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. This may be a clue of coevolution between nuclear and mitochondrial genes. In this work we inferred the phylogenetic signal from mitochondrial and nuclear oxidative phosphorylation markers exploiting different phylogenetic approaches and added two more datasets for comparison: genes of the glycolytic pathway and genes related to the biogenesis of regulative small noncoding RNAs. All trees inferred from mitochondrial and nuclear subunits of the mitochondrial complexes support the monophyly of Amarsipobranchia, regardless of the phylogenetic pipeline. However, not every single marker agrees with this topology: this is clearly visible in nuclear subunits that do not directly interact with the mitochondrial counterparts. Overall, our data support the hypothesis of a coevolution between nuclear and mitochondrial genes for the oxidative phosphorylation. Moreover, we suggest a relationship between mitochondrial topology and different nucleotide composition between clades, which could be associated to the highly variable gene arrangement in Bivalvia

Mitochondrial genomic landscape: A portrait of the mitochondrial genome 40 years after the first complete sequence

open3noNotwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.openFormaggioni A.; Luchetti A.; Plazzi F.Formaggioni A.; Luchetti A.; Plazzi F

Influence of milk somatic cell content on Parmigiano-Reggiano cheese yield

The aim of this study was to determine the influence of the somatic cell content (SCC) of milk on Parmigiano-Reggiano cheese yield, produced in commercial cheese factories under field conditions. The study was carried out following the production of 56 batches of Parmigiano-Reggiano in 13 commercial cheese factories by processing milk collected from Italian Friesian cattle herds. The vat-milk (V-milk) used for making each cheese batch was obtained by mixing evening milk (partially skimmed following spontaneous separation of fat overnight, natural creaming) and morning milk. The batches of cheese produced were divided into 5 classes according to the SCC value of the evening milk determined prior to natural creaming (class 1, from 0 to 200 000; 2, 201 000-300 000; 3, 301 000-400 000; 4, 401 000-500 000; 5, over 501 000 cells/ml). The cheese yield was calculated as the amount of 24-h cheese, expressed in kilograms, obtained from 100 kg of V-milk (24 h ACY). The values of fat, crude protein, true protein, casein and 24 h ACY of V-milk were negatively correlated with the somatic cell score (SCS) of the evening milk. Conversely, a positive correlation was observed between chloride and SCS. Fat, protein fractions (crude protein, casein and whey proteins), P and titratable acidity of V-milk were positively correlated with its 24 h ACY, while chloride, pH and SCS showed a negative correlation. A significant drop in 24 h ACY was observed in classes 3, 4 and 5, therefore when the SCC of the evening milk exceeded 300 000 cells/ml. Finally a lower recovery of milk fat in cheese was observed as SCC of evening milk increase

Milk of Italian Saddle and Haflinger nursing mares: physico – chemical characteristics, nitrogen composition and mineral elements at the end of lactation

Aim of this work was to investigate nursing mares milk characteristics at the end of lactation (D) and to make a comparisonwith milk taken during early lactation (3 to 30 d post partum) (E). The survey was carried out on 17 Italian Saddlemares (IS) (193 days in milk; 147 pregnancy days) and on 12 Haflinger mares (H) (174 days in milk; 146 pregnancydays). N fractions were determined by means of Kjeldahl; fat and lactose by means of mid infrared lectures; mineral elementswere determined by Atomic Absorption Spectrophotometry; P by colorimetry. Data referring to 58 individual milksamples were analyzed by ANCOVA. Significant variations, similar in both breeds, were observed (E vs D) for density at15°C (1.036 vs 1.034), pH (6.94 vs 7.24), titratable acidity (3.56 vs 1.70 °SH), fat (1.17 vs 0.76% g/100g of milk),crude protein (2.31 vs 1.68% g/100g), casein number (52.37 vs 46.59) and ash (0.50 vs 0.30% g/100g); similarly(mg/100g) for non casein N (172.31 vs 142.05), non protein N (34.43 vs 29.09), P (61.30 vs 32.48), Ca (112.88 vs54.42), Mg (8.40 vs 4.38) and K (60.77 vs 41.31). Freezing point, lactose and Na showed no significant variations. Atthe end of lactation, milk resulted poorer in all main organic components, except lactose, and in all mineral components,except Na. Only freezing point and phosphorus variations differed in IS from H. Breed significantly affected fat, casein Nand ash mean contents

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. Since miRNA genes evolve easily de novo with respect to protein-coding genes, in the present work we estimate the probability with which a newly arisen smithRNA finds a suitable target in the nuclear transcriptome. Simulations with transcriptomes of 12 bivalve species suggest that this probability is high and not species specific: one in a hundred million (1 x 10-8) if five mismatches between the smithRNA and the 3' mRNA are allowed, yet many more are allowed in animals. We propose that novel smithRNAs may easily evolve as exaptation of the pre-existing mitochondrial RNAs. In turn, the ability of evolving novel smithRNAs may have played a pivotal role in mito-nuclear interactions during animal evolution, including the intriguing possibility of acting as speciation trigger

Characterization and evolution of mito-nuclear interactions

Since the emergence of the first eukaryotic cell, two genomes have coexisted and coevolved within the same cellular environment, resulting in a complex network of interactions. The aim of my thesis is to investigate these interactions and their biological implications. RNA-RNA interactions play a key role in cellular homeostasis regulation. The Small Mitochondrial Highly Transcribed RNAs (smithRNAs), transcribed from the mitochondrial genome, target nuclear transcripts. However, their regulatory mechanisms are not fully understood. I focused on identifying proteins involved in the maturation and regulation of smithRNAs. To this end, I analyzed RNA immunoprecipitation (RIP) from various organisms and performed co-immunoprecipitation experiments between the identified smithRNAs in R. philippinarum and protein lysates. In the second part of my project, I examined protein-protein interactions between mitochondrial and nuclear OXPHOS subunits. Twelve subunits are encoded by the mitochondrial genome, while approximately 70 are encoded by the nuclear genome. I studied two mito-nuclear discordances in deep lineages, where mitochondrial markers support one phylogenetic hypothesis, but phylogenomic analyses reject it. I analyzed the phylogenetic signal of nuclear OXPHOS genes. In both Bivalvia and Squamata, the close interaction between OXPHOS subunits caused nuclear OXPHOS genes to support the biased mitochondrial topology. The tight interactions between the nuclear and mitochondrial genomes impact many biological processes. By co-opting nuclear proteins, the mitochondrial genome has evolved an internal RNAi pathway, possibly linked to sex determination in R. philippinarum. In snakes, adaptive selection on OXPHOS genes is likely linked to their extreme radiation. Over the course of my three-year project, I explored these interactions, highlighting their importance in key evolutionary processes

Milk acidity, curd firming time, curd firmness and protein and fat losses in the Parmigiano- Reggiano cheesemaking

The cheese yield depends on the milk casein content and on the fat to casein ratio. The efficiency of the milk transformation depends on curd particles ("curd fines") that remain in the cooked whey and on the losses of fat and casein as it is

Effects of milk storage temperature at the farm on the characteristics of Parmigiano Reggiano cheese: chemical composition and proteolysis.

Parmigiano Reggiano is a Protected Designation of Origin (PDO) cheese whose official production protocol provides that milk cannot be stored at less than 18 °C at the farm. The possibility of refrigerating milk at the farm is highly debated, since it should allow for the limiting of bacterial growth, thus improving the quality of the cheese. The present research aimed to study the influence of storing the milk at 9 °C on the chemical composition and proteolysis during the ripening of Parmigiano Reggiano cheese. The experimentation considered six cheese-making trials, in which both evening and morning milks were subdivided into two parts that were maintained at 9 and 20 °C. After Parmigiano Reggiano cheese-making, one of the twin wheels obtained was analyzed after 21 months of ripening. From each cheese, two different samples were taken, one from the inner zone, and the other from the outer zone. The results of the chemical analyses evidenced that milk storage at 9 °C significantly (p ≤ 0.05) influenced fat, crude protein, soluble nitrogen and peptone nitrogen contents. Nevertheless, the differences observed with respect to the cheese obtained with milk stored under standard condition were very small and should be considered within the “normal variations” of Parmigiano Reggiano chemical characteristics