Biology subjects

Faino, L.

Publications and source records attributed to Faino, L..

12 recordsLinked to original sources

bioRxiv2026

Genome-wide structural variants uncover strain-specific genes and evolutionary genomic determinants of a fungal maize pathogen

Genomic structural variants (SVs) are important sources of genetic diversity and contribute to the adaptation and evolution of plant-pathogenic fungi. Colletotrichum graminicola, the causal agent of maize (Zea mays L.) anthracnose, causes significant yield losses and serves as an important model for genetic studies. To investigate genomic plasticity in this pathogen, long-read genome assemblies were generated for four C. graminicola field strains collected in France, Croatia, Brazil, and Argentina and compared with the chromosome-level reference genome from the USA. Comparative analyses revealed extensive structural variation across core chromosomes, including large-scale translocations, inversions, duplications, and insertions and deletions, whereas minichromosomes showed markedly reduced collinearity among strains. Secreted proteins and predicted effectors were located significantly closer to regions affected by SVs. Approximately 174 kb of segmental duplications lacking genes were shared between core chromosome 04 and minichromosomes 11 and 13 in the reference genome but were absent from the other field strains, revealing a strain-specific structural link between core and minichromosomes. Protein clustering identified 733 candidate strain-specific genes across the reference genome. Approximately 72% of the genes annotated on the minichromosomes were strain-specific, indicating that most of their annotated genes lacked orthologous gene models in the other strains. Of the 733 candidate strain-specific genes, 492 retained homologous genomic sequences in at least one other strain and many also showed evidence of gene disruption. This pattern is consistent with lineage-specific pseudogenization and suggests that apparent gene presence-absence variation may arise through several evolutionary processes, including gene gain, gene loss and loss of gene function. Insertions and deletions in potentially regulatory flanking regions were associated with plant-pathogen interaction genes. In addition, interpretable machine learning analyses revealed a co-occurrence of duplications and LTR retrotransposons in genomic regions associated with secreted genes. This study shows that structural variation, transposable elements, and lineage-specific pseudogenization are important features of genome evolution in C. graminicola and identifies associations between genomic variation and genes involved in plant-pathogen interactions.

genomics↗

bioRxiv2026

A structurally unique effector shared between Verticillium dahliae and Fusarium oxysporum is involved in cotton defoliation and virulence on other hosts

Defoliating (D) strains of the vascular wilt fungus Verticillium dahliae cause severe yield losses in cotton and olive worldwide, yet the genetic basis underlying this pathotype has remained unknown. Here, we combined comparative genomics, functional genetics, structural analysis, and phylogenomics to uncover the molecular determinant of defoliation. We identified a small, D pathotype-specific genomic region encoding two duplicated secreted effector genes. Simultaneous deletion of both gene copies abolished pathogenicity and defoliation in cotton, olive, Nicotiana benthamiana, and Arabidopsis thaliana, whereas single deletions reduced virulence and genetic complementation restored disease symptoms. Conversely, expression of the D effector in non-defoliating strains was sufficient to induce defoliation. Moreover, or exogenous application of the purified protein, induced wilting and defoliation as well. Structural analyses revealed that D homologs share a conserved but previously uncharacterized protein fold and are distributed across Verticillium and Fusarium species, exhibiting functional diversification and host-specific activity. Phylogenomic and genomic context analyses indicate repeated horizontal transfer events mediated by giant transposable elements known as Starships. Together, our findings identify the D effector as a central pathogenicity factor that drives defoliation and virulence, and demonstrate how Starship-mediated horizontal gene transfer shapes the emergence and dissemination of an agriculturally devastating fungal trait.

plant biology↗

bioRxiv2025

In genomes we trust: assessing genomic reliability within the family Nectriaceae

The Nectriaceae includes major plant and human pathogens, yet the genomic foundation underpinning its taxonomy remains uneven and largely unassessed. We analysed 1,530 genome sequence assemblies to quantify metadata completeness, geographic and taxonomic bias, and assembly quality across the family. One-third of the assemblies lacked essential metadata, sequencing was heavily skewed toward a few agriculturally important lineages, and sampling of many genera was limited or nonexistent. BUSCO and QUAST metrics revealed striking heterogeneity in assembly quality, with widespread fragmentation and a substantial subset of genomes falling outside the expected quality thresholds. From orthologous protein sequences of 763 single-copy genes in 576 high-quality genomes, we reconstructed a phylogenomic backbone for the Nectriaceae and quantified gene- and site-level concordance. While major clades broadly match current concepts, extensive gene-tree discordance and a polyphyletic Nisikadoi complex highlight unresolved evolutionary and taxonomic boundaries. Our study delivers the first integrated, family-wide evaluation of Nectriaceae genomic resources and outlines a framework for quality standards, curated metadata, and stable phylogenomic inference to support future taxonomic and comparative work.

genomics↗

bioRxiv2024

The Zymoseptoria tritici avirulence factor AvrStb6 accumulates in hyphae close to stomata and triggers a wheat defense response hindering fungal penetration

Zymoseptoria tritici, the causal agent of septoria tritici blotch, is one of Europes most damaging wheat pathogens, causing significant economic losses. Genetic resistance is a common strategy to control the disease, Stb6 being a resistance gene used for over 100 years in Europe. This study investigates the molecular mechanisms underlying Stb6-mediated resistance. Utilizing confocal microscopy imaging, we identified that Z. tritici epiphytic hyphae mainly accumulates the corresponding avirulence factor AvrStb6 in close proximity to stomata. Consequently, the progression of AvrStb6-expressing avirulent strains is hampered during penetration. The fungal growth inhibition co-occurs with a transcriptional reprogramming in wheat characterized by an induction of immune responses, genes involved in stomata regulation, and cell wall-related genes. Overall, we shed light on the gene-for-gene resistance mechanisms in the wheat - Z. tritici pathosystem at the cytological and transcriptomic level, and our results highlight that stomata penetration is a critical process for pathogenicity and resistance.

plant biology↗

bioRxiv2022

A single Verticillium dahliae effector determines pathogenicity on tomato by targeting auxin response factors

SUMMARYVerticillium dahliae is a xylem-invading fungal pathogen that causes devastating vascular wilt diseases on hundreds of plant hosts, including tomato (Solanum lycopersicum). Although individual V. dahliae strains are typically characterized by their broad host range, differential pathogenicity occurs on nearly all hosts. Currently, the molecular basis underlying such pathogenicity differences remains unknown. We used comparative genomics to identify a single effector gene that specifically occurs in tomato-pathogenic V. dahliae strains and is expressed during tomato colonization. Functional analyses showed that this Tom1 effector governs pathogenicity on tomato, as Tom1 deletion prohibited tomato colonization, while introduction of Tom1 into non-pathogenic V. dahliae or into saprophytic sister species V. tricorpus and V. nubilum resulted in disease. Through proteomics-based approaches, auxin response factors (ARFs) were identified as in planta targets of Tom1. Intriguingly, repression of SlARF2a expression by virus-induced gene silencing fully impaired V. dahliae colonization of tomato, solidifying its role as susceptibility target.Collectively, our findings indicate that a single effector, Tom1, mediates pathogenicity of V. dahliae on tomato by targeting auxin response factors.

plant biology↗

bioRxiv2022

A highly polymorphic effector protein promotes fungal virulence through suppression of plant-associated Actinobacteria

Plant pathogens secrete effector proteins to support host colonization through a wide range of molecular mechanisms, while plant immune systems evolved receptors to recognize effectors or their activities to mount immune responses to halt pathogens. Importantly, plants do not act as single organisms, but rather as holobionts that actively shape their microbiota as a determinant of health, and may thus be targeted by pathogen effectors as such. The soil-borne fungal pathogen Verticillium dahliae was recently demonstrated to exploit the VdAve1 effector to manipulate the host microbiota to promote vascular wilt disease in absence of the corresponding immune receptor Ve1. We now identified a multiallelic V. dahliae gene displaying ~65% sequence similarity to VdAve1, named VdAve1-like (VdAve1L). Interestingly, VdAve1L shows extreme sequence variation, including alleles that encode dysfunctional proteins, indicative of selection pressure to overcome host recognition. We show that the orphan cell surface receptor Ve2, encoded at the Ve1 locus, does not recognize VdAve1L. Furthermore, we show that the full-length variant VdAve1L2 possesses antimicrobial activity, like VdAve1, yet with a divergent activity spectrum. Altogether, VdAve1L2 is exploited by V. dahliae to mediate tomato colonization through the direct suppression of antagonistic Actinobacteria in the host microbiota. Our findings open up strategies for more targeted biocontrol against microbial plant pathogens.

plant biology↗

bioRxiv2022

ANTARCTIC FUNGI: A BIO-SOURCE ALTERNATIVE TO PRODUCE POLYUNSATURATED FATTY ACIDS (PUFAs)

The Antarctic ecosystem is a combination of conditions including extremely low values of temperature. The environmental temperature is one of the parameters thoroughly affecting the structure and composition of fungal membranes lipids. The psychrophilic fungi generally increase the disorder within macromolecules to maintain membrane fluidity at low temperatures. The strategy adopted by Antarctic fungi is to increase the proportion of unsaturated fatty acid that allows maintaining a semi-fluid state of the membranes. This ecological feature might be exploited for using Antarctic fungi as potential alternative source of polyunsaturated fatty acids (PUFAs) for human diet. This study provides both the characterization of fungal strains isolated from Antarctica by lipidomic analysis and the laboratory/large-scale production of fungal biomass with high content of beneficial PUFAs. In detail, three fungal species isolated from environmental matrices from Antarctica were tested and identified at genome level. Growth experiments to evaluate the influence of temperature and substrate in the yield in biomass and unsaturated fatty acid (UFA) were conducted. The results showed that the selected fungi have a high percentage of UFA compared to saturated ones; low growth temperatures increase the yield in linolenic fatty acid (C18:3); the biomass yield depends on the composition of the growth substrate and a satisfying qualitative-quantitative yield has also been obtained by using an agri-food chain waste product as growth substrate. IMPORTANCEThe presence of polyunsaturated fatty acids (PUFAs) in human and animal diet is gaining attention because PUFAs have several recognized functional properties: they modulate immune response, have anti-allergic and anti-inflammatory activity, cardio-protective effect and reduce blood LDL cholesterol levels. Human diets typically do not contain sufficient PUFAs because foods rich in PUFAs are few and it is therefore necessary to supplement this diet. Food supplements with these types of fatty acid currently commercially available come from marine fish oils and this source is no longer sustainable. It is necessary to develop efficient industrial processes capable of producing good quality PUFAs and in quantity, even using as carbon and nitrogen sources agro-industrial chains (in our case spent yeast from brewing and whey waste) waste products. Like microorganisms we used Antarctic fungi because they are adapted at very low temperature increasing the proportion of unsaturated fatty acid that allows maintaining a semi-fluid state of the membranes.

ecology↗

bioRxiv2020

Centromere evolution in the fungal genus Verticillium

ABSTRACTCentromeres are chromosomal regions that are crucial for chromosome segregation during mitosis and meiosis, and failed centromere formation can contribute to chromosomal anomalies. Despite this conserved function, centromeres differ significantly between and even within species. Thus far, systematic studies into the organization and evolution of fungal centromeres remain scarce. In this study, we identified the centromeres in each of the ten species of the fungal genus Verticillium and characterized their organization and evolution. Chromatin immunoprecipitation of the centromere-specific histone CenH3 (ChIP-seq) and chromatin conformation capture (Hi-C) followed by high-throughput sequencing identified eight conserved, large (∼150 kb), AT-, and repeat-rich regional centromeres that are embedded in heterochromatin in the plant pathogen V. dahliae. Using Hi-C, we similarly identified repeat-rich centromeres in the other Verticillium species. Strikingly, a single repetitive element is strongly associated with centromeric regions in some but not all Verticillium species. Extensive chromosomal rearrangements occurred during Verticillium evolution, yet only a minority could be linked to centromeres, suggesting that centromeres played a minor role in chromosomal evolution. Nevertheless, the size and organization of centromeres differ considerably between species, and centromere size was found to correlate with the genome-wide repeat content. Overall, our study highlights the contribution of repetitive elements to the diversity and rapid evolution of centromeres within the fungal genus Verticillium.IMPORTANCE The genus Verticillium contains ten species of plant-associated fungi, some of which are notorious pathogens. Verticillium species evolved by frequent chromosomal rearrangements that contribute to genome plasticity. Centromeres are instrumental for separation of chromosomes during mitosis and meiosis, and failed centromere functionality can lead to chromosomal anomalies. Here, we used a combination of experimental techniques to identify and characterize centromeres in each of the Verticillium species. Intriguingly, we could strongly associate a single repetitive element to the centromeres of some of the Verticillium species. The presence of this element in the centromeres coincides with increased centromere sizes and genome-wide repeat expansions. Collectively, our findings signify a role of repetitive elements in the function, organization and rapid evolution of centromeres in a set of closely related fungal species.View Full Text

genetics↗

bioRxiv2019

Nanopore sequencing for the detection and the identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material

Xylella fastidiosa (Xf) is a polyphagous gram-negative bacterial plant pathogen that can infect more than 300 plant species. It is endemic in America while, in 2013, Xf subsp. pauca was for the first time reported in Europe on olive tree in the Southern Italy. The availability of fast and reliable diagnostic tools is indispensable for managing current and future outbreaks of Xf. In this work, we used the Oxford Nanopore Technologies (ONT) device MinION platform for detecting and identifying Xf at species, subspecies and Sequence Type (ST) level straight from infected plant material. The study showed the possibility to detect Xf by direct DNA sequencing and identify the subspecies in highly infected samples. In order to improve sensitivity, Nanopore amplicon sequencing was assessed. Using primers within the set of the seven MLST officially adopted for identifying Xf at type strain level, we developed a workflow consisting in a multiple PCR and an ad hoc pipeline to generate MLST consensus after Nanopore-sequencing of the amplicons. The here-developed combined approach achieved a sensitivity higher than real-time PCR allowing within few hours, the detection and identification of Xf at ST level in infected plant material, also at low level of contamination. Originality Significance StatementIn this work we developed a methodology that allows the detection and identification of Xylella fastidiosa in plant using the Nanopore technology portable device MinION. The approach that we develop resulted more sensitive than methods currently used for detecting X. fastidiosa, like real-time PCR. This approach can be extensively used for X. fastidiosa detection and it may pave the road for the detection of other tedious vascular pathogens.

pathology↗

bioRxiv2018

Dynamic virulence-related regions of the fungal plant pathogen Verticillium dahliae display remarkably enhanced sequence conservation

Selection pressure impacts genomes unevenly, as different genes adapt with differential speed to establish an organisms optimal fitness. Plant pathogens co-evolve with their hosts, which implies continuously adaption to evade host immunity. Effectors are secreted proteins that mediate immunity evasion, but may also typically become recognized by host immune receptors. To facilitate effector repertoire alterations, in many pathogens, effector genes reside in dynamic genomic regions that are thought to display accelerated evolution, a phenomenon that is captured by the two-speed genome hypothesis. The genome of the vascular wilt pathogen Verticillium dahliae has been proposed to obey to a similar two-speed regime with dynamic, lineage-specific regions that are characterized by genomic rearrangements, increased transposable element activity and enrichment in in planta-induced effector genes. However, little is known of the origin of, and sequence diversification within, these lineage-specific regions. Based on comparative genomics among Verticillium spp. we now show differential sequence divergence between core and lineage-specific genomic regions of V. dahliae. Surprisingly, we observed that lineage-specific regions display markedly increased sequence conservation. Since single nucleotide diversity is reduced in these regions, host adaptation seems to be merely achieved through presence/absence polymorphisms. Increased sequence conservation of genomic regions important for pathogenicity is an unprecedented finding for filamentous plant pathogens and signifies the diversity of genomic dynamics in host-pathogen co-evolution.

microbiology↗

bioRxiv2017

Long Read Annotation (LoReAn): automated eukaryotic genome annotation based on long-read cDNA sequencing

Single-molecule full-length cDNA sequencing can aid genome annotation by revealing transcript structure and alternative splice-forms, yet current annotation pipelines do not incorporate such information. Here we present LoReAn (Long Read Annotation) software, an automated annotation pipeline utilizing short- and long-read cDNA sequencing, protein evidence, and ab initio prediction to generate accurate genome annotations. Based on annotations of two fungal and two plant genomes, we show that LoReAn outperforms popular annotation pipelines by integrating single-molecule cDNA sequencing data generated from either the PacBio or MinION sequencing platforms, and correctly predicting gene structure and capturing genes missed by other annotation pipelines.

bioinformatics↗

bioRxiv2017

Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss

The fungal genus Verticillium contains ten species, some of which are notorious plant pathogens causing vascular wilt diseases in host plants, while others are known as saprophytes and opportunistic plant pathogens. Whereas the genome of V. dahliae, the most notorious plan pathogen of the genus, has been well characterized, evolution and speciation of other members of the genus received little attention thus far. Here, we sequenced the genomes of the nine haploid Verticillium spp. to study evolutionary trajectories of their divergence from a last common ancestor. Frequent occurrence of chromosomal rearrangement and gene family loss was identified. In addition to ~11,000 core genes that are shared among all species, only 200-600 species-specific genes occur. Intriguingly, these species-specific genes show different features than core genes.

microbiology↗