Biology subjects

Formaggioni, A.

Publications and source records attributed to Formaggioni, A..

3 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↗

bioRxiv2024

MirGeneDB 3.0: Improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families, and updated covariance models.

We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to a new server and the creation of a computational mirror, we have expanded the database with the addition of 33 invertebrate species, including representatives of 5 previously unsampled phyla, and 6 mammal species. MirGeneDB now contains entries for 21, 822 microRNA genes (5, 160 of these from the new species) belonging to 1743 microRNA families. The inclusion of these new species allowed us to refine both the evolutionary node of appearance of a number of microRNA genes/families, as well as MirGeneDBs phylogenetically informed nomenclature system. Updated covariance models of all microRNA families, along with all smallRNA read data are now downloadable. These enhanced annotations will allow researchers to analyze microRNA properties such as secondary structure and features of their biogenesis within a robust phylogenetic context and without the database plagued with numerous false positives and false negatives. In light of these improvements, MirGeneDB 3.0 will assume the responsibility for naming conserved novel metazoan microRNAs. MirGeneDB is part of RNAcentral and Elixir Norway, and is publicly and freely available at master.cloud.mirgenedb.org. Key PointsO_LIMajor update to the manually curated and uniformly named microRNA gene database MirGeneDB C_LIO_LI114 animal species, >1700 microRNA families and [~]20 000 genes searchable, browsable and downloadable C_LIO_LINew features to download all smallRNA read data and updated covariance models for each family C_LI

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↗