Biology subjects

Passamonti, M.

Publications and source records attributed to Passamonti, M..

4 recordsLinked to original sources

bioRxiv2024

Evidence of convergent evolution in the nuclear and mitochondrial OXPHOS subunits across the deep lineages of Squamata

The OXidative PHosphorylation System (OXPHOS) is composed of subunits encoded by both the nuclear and mitochondrial genomes, which are subject to distinct evolutionary pressures. Nevertheless, the cooperation between OXPHOS subunits is essential for proper OXPHOS function, as incompatibilities between subunits can be highly deleterious. The order Squamata is a good candidate for studying unusual patterns of mitochondrial evolution. The lineages leading to the snake and agamid clades likely experienced convergent evolution in mitochondrial OXPHOS genes, potentially linked to their distinctive feeding strategies. This deep signal of convergence can also be inferred from mitochondrial markers, which provide strong support for the monophyly of these two groups. In the present study, we annotated the mitochondrial and nuclear OXPHOS genes of 56 Squamata species. The nuclear OXPHOS subunits that physically interact with mitochondrial proteins also support the clade clustering snakes and agamids. Additionally, we found a significant number of convergent amino acid changes between agamids and snakes, not only in mitochondrial OXPHOS genes but also in nuclear ones, with a higher rate of convergence in the nuclear OXPHOS subunits that play central roles in the OXPHOS complexes. Overall, the common selective pressures in two distinct lineages can lead two sets of genes, encoded by two different genomes, to exhibit similar patterns of convergent evolution, affecting the phylogenetic signal of these genes. Thus, we highlight how the phylogenetic signal of OXPHOS genes, through the coevolution of subunits and their adaptation to specific evolutionary pressures, can be influenced and may diverge from the signal supported by most other genes. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/623538v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@13753aforg.highwire.dtl.DTLVardef@15734f2org.highwire.dtl.DTLVardef@5502b5org.highwire.dtl.DTLVardef@124e661_HPS_FORMAT_FIGEXP M_FIG In Squamata, nuclear genes support the monophyly of Pleurodonta and Acrodonta. However, OXPHOS genes, bot nuclear and mitochondrial, place Acrodonta in sister relationship with Serpentes. This phylogenetic discordance is likely due to convergent evolution along the that leading to Serpentes and Acrodonta. C_FIG

evolutionary biology↗

bioRxiv2023

The evolution of RNA interference among Metazoa

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 loaded by a specific Argonaute homolog protein. 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. Among Metazoa, the distribution of these families has been only studied in major groups, and there are very few data for clades like Lophotrochozoa. Thus, we here inferred the evolutionary history of the animal Argonaute and DICER families including 43 lophotrochozoan species. Phylogenetic analyses along with newly sequenced sncRNA libraries depicted a loss of the endo-siRNA pathway along the Lophotrochozoa evolution, with the absence of DICER2 in Nematoda and Polyzoa, and with the absence of DICER2 and the Argonaute homolog in the rest of Trochozoa phyla. On the contrary, early diverging phyla, Platyhelminthes and Syndermata, showed a complete endo-siRNA pathway. On the other hand, miRNAs were revealed the most conserved and ubiquitous mechanism of the metazoan RNA interference machinery, confirming their pivotal role in animal cell regulation.

evolutionary biology↗

bioRxiv2021

Polyacrylamide co-N,N'-methylene bisacrylamide monoliths for high peak capacity HILIC-HRMS of intact proteins at low trifluoroacetic acid content

In this study, we optimized a polymerization mixture to synthesize polyacrylamide-co-N,N-methylene bisacrylamide monolithic stationary phases for hydrophilic-interaction chromatography (HILIC) of intact proteins. Thermal polymerization was performed, and the effects of varying the amount of crosslinker and the porogen composition on the separation performance of the resulting columns were studied. The homogeneity of the structure and the different porosities were examined through scanning electron microscopy. Further characterization of the monolithic structure revealed a permeable (Kf between 2.5 x 10-15 and 1.40 x 10-13 m2) and polar stationary phase suitable for HILIC. The HILIC separation performance of the different columns was assessed using gradient separation of a sample containing four intact proteins, with the best performing stationary phase exhibiting a peak capacity of 51 in a gradient of 25 min. Polyacrylamide-based materials were compared with a silica-based particulate amide phase (2.7 m core-shell particles). The monolith has no residual silanol sites and, therefore, fewer sites for ion-exchange interactions with proteins. Thus, it required lower concentrations of ion-pair reagent in HILIC of intact proteins. When using 0.1% of trifluoroacetic acid (TFA) the peak capacities of the two columns were similar (31 and 36 for the monolithic and packed column, respectively). However, when decreasing the concentration of TFA to 0.005%, the monolithic column maintained its separation performance and selectivity (peak capacity 26), whereas the packed column showed greatly reduced performance (peak capacity 7), lower selectivity, and inability to elute all four reference proteins. Finally, using a mobile phase containing 0.1% formic acid and 0.005% TFA the HILIC separation on the monolithic column was successfully hyphenated with high-resolution mass spectrometry. Detection sensitivity for protein and glycoproteins was increased and the amount of adducts formed was decreased in comparison with separations performed at 0.1% TFA.

biochemistry↗

bioRxiv2018

Hybrid de novo assembly of the draft genome of the freshwater mussel Venustaconcha ellipsiformis (Bivalvia: Unionida).

Freshwater mussels (Bivalvia: Unionida) serve an important role as aquatic ecosystem engineers but are one of the most critically imperilled groups of animals. Here, we used a combination of sequencing strategies to assemble and annotate a draft genome of Venustaconcha ellipsiformis, which will serve as a valuable genomic resource given the ecological value and unique \"doubly uniparental inheritance\" mode of mitochondrial DNA transmission of freshwater mussels. The genome described here was obtained by combining high coverage short reads (65X genome coverage of Illumina paired-end and 11X genome coverage of mate-pairs sequences) with low coverage Pacific Biosciences long reads (0.3X genome coverage). Briefly, the final scaffold assembly accounted for a total size of 1.54Gb (366,926 scaffolds, N50 = 6.5Kb, with 2.3% of \"N\" nucleotides), representing 86% of the predicted genome size of 1.80Gb, while over one third of the genome (37.5%) consisted of repeated elements and more than 85% of the core eukaryotic genes were recovered. Given the repeated genetic bottlenecks of V. ellipsiformis populations as a result of glaciations events, heterozygosity was also found to be remarkably low (0.6%), in contrast to most other sequenced bivalve species. Finally, we reassembled the full mitochondrial genome and found six polymorphic sites with respect to the previously published reference. This resource opens the way to comparative genomics studies to identify genes related to the unique adaptations of freshwater mussels and their distinctive mitochondrial inheritance mechanism.

genomics↗