Biology subjects

Poretti, M.

Publications and source records attributed to Poretti, M..

4 recordsLinked to original sources

bioRxiv2026

Light-harvesting strategies and competition drive niche partitioning among Ostreobium lineages in the spectral architecture of the coral reef

Ostreobium, a siphonous green alga capable of living inside of calcium carbonate substrates, including the skeletons of reef-building corals. This study investigates spectral niche preferences and physiological strategies of Ostreobium using community-wide experiments. We exposed natural Ostreobium communities from Porites lutea collected across shallow, mid, and deeper-water sites to three light conditions: far-red, blue, and white light, simulating healthy shallow-water corals, deeper water conditions, and bleached coral skeletons respectively. Using 16S rRNA metabarcoding and chlorophyll analysis, we assessed community changes and physiological responses over 16 weeks. We show significant variation in spectral preferences among Ostreobium OTUs, with clear evidence for both generalist and specialist strategies. Chlorophyll analysis showed photoacclimation responses through changes in pigment compositions. Our work shows that the spectral architecture of the reef plays a role in structuring Ostreobium communities, but the many mismatches between spectral preferences of OTUs and their observed presence in nature, suggests that inter-species competition is likely to be an even stronger contributor to community structure across the reefs microhabitats. We show that physiological heterogeneity within Ostreobium is strongly phylogenetically structured, and our results clearly highlight the importance of considering OTU-level differences when predicting community responses to environmental disturbances such as coral bleaching. While generalist OTUs dominate natural communities, these do poorly in incubations, and we hypothesise that white light specialists may become key players during coral bleaching events. Our work is a substantial advance in our understanding of Ostreobium ecology and provides a framework for interpreting future environmental sequencing data, offering insights into the functional roles of the different OTUs.

ecology↗

bioRxiv2025

Coral genetic structure in the Western Indian Ocean mirrors ocean circulation and thermal stress

Global warming and rising sea temperatures are pushing many reef-building coral species towards extinction. As thermal tolerance in corals is partially heritable, identifying genes under thermal selection is critical for targeted biodiversity management. However, it remains unclear how large breaks in connectivity (>100 km of open sea) affect the spread of adaptive alleles for different coral species in discontinuous reef networks such as the West Indian Ocean (WIO). To address this, we applied a seascape genomics approach to model (i) population connectivity and (ii) thermal adaptive potentials for two keystone coral species, Acropora muricata and Pocillopora damicornis, across the WIO. For both species, corals from the Seychelles were predominantly genetically isolated from corals in Rodrigues and Mauritius, putatively an effect of regional oceanographic barriers. Furthermore, sea currents during reproductive periods better predicted genetic connectivity than did Euclidean distances for both species, highlighting that connectivity models can serve as proxies to understand dispersal potential depending on reproductive strategies. Spatial patterns of neutral genetic variation were best explained by sea surface temperature variability and mean degree heating weeks. When used in genotype- environment association (GEA) analyses, we identified hundreds of loci under putative thermal selection from linked to known heat stress responses. In A. muricata, five Sacsin genes--co- chaperones of the Hsp70 heat-shock protein involved in thermal stress response--were identified, alongside genes related to immune defence, antioxidant response, signalling, and protein folding. In contrast, only the centromere protein V, involved in mitosis, was enriched in P. damicornis. By integrating patterns of gene flow with molecular adaptations to estimate species-specific adaptive potentials, we found that large sea distances and strong oceanographic barriers inhibit the genetic exchange of adapted genotypes across the WIO, providing valuable insights to guide local and regional biodiversity management in this region.

evolutionary biology↗

bioRxiv2024

A reference metagenome sequence of the lichen Cladonia rangiformis

[bullet] Lichens are an ancient symbiosis comprising the thalli of lichen-forming fungi, their photoautotrophic partners and their microbiome. So far, they were poorly studied at the genome sequence level. Here, we present a reference metagenome for the holobiont of Cladonia rangiformis. [bullet]Using long read sequences from an entire symbiotic complex, plus short read libraries from 28 additional diverse European lichen samples, we were able to separate genome sequences of 20 individual species. [bullet]We constructed chromosome-scale assemblies of the C. rangiformis fungus and its trebouxioid green algal photobiont Asterochloris mediterranea. The genome of the fungus comprises [~]22% transposable elements and is highly compartmentalized into genic regions and large TE-derived segments which show extensive signatures of repeat-induced point mutations (RIP). We found that A. mediterranea centromeres are predominantly derived from two interacting retrotransposon families. We also identified strong candidates for genes that were horizontally transferred from bacteria to both alga and fungus. Furthermore, we isolated 18 near-complete bacterial genomes, of which 13 are enriched in the lichen compared to surrounding soil. [bullet]Our study revealed that the thalli of C. rangiformis have a highly complex microbiome, comprising a mix of species that may include opportunists, ecologically obligate symbionts and possibly even lichen-beneficial bacteria.

evolutionary biology↗

bioRxiv2022

A survey of lineage-specific genes in Triticeae reveals de novo gene evolution from genomic raw material

Plant genomes typically contain [~]35,000 genes, almost all belonging to highly-conserved gene families. Only a small fraction are lineage-specific, which are found in only one or few closely related species. Little is known about how genes arise de novo in plant genomes and how often this occurs, however they are believed to be important for plants diversification and adaptation. We developed a pipeline to identify lineage-specific genes in Triticeae, using newly available genome assemblies of wheat, barley and rye. Applying a set of stringent criteria, we identified 5,942 candidate Triticeae-specific genes (TSGs), of which 2,337 were validated as protein-coding genes in wheat. Differential gene expression analyses revealed that stress-induced wheat TSGs are strongly enriched in secreted proteins. Some were previously described to be involved in Triticeae non-host resistance and cold adaptation. Additionally, we show that 1,079 TSGs have sequence homology to transposable elements (TEs), [~]68% of them deriving from regulatory non-coding regions of Gypsy retrotransposons. Most importantly, we demonstrate that these TSGs are enriched in transmembrane domains and are among the most highly expressed wheat genes overall. To summarize, we conclude that de novo gene formation is relatively rare and that Triticeae probably possess [~]779 lineage-specific genes per haploid genome. TSGs which respond to pathogen and environmental stresses, may be interesting candidates for future targeted resistance breeding in Triticeae. Finally, we propose that non-coding regions of TEs might provide important genetic raw material for the functional innovation of TM domains and the evolution of novel secreted proteins.

evolutionary biology↗