performed. To compare the mitochondrial genome evolution at two hierarchical levels: within and among closely related species, we focused on five species of the Lachancea genus, which are close relatives of L. kluyveri. Hence, we sequenced the complete mt genome of L. dasiensis, L. nothofagi, L. mirantina, L. fantastica and L. meyersii. The phylogeny of the Lachancea genus was explored using these data. Analysis of intra- and interspecific variability across the whole Lachancea genus led to the same conclusions regarding the mitochondrial genome evolution. These genomes exhibit a similar architecture and are completely syntenic. Nevertheless, genome sizes vary considerably because of the variations of the intergenic regions and the intron content, contributing to mitochondrial genome plasticity. The high variability of the intergenic regions stands in contrast to the high level of similarity of protein sequences. Quantification of the selective constraints clearly revealed that most of the mitochondrial genes are under purifying selection in the whole genus.

Mobile Introns Shape the Genetic Diversity of Their Host Genes

“…In L. kluyveri , a recent study found evidence for mobility of both cox1 and cob introns, noting presence/absence polymorphisms for three out of four cob and three out of five cox1 introns (Jung et al 2012). In line with widespread mobility in this species, all introns with the exception of the first cob intron encode endonucleases (Friedrich et al 2012). As predicted under a model where gene identity is secondary but mobility plays a pivotal role in nonrandom nucleotide diversity at intron–exon boundaries, we observe SNP density gradients across both cob (τ = −0.21, P = 0.03, Figure 2D) and cox1 exons (τ = −0.29, P = 0.002) in L. kluyveri , whereas in S. pombe a negative SNP gradient is evident for cob (τ = −0.31, P = 0.002) but not cox1 (τ = 0.16, P = 0.1).…”

Population structure of mitochondrial genomes in Saccharomyces cerevisiae

“…Few population genetic investigations on intraspecific mtDNAs in yeasts exist [45–47], and none for Saccharomyces species. To provide a window onto recent evolutionary changes in the mtDNA, we compared the intraspecific genetic variation in mitochondrial genomes from 100 strains of S. cerevisiae.…”

Discordant evolution of mitochondrial and nuclear yeast genomes at population level

“…Recent report suggested that the alteration of the gene order within yeast genera could be related to the mitochondrial genome size (Sulo et al 2017). While the Lachancea and Yarrowia clades, with mitochondrial genome less than 50 kb, show high synteny across species (Friedrich et al 2012;Gaillardin et al 2012), the Saccharomyces clade (mitochondrial genome size > 65 kb) is more prone to rearrangements (Sulo et al 2017). Indeed structural rearrangements were also detected in the mitochondrial genome of S. paradoxus (Yue et al 2017).…”