Biology subjects

Dal Grande, F.

Publications and source records attributed to Dal Grande, F..

11 recordsLinked to original sources

bioRxiv2025

Sequencing a botanical monument: a chromosome-level assembly of the 400-year-old Goethe's Palm (Chamaerops humilis L.) at the Botanical Garden of the University of Padua (Italy)

The rapid decline in global biodiversity highlights the urgent need for conservation efforts, with botanical gardens playing a crucial role in ex situ plant preservation. Monumental plants, such as the 400-year-old Goethes Palm (Chamaerops humilis L.) at the UNESCO Botanical Garden of the University of Padua (Italy), serve as vital flagship species with significant ecological and cultural value. In this study, we present the first high-quality, chromosome-level genome assembly of C. humilis, using PacBio HiFi and Arima Hi-C sequencing technologies. This genome is the most contiguous and complete within the Arecaceae family to date, with an exceptionally high repeat content of 88%, of which 63% is attributed to Long Terminal Repeat (LTR) elements. Comparative analysis of the transposable element (TE) landscape in palms suggests that the LTR expansion in C. humilis is likely the result of recent TE bursts. Furthermore, we provide the first comprehensive annotation of microRNAs (miRNAs) in the Arecaceae family, identifying, for the first time in palms, the miRNA family miR827, which plays a key role in nutrient regulation. Microsatellite analysis suggests that it probably belongs to the Western genetic lineage of C. humilis. These findings represent a significant advancement in the conservation genomics of this species, laying the groundwork for enhanced preservation strategies, with botanical gardens as pivotal actors in the fight to safeguard global biodiversity.

genomics↗

bioRxiv2025

AI-based prediction of herbarium sequencing success across the plant tree of life

DNA recovered from herbarium specimens represents a vital asset in botanical research, playing a pivotal role in unravelling the evolution, diversity, and ecological dynamics of plants. Despite its importance, challenges such as fragmented DNA and insufficient sequencing yields render molecular data retrieval a high-risk and costly endeavour involving the use of non-replaceable herbarium specimens. Here, we propose a framework based on Artificial Intelligence (AI) to forecast the success of genomic DNA extraction suitable for sequencing from herbarium samples. Our model integrates morphological characteristics and sample colour derived from scanned herbarium images, metadata including sample age and locality, and DNA quantity measurements of samples. We train a deep learning algorithm with ca. 2,000 specimens that have been digitized and sequenced in the framework of the Plant and Fungal Trees of Life (PAFTOL) Project, spanning from year 1832 to the present. As training datasets increase with ongoing digitization and genomic sequencing efforts, our AI predictive model can support researchers in selecting the herbarium samples with the highest likelihood of yielding high-quality genomic DNA from amongst a vast array of globally distributed candidate specimens. Our approach enhances the contribution of herbarium-derived DNA in large-scale studies and facilitates the utilisation of historical collections for a deeper understanding of plant evolution and ecology, with implications for conservation.

plant biology↗

bioRxiv2022

Protein kinase gene declines linearly with elevation: a shared genomic feature across species and continents in lichenized fungi suggests role in climate adaptation

Intraspecific genomic variability affects a species adaptive potential towards climatic conditions. Variation in gene content across populations and environments may point at genomic adaptations to specific environments. The lichen symbiosis, a stable association of fungal and photobiont partners, offers an excellent system to study environmentally driven gene content variation. Many species have remarkable environmental tolerances, and often form populations in different climate zones. Here we combine comparative and population genomics to assess the presence and absence of genes in high elevation and low elevation genomes of two lichenized fungi of the genus Umbilicaria. The two species have non-overlapping ranges, but occupy similar climatic niches in North America (U. phaea) and Europe (U. pustulata): high elevation populations are located in the cold temperate zone and low elevation populations in the Mediterranean zone. We assessed gene content variation along replicated elevation gradients in each of the two species, based on a total of 2050 individuals across 26 populations. Specifically, we assessed shared orthologs across species within the same climate zone, and tracked which genes increase or decrease in abundance within populations along elevation. In total, we found 16 orthogroups with shared orthologous genes in genomes at low elevation and 13 at high elevation. Coverage analysis revealed one ortholog that is exclusive to genomes at low elevation. Conserved domain search revealed domains common to the protein kinases (PKs) superfamily. We traced the discovered ortholog in populations along five replicated elevation gradients on both continents. The protein kinase gene linearly declined in abundance with increasing elevation, and was absent in the highest populations. We consider the parallel loss of an ortholog in two species and in two geographic settings a rare find, and a step forward in understanding the genomic underpinnings of climatic tolerances in lichenized fungi. In addition, the tracking of gene content variation provides a widely applicable framework for retrieving biogeographical determinants of gene presence/absence patterns. Our work provides insights into gene content variation of lichenized fungi in relation to climatic gradients, suggesting a new research direction with implications for understanding evolutionary trajectories of complex symbioses in relation to climatic change.

genomics↗

bioRxiv2022

Genome mining as a biotechnological tool for the discovery of novel biosynthetic genes in lichens

The ever-increasing demand for novel drugs highlights the need for bioprospecting unexplored taxa for their biosynthetic potential. Lichen-forming fungi (LFF) are a rich source of natural products but their implementation in pharmaceutical industry is limited, mostly because the genes corresponding to a majority of their natural products is unknown. Furthermore, it is not known to what extent these genes encode structurally novel molecules. Advance in next-generation sequencing technologies has expanded the range of organisms that could be exploited for their biosynthetic potential. In this study, we mine the genomes of nine lichen-forming fungal species of the genus Umbilicaria for biosynthetic genes, and categorize the BGCs as "associated product structurally known", and "associated product putatively novel". We found that about 25-30% of the biosynthetic genes are divergent when compared to the global database of BGCs comprising of 1,200,000 characterized biosynthetic genes from planta, bacteria and fungi. Out of 217 total BGCs, 43 were only distantly related to known BGCs, suggesting they encode structurally and functionally unknown natural products. Clusters encoding the putatively novel metabolic diversity comprise PKSs (30), NRPSs (12) and terpenes (1). Our study emphasizes the utility of genomic data in bioprospecting microorganisms for their biosynthetic potential and in advancing the industrial application of unexplored taxa. We highlight the untapped structural metabolic diversity encoded in the lichenized fungal genomes. To the best of our knowledge, this is the first investigation identifying genes coding for NPs with potentially novel therapeutic properties in LFF.

genomics↗

bioRxiv2022

Tree size drives diversity and community structure of microbial communities on the bark of beech (Fagus sylvatica)

Tree bark constitutes ideal habitat for microbial communities, because it is a stable substrate, rich in micro-niches. Bacteria, fungi, and terrestrial microalgae together form microbial communities, which in turn support more bark-associated organisms, such as mosses, lichens, and invertebrates, thus contributing to forest biodiversity. We have a limited understanding of the diversity and biotic interactions of the bark-associated microbiome, as investigations have mainly focussed on agriculturally relevant systems and on single taxonomic groups. Here we implemented a multi-kingdom metabarcoding approach to analyse diversity and community structure of the green algal, bacterial, and fungal components of the bark-associated microbial communities of beech, the most common broadleaved tree of Central European forests. We identified the most abundant taxa, hub taxa, and co-occurring taxa. We found that tree size (as a proxy for age) is an important driver of community assembly, suggesting that environmental filtering leads to less diverse fungal and algal communities over time. Conversely, forest management intensity had negligible effects on microbial communities on bark. Our study suggests the presence of undescribed, yet ecologically meaningful taxa, especially in the fungi, and highlights the importance of bark surfaces as a reservoir of microbial diversity. Our results constitute a first, essential step towards an integrated framework for understanding microbial community assembly processes on bark surfaces, an understudied habitat and neglected component of terrestrial biodiversity. Finally, we propose a cost-effective sampling strategy to study bark-associated microbial communities across large spatial or environmental scales.

ecology↗

bioRxiv2022

A candidate gene cluster for the bioactive natural product gyrophoric acid in lichen-forming fungi

Natural products of lichen-forming fungi are structurally diverse and have a variety of medicinal properties. Despite this, they a have limited implementation in industry, because the corresponding genes remain unknown for most of the natural products. Here we implement a long-read sequencing and bioinformatic approach to identify the biosynthetic gene cluster of the bioactive natural product gyrophoric acid (GA). Using 15 high-quality genomes representing nine GA-producing species of the lichen-forming fungal genus Umbilicaria, we identify the most likely GA cluster and investigate cluster gene organization and composition across the nine species. Our results show that GA clusters are promiscuous within Umbilicaria, with only three genes that are conserved across species, including the PKS gene. In addition, our results suggest that the same cluster codes for different but structurally similar NPs, i.e., GA, umbilicaric acid and hiascic acid, bringing new evidence that lichen metabolite diversity is also generated through regulatory mechanisms at the molecular level. Ours is the first study to identify the most likely GA cluster, and thus provides essential information to open new avenues for biotechnological approaches to producing and modifying GA and similar lichen-derived compounds. We show that bioinformatics approaches are useful in linking genes and potentially associated natural products. Genome analyses help unlocking the pharmaceutical potential of organisms such as lichens, which are biosynthetically diverse but slow growing, and difficult to cultivate due to their symbiotic nature. ImportanceThe implementation of natural products in the pharmaceutical industry relies on the possibility of modifying the natural product (NP) pathway to optimize yields and pharmacological effects. Characterization of genes and pathways underlying natural product biosynthesis is a major bottleneck for the use of natural products in the pharmaceutical industry. Genome mining is a promising and relatively cost- and time-effective approach to exploit unexplored NP resources for drug discovery. In this study, we identify the most likely gene cluster for the lichen-forming fungal depside gyrophoric acid in nine Umbilicaria species. This compound shows cytotoxic and antiproliferative properties against several cancer cell lines, and is also a broad-spectrum antimicrobial agent. We identify the putative GA cluster from nine Umbilicaria species. This information paves the way for generating GA analogs with modified properties by selective activation/deactivation of genes.

genomics↗

bioRxiv2022

Phylogenomics reveals the evolutionary origin of lichenization in chlorophyte algae

Mutualistic symbioses have contributed to major transitions in the evolution of life. Here, we investigate the evolutionary history and the molecular innovations at the origin of lichens, which are a symbiosis established between fungi and green algae or cyanobacteria. We de novo sequence the genomes or transcriptomes of 12 lichen algal symbiont (LAS) and closely related non-symbiotic algae (NSA) to improve the genomic coverage of Chlorophyte algae. We then perform ancestral state reconstruction and comparative phylogenomics. We identify at least three independent gains of the ability to engage in the lichen symbiosis, one in Trebouxiophyceae and two in Ulvophyceae, confirming the convergent evolution of the lichen symbioses. A carbohydrate-active enzyme from the glycoside hydrolase 8 (GH8) family was identified as a top candidate for the molecular-mechanism underlying lichen symbiosis in Trebouxiophyceae. This GH8 was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer, concomitantly with the ability to associate with lichens fungal symbionts (LFS) and is able to degrade polysaccharides found in the cell wall of LFS. These findings indicate that a combination of gene family expansion and horizontal gene transfer provided the basis for lichenization to evolve in chlorophyte algae.

plant biology↗

bioRxiv2021

Elevation drives activity of soil bacteria, but not of bacterial viruses

Soil microbial diversity affects ecosystem functioning and global biogeochemical cycles. Soil bacterial communities catalyze a diversity of biogeochemical reactions and have thus sparked considerable scientific interest. One driver of bacterial community dynamics in natural ecosystems has so far been largely neglected: the predator-prey interactions between bacterial viruses (bacteriophages) and bacteria. To generate ground level knowledge on environmental drivers of these particular predator-prey dynamics we propose an activity-based ecological framework to simultaneous capture community dynamics of bacteria and bacteriophages in soils. An ecological framework and specifically the analyses of community dynamics across latitudinal and altitudinal gradients have been widely used in ecology to understand community-wide responses of innumerable taxa to environmental change, in particular to climate. Here, we tested the hypothesis that the activity of bacteria and bacteriophages co-decline across an elevational gradient. We used metatranscriptomics to investigate bacterial and bacteriophage activity patterns at 5 sites across 400 elevational meters in the Swiss Alps in 2015 and 2017. We found that metabolic activity (transcription levels) of bacteria declined significantly with increasing elevation, but activity of bacteriophages did not. We showed that bacteriophages are consistently active in soil along the entire gradient. Bacteriophage activity pattern, however, is divergent from that of their putative bacterial prey. Future efforts will be necessary to link the environment-activity relationship to predator-prey dynamics, to understand the magnitude of viral contributions to mobilize bacterial cell carbon when infection causes bacterial cell death, a process that may represent an overlooked component of soil biogeochemical cycles.

ecology↗

bioRxiv2021

Depside and depsidone synthesis in lichenized fungi comes into focus through a genome-wide comparison of the olivetoric and physodic acid chemotype of Pseudevernia furfuracea

Primary biosynthetic enzymes involved in the synthesis of lichen polyphenolic compounds depsides and depsidones are Non-Reducing Polyketide Synthases (NR-PKSs), and cytochrome P450s (CytP450). However, for most depsides and depsidones the corresponding PKSs are unknown. Additionally, in non-lichenized fungi specific fatty acyl synthases (FASs) provide starters to the PKSs. Yet, the presence of such FASs in lichenized fungi remains to be investigated. Here we implement comparative genomics and metatranscriptomics to identify the most likely PKS and FASs for the synthesis of olivetoric and physodic acid, the primary depside and depsidone defining the two chemotypes of the lichen Pseudevernia furfuracea. We propose that the gene cluster PF33-1_006185, found in both chemotypes, is the most likely candidate for olivetoric and physodic acid biosynthesis. This is the first study to identify the gene cluster and the FAS likely responsible for physodic and olivetoric acid biosynthesis in a lichenized fungus. Our findings suggest that gene regulation and other epigenetic factors determine whether the mycobiont produces the depside or the depsidone, providing the first direct indication that chemotype diversity in lichens can arise through regulatory and not only through genetic diversity. Combining these results and existing literature, we propose a detailed scheme for depside/depsidone synthesis.

genomics↗

bioRxiv2021

Transposable elements in the genome of the lichen-forming fungus Umbilicaria pustulata, and their distribution in different climate zones along elevation

BackgroundTransposable elements (TEs) are an important source of genome plasticity across the tree of life. Accumulating evidence suggests that TEs may not be randomly distributed in the genome. Drift and natural selection are important forces shaping TE distribution and accumulation, acting directly on the TE element or indirectly on the host species. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the hosts ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold-temperate. We trace the occurrence of the newly identified TEs in populations along three replicated elevation gradients using a Pool-Seq approach, to identify TE insertions of potential adaptive significance. ResultsWe found that TEs cover 21.26 % of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. Out of a total of 182 TE copies we identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. ConclusionsThis pioneering study into the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution. Particularly, it may serve as a foundation for assessing the impact of TE dynamics on fungal adaptation to the abiotic environment, and the impact of TE activity on the evolution and maintenance of a symbiotic lifestyle.

genomics↗

bioRxiv2019

What is in a lichen? A metagenomic approach to reconstruct the holo-genome of Umbilicaria pustulata

Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are generally poor candidates for experimentation. Obtaining contiguous, high quality genomes for such symbiotic communities is technically challenging. Here we present the first assembly of a lichen holo-genome from metagenomic whole genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis - the fungus Umbilicaria pustulata (33 Mbp) and the green alga Trebouxia sp. (53 Mbp) - were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative cellular abundance of approximately 20:1 (fungus:alga). Gap-free, circular sequences for all organellar genomes were obtained. The community of lichen-associated bacteria is dominated by Acidobacteriaceae, and the two largest bacterial contigs belong to the genus Acidobacterium. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that G/C-rich inverted repeats paired with non-random sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.

genomics↗