Structure, transcription and variability of metazoan mitochondrial genome: perspectives from an unusual mitochondrial inheritance system

Despite its functional conservation, mtDNA presents strikingly different features among eukaryotes, such as size, rearrangement frequency, and amount of intergenic regions. The reasons beyond this diversity have been object of extensive studies that have investigated the correlation between different mtDNA evolutionary patterns and body mass, metabolic rate, reactive oxygen species production, lifespan, etc. The fundamental role of non-adaptive processes such as random genetic drift and mutation rate in genome evolution has been recently highlighted by the work of several Authors. Under this light, mitochondrial bottlenecks and number of germ line replications are critical factors for mtDNA evolution, and different patterns of germ line differentiation could be responsible for the mtDNA diversity observed across eukaryotic lineages. Among metazoans, bivalve mollusc mtDNAs show unusual features, like hypervariable gene arrangement, high mutation rate, large amount of intergenic regions and, in some species, an unique inheritance system, the Doubly Uniparental Inheritance (DUI). In DUI species, two mitochondrial lineages are present: one is transmitted maternally (F-type), the other paternally (M-type). We exploited the DUI species Ruditapes philippinarumto study intergenic mtDNA functions, and to assess mitochondrial transcription and polymorphism in gonads. The coupling of high mutation rate with quite large genomes (i.e., large proportion of intergenic DNA) would be in contrast with the Mutation Pressure theory, but this is not true if most of that intergenic DNA has a function. We observed the presence of conserved functional elements and novel ORFs that could explain the evolutionary persistence of such regions and possibly be involved in DUI-specific aspects. Accordingly, the RNA-Seq analysis showed that mtDNA transcription is lineage-specific and it is independent from the nuclear background. This is consistent with an involvement in transcriptional control of the lineage- specific structures found inside the intergenic regions. We also found that male-transmitted and female- transmitted mtDNAs have a similar amount of polymorphism, but of a different kind. In contrast with organisms that show male-driven evolution, in this species male and female germ cells undergo a similar number of replication events due to gonad physiology, and this is reflected by the number of SNPs in M and F mtDNAs. The different kind of polymorphism is instead an effect of a different population size (different bottlenecks) and of a different efficiency of selection on the two mitochondrial lineages. Our results are consistent with the hypothesis that mtDNA evolution is strongly dependent on the dynamics of germ line formation. The DUI system offers the possibility to study the evolutionary dynamics of mtDNAs that, despite being in the same organism, experience different genetic drifts (due to different mitochondrial population size in gametes), but also different selective pressures. Actually, DUI animals are the only known organisms in which the mtDNA (i.e. the M-type) is subject to selection for male function. In a broadcast spawning organism the performance of spermatozoa is extremely important and selection for viable sperm, as well as sperm competition, is more efficient on a mtDNA which is transmitted through males. For this reason, we think that even if DUI probably arose by chance through completely stochastic events, its evolutionary persistence may be adaptive, because an increased male fitness would be beneficial for the whole species.