SmithHunter: a workflow for the identification of candidate smithRNAs and their targets.

Background: SmithRNAs (Small MITochondrial Highly-transcribed RNAs) are a novel class of small RNA molecules that are encoded in the mitochondrial genome and regulate the expression of nuclear transcripts. Initial evidence for their existence came from the Manila clam Ruditapes philippinarum, where they have been described and whose activity has been biologically validated through RNA injection experiments. Current evidence on the existence of these RNAs in other species is based only on small RNA sequencing.

Mitochondrion-to-nucleus communication mediated by RNA export: a survey of potential mechanisms and players across eukaryotes.

The nucleus interacts with the other organelles to perform essential functions of the eukaryotic cell. Mitochondria have their own genome and communicate back to the nucleus in what is known as mitochondrial retrograde response. Information is transferred to the nucleus in many ways, leading to wide-ranging changes in nuclear gene expression and culminating with changes in metabolic, regulatory or stress-related pathways.

The Evolution and Characterization of the RNA Interference Pathways in Lophotrochozoa.

In animals, three main RNA interference mechanisms have been described so far, which respectively maturate three types of small noncoding RNAs (sncRNAs): miRNAs, piRNAs, and endo-siRNAs. The diversification of these mechanisms is deeply linked with the evolution of the Argonaute gene superfamily since each type of sncRNA is typically loaded by a specific Argonaute homolog. Moreover, other protein families play pivotal roles in the maturation of sncRNAs, like the DICER ribonuclease family, whose DICER1 and DICER2 paralogs maturate respectively miRNAs and endo-siRNAs.

Biodiversity of extant snails (Gastropoda, Mollusca) in the Pliocene Mountain Spur Natural Reserve (Northern Apennine, Italy).

Background: To date, there is a substantial lack of information about gastropods from the Tuscan-Emilian Apennine in the north of Italy, notwithstanding the availability of detailed and comprehensive literature on this molluscan class. We present a gastropod fauna from the Natural Reserve of the Pliocene Mountain Spur: to our knowledge, this is the first investigation of the extant gastropod fauna in the Tuscan-Emilian Apennine and one of the few in the Apennine's mountain chain as a whole.

New Information: We describe a gastropod fauna comprised by 25 species, belonging to 18 genera and 10 families: the general figure which is emerging is an assemblage of European and Mediterranean-European species, with a single Asian contribution.

Mitochondrially mediated RNA interference, a retrograde signaling system affecting nuclear gene expression.

Several functional classes of short noncoding RNAs are involved in manifold regulatory processes in eukaryotes, including, among the best characterized, miRNAs. One of the most intriguing regulatory networks in the eukaryotic cell is the mito-nuclear crosstalk: recently, miRNA-like elements of mitochondrial origin, called smithRNAs, were detected in a bivalve species, Ruditapes philippinarum. These RNA molecules originate in the organelle but were shown in vivo to regulate nuclear genes.

Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks.

Mito-nuclear phylogenetic discordance in Bivalvia is well known. In particular, the monophyly of Amarsipobranchia (Heterodonta + Pteriomorphia), retrieved from mitochondrial markers, contrasts with the monophyly of Heteroconchia (Heterodonta + Palaeoheterodonta), retrieved from nuclear markers. However, since oxidative phosphorylation nuclear markers support the Amarsipobranchia hypothesis instead of the Heteroconchia one, interacting subunits of the mitochondrial complexes ought to share the same phylogenetic signal notwithstanding the genomic source, which is different from the signal obtained from other nuclear markers.

Molecular Phylogenetics and Mitochondrial Evolution.

The myth of a "typical" mitochondrial genome (mtDNA) is a rock-hard belief in the field of genetics, at least for the animal kingdom [...

One in a Million: Genetic Diversity and Conservation of the Reference Population in Europe from the Sado Estuary (Portugal).

The production of cupped oysters is an important component of European aquaculture. Most of the production relies on the cultivation of the Pacific oyster , although the Portuguese oyster represents a valuable product with both cultural and economic relevance, especially in Portugal. The authors of the present study investigated the genetic diversity of Portuguese oyster populations of the Sado estuary, both from natural oyster beds and aquaculture facilities, through gene fragment sequencing.

Mitochondrial phylogeny and taxonomic revision of Italian and Slovenian fluvio-lacustrine barbels, Barbus sp. (Cypriniformes, Cyprinidae).

Background: Barbels are ray finned cyprinid fishes of the Old-World with partially unresolved, intricate taxonomy. Within the Barbus sensu lato paraphyletic assemblage, Barbus sensu stricto is a monophyletic tetraploid lineage of Europe, northern Africa and Middle East, including two monophyletic sibling genera: Barbus and Luciobarbus. Italy, Slovenia and northern Croatia are natively inhabited by several entities of the genus Barbus, whose relationships and taxonomic ranks are still unclear.

HERMES: An improved method to test mitochondrial genome molecular synapomorphies among clades.

Mitochondrial chromosomes have diversified among eukaryotes and many different architectures and features are now acknowledged for this genome. Here we present the improved HERMES index, which can measure and quantify the amount of molecular change experienced by mitochondrial genomes. We test the improved approach with ten molecular phylogenetic studies based on complete mitochondrial genomes, representing six bilaterian Phyla.

Mitonuclear Coevolution, but not Nuclear Compensation, Drives Evolution of OXPHOS Complexes in Bivalves.

In Metazoa, four out of five complexes involved in oxidative phosphorylation (OXPHOS) are formed by subunits encoded by both the mitochondrial (mtDNA) and nuclear (nuDNA) genomes, leading to the expectation of mitonuclear coevolution. Previous studies have supported coadaptation of mitochondria-encoded (mtOXPHOS) and nuclear-encoded OXPHOS (nuOXPHOS) subunits, often specifically interpreted with regard to the "nuclear compensation hypothesis," a specific form of mitonuclear coevolution where nuclear genes compensate for deleterious mitochondrial mutations due to less efficient mitochondrial selection. In this study, we analyzed patterns of sequence evolution of 79 OXPHOS subunits in 31 bivalve species, a taxon showing extraordinary mtDNA variability and including species with "doubly uniparental" mtDNA inheritance.

Phylomitogenomics provides new perspectives on the Euphasmatodea radiation (Insecta: Phasmatodea).

Phasmatodea species diversity lies almost entirely within its suborder Euphasmatodea, which exhibits a pantropical distribution and is considered to derive from a recent and rapid evolutionary radiation. To shed light on Euphasmatodea origins and diversification, we assembled the mitogenomes of 17 species from transcriptomic sequencing data and analysed them along with 22 already available Phasmatodea mitogenomes and 33 mitogenomes representing most of the Polyneoptera lineages. Maximum Likelihood and Bayesian Inference approaches retrieved consistent topologies, both showing the widespread conflict between phylogenetic approaches and traditional systematics.

Clues of in vivo nuclear gene regulation by mitochondrial short non-coding RNAs.

Gene expression involves multiple processes, from transcription to translation to the mature, functional peptide, and it is regulated at multiple levels. Small RNA molecules are known to bind RNA messengers affecting their fate in the cytoplasm (a process generically termed 'RNA interference'). Such small regulatory RNAs are well-known to be originated from the nuclear genome, while the role of mitochondrial genome in RNA interference was largely overlooked.

Comparative Transcriptomics in Two Bivalve Species Offers Different Perspectives on the Evolution of Sex-Biased Genes.

Comparative genomics has become a central tool for evolutionary biology, and a better knowledge of understudied taxa represents the foundation for future work. In this study, we characterized the transcriptome of male and female mature gonads in the European clam Ruditapes decussatus, compared with that in the Manila clam Ruditapes philippinarum providing, for the first time in bivalves, information about transcription dynamics and sequence evolution of sex-biased genes. In both the species, we found a relatively low number of sex-biased genes (1,284, corresponding to 41.

SmithRNAs: Could Mitochondria "Bend" Nuclear Regulation?

Typically, animal mitochondria have very compact genomes, with few short intergenic regions, and no introns. Hence, it may seem that there is little space for unknown functions in mitochondrial DNA (mtDNA). However, mtDNA can also operate through RNA interference, as small non coding RNAs (sncRNAs) produced by mtDNA have already been proposed for humans.

Burrowers from the Past: Mitochondrial Signatures of Ordovician Bivalve Infaunalization.

Bivalves and gastropods are the two largest classes of extant molluscs. Despite sharing a huge number of features, they do not share a key ecological one: gastropods are essentially epibenthic, although most bivalves are infaunal. However, this is not the ancestral bivalve condition; Cambrian forms were surface crawlers and only during the Ordovician a fundamental infaunalization process took place, leading to bivalves as we currently know them.

The Complete Female- and Male-Transmitted Mitochondrial Genome of Meretrix lamarckii.

Bivalve mitochondrial genomes show many uncommon features, like additional genes, high rates of gene rearrangement, high A-T content. Moreover, Doubly Uniparental Inheritance (DUI) is a distinctive inheritance mechanism allowing some bivalves to maintain and transmit two separate sex-linked mitochondrial genomes. Many bivalve mitochondrial features, such as gene extensions or additional ORFs, have been proposed to be related to DUI but, up to now, this topic is far from being understood.