Biology subjects

Abraham, L. N.

Publications and source records attributed to Abraham, L. N..

8 recordsLinked to original sources

bioRxiv2025

Wheat infection by Fusarium graminearum species complex members is facilitated by a transcriptionally conserved non-ribosomal peptide synthetase gene cluster

Biosynthetic gene clusters (BGCs) are often found in fungal pathogens and encode secondary (or specialized) metabolites that play crucial roles in host and niche adaptation. However, the regulatory dynamics and functions of these BGCs during host infection remain largely unknown. To address this gap, we employed interspecies comparative transcriptomics to identify BGCs involved in host-pathogen interactions mediated by the Fusarium graminearum species complex (FGSC). We conducted joint transcriptomic and metabolomic analyses during wheat infection and in vitro experiments with five members of the FGSC to understand gene regulation during host infection. Our findings revealed that expression regulation was predominantly species-specific, but we also identified a set of shared upregulated genes that were common to all five FGSC species showing enrichment for metabolic and pathogenicity-associated functions. We focused on jointly upregulated BGC during infection and identified a NRPS-like gene cluster named SM3. The cluster was highly conserved within FGSC and shared by the more distant F. sambucinum species complex. We show that inactivation of the BGC core gene significantly impairs F. graminearum sensu stricto (s.s.) spore production, reduces fungal spread and Fusarium Head Blight symptoms on wheat kernels. Our results highlight that comparative infection transcriptomes can reveal conserved metabolic functions mediating the host infection process of a plant pathogen.

microbiology↗

bioRxiv2023

Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen

BackgroundIn agricultural ecosystems, outbreaks of diseases are frequent and pose a significant threat to food security. A successful pathogen undergoes a complex and well-timed sequence of regulatory changes to avoid detection by the host immune system, hence well-tuned gene regulation is essential for survival. However, the extent to which the regulatory polymorphisms in a pathogen population provide an adaptive advantage is poorly understood. ResultsWe used Zymoseptoria tritici, one of the most important pathogens of wheat, to generate a genome-wide map of regulatory polymorphism governing gene expression. We investigated genome-wide transcription levels of 146 strains grown under nutrient starvation and performed expression quantitative trait loci (eQTL) mapping. We identified cis-eQTLs for 65.3% of all genes and the majority of all eQTL loci are within 2kb upstream and downstream of the transcription start site (TSS). We also show that polymorphism in different gene elements contributes disproportionally to gene expression variation. Investigating regulatory polymorphism in gene categories, we found an enrichment of regulatory variants for genes predicted to be important for fungal pathogenesis but with comparatively low effect size, suggesting a separate layer of gene regulation involving epigenetics. We also show that previously reported trait-associated SNPs in pathogen populations are frequently cis-regulatory variants of neighboring genes with implications for the trait architecture. ConclusionsOverall, our study provides extensive evidence that single populations segregate large-scale regulatory variation and are likely to fuel rapid adaptation to resistant hosts and environmental change.

genomics↗

bioRxiv2023

Improved gene annotation of the fungal wheat pathogen Zymoseptoria tritici based on combined Iso-Seq and RNA-Seq evidence

Despite large omics datasets, the establishment of a reliable gene annotation is still challenging for eukaryotic genomes. Here, we used the reference genome of the major fungal wheat pathogen Zymoseptoria tritici (isolate IPO323) as a case study to develop methods to improve eukaryotic gene prediction. Four previous IPO323 annotations identified 10,933 to 13,260 gene models, but only one third of these coding sequences (CDS) have identical structures. To resolve these discrepancies and improve gene models, we generated full-length transcripts using long-read sequencing. This dataset was used together with other evidence (RNA-Seq transcripts and protein sequences) to generate novel ab initio gene models. The selection of the best structure among novel and existing gene models was performed according to transcript and protein evidence using InGenAnnot, a novel bioinformatics suite. Overall, 13,414 re-annotated gene models (RGMs) were predicted, including 671 new genes among which 53 encoded effector candidates. This process corrected many of the errors (15%) observed in previous gene models (coding sequence fusions, false introns, missing exons). While fungal genomes have poor annotations of untranslated regions (UTRs), our Iso-Seq long-read sequences outlined 5 and 3UTRs for 73% of the RGMs. Alternative transcripts were identified for 13% of RGMs, mostly due to intron retention (75%), likely corresponding to unprocessed pre-mRNAs. A total of 353 genes displayed alternative transcripts with combinations of previously predicted or novel exons. Long non-coding transcripts (lncRNAs) and double-stranded RNAs from two fungal viruses were also identified. Most lncRNAs corresponded to antisense transcripts of genes (52%). lncRNAs that were up or down regulated during infection were enriched in antisense transcripts (70%), suggesting their involvement in the control of gene expression. Our results showed that combining different ab initio gene predictions and evidence-driven curation using InGenAnnot improved the quality of gene annotations of a compact eukaryotic genome. Our analysis also provided new insights into the transcriptional landscape of Z. tritici, helping develop an increasingly complex picture of its biology.

genomics↗

bioRxiv2023

Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen

Rapid adaptive evolution is driven by strong selection pressure acting on standing genetic variation within populations. How adaptive genetic variation is generated within species and how such variation influences phenotypic trait expression is often not well understood though. Here, we focused on recent activity of transposable elements (TEs) using deep population genomics and transcriptomics analyses of a fungal plant pathogen with a highly active content of TEs in the genome. Zymoseptoria tritici causes one of the most damaging diseases on wheat, with recent adaptation to the host and environment being facilitated by TE-associated mutations. We obtained genomic and RNA-sequencing data from 146 isolates collected from a single wheat field. We established a genome-wide map of TE insertion polymorphisms in the population by analyzing recent TE insertions among individuals. We quantified the locus-specific transcription of individual TEs within the population and revealed considerable variation in transcription across individual TE loci. About 20% of all TE copies show activity in the genome implying that genomic defenses such as repressive epigenetic marks and repeat-induced polymorphisms are ineffective at preventing the proliferation of TEs in the genome. A quarter of recent TE insertions are associated with expression variation of neighboring genes providing broad potential to influence trait expression. We indeed found that TE insertions are likely responsible for variation in virulence on the host and secondary metabolite production. Our study emphasizes how TE-derived polymorphisms segregate even in individual populations and broadly underpin transcription and adaptive trait variation in a species.

genomics↗

bioRxiv2022

Genome-wide association mapping reveals genes underlying population-level metabolome diversity in a fungal crop pathogen

BackgroundFungi produce a wide range of specialized metabolites (SMs) involved in biotic interactions. Pathways for the production of SMs are often encoded in clusters of tightly arranged genes identified as biosynthetic gene clusters. Such gene clusters can undergo horizontal gene transfers between species and rapid evolutionary change within species. The acquisition, rearrangement and deletion of gene clusters can generate significant metabolome diversity. However, the genetic basis underlying variation in SM production remains poorly understood. ResultsHere, we analyzed metabolite production of a large population of the fungal pathogen of wheat, Zymoseptoria tritici. The pathogen causes major yield losses and shows variation in gene clusters. We performed untargeted ultra-high performance liquid chromatography-high resolution mass spectrometry to profile the metabolite diversity among 102 isolates of the same species. We found substantial variation in the abundance of the detected metabolites among isolates. Integrating whole-genome sequencing data, we performed metabolite genome-wide association mapping to identify loci underlying variation in metabolite production (i.e. metabolite-GWAS). We found that significantly associated SNP reside mostly in coding and gene regulatory regions. Associated genes encode mainly transport and catalytic activities. The metabolite-GWAS identified also a polymorphism in the 3UTR region of a virulence gene related to metabolite production and showing expression variation. ConclusionsTaken together, our study provides a significant resource to unravel polymorphism underlying metabolome diversity within a species. Integrating metabolome screens should be feasible for a range of different plant pathogens and help prioritize molecular studies.

microbiology↗

bioRxiv2021

Histone H3K27 methylation perturbs transcriptional robustness and underpins dispensability of highly conserved genes in fungi

Epigenetic modifications are key regulators of gene expression and underpin genome integrity. Yet, how epigenetic changes affect the evolution and transcriptional robustness of genes remains largely unknown. Here, we show how the repressive histone mark H3K27me3 influences the trajectory of highly conserved genes in fungi. We first performed transcriptomic profiling on closely related species of the plant pathogen Fusarium graminearum species complex. We determined transcriptional responsiveness of genes across environmental conditions to determine expression robustness. To infer evolutionary conservation of coding sequences, we used a comparative genomics framework of 23 species across the Fusarium genus. We integrated histone methylation data from three Fusarium species across the phylogenetic breadth of the genus. Gene expression variation is negatively correlated with gene conservation confirming that highly conserved genes show higher expression robustness. Furthermore, we show that highly conserved genes marked by H3K27me3 deviate from the typical housekeeping gene archetype. Compared to the genomic background, H3K27me3 marked genes encode smaller proteins, exhibit lower GC content, weaker codon usage bias, higher levels of hydrophobicity and are enriched for functions related to regulation and membrane transport. The evolutionary age of conserved genes with H3K27me3 histone marks falls typically within the origins of the Fusarium genus. We show that highly conserved genes marked by H3K27me3 are more likely to be dispensable for survival. Lastly, we show that conserved genes exposed to repressive H3K27me3 marks across distantly related fungi predict transcriptional perturbation at the microevolutionary scale in Fusarium fungi. In conclusion, we establish how repressive histone marks determine the evolutionary fate of highly conserved genes across evolutionary timescales.

genomics↗

bioRxiv2021

Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen

Background: Plant pathogens cause substantial crop losses in agriculture production and threaten food security. Plants evolved the ability to recognize virulence factors and pathogens have repeatedly escaped recognition due rapid evolutionary change at pathogen virulence loci (i.e. effector genes). The presence of transposable elements (TEs) in close physical proximity of effector genes can have important consequences for gene regulation and sequence evolution. Species-wide investigations of effector gene loci remain rare hindering our ability to predict pathogen evolvability. Results: Here, we performed genome-wide association studies (GWAS) on a highly polymorphic mapping population of 120 isolates of Zymoseptoria tritici, the most damaging pathogen of wheat in Europe. We identified a major locus underlying significant variation in reproductive success of the pathogen and damage caused on the wheat cultivar Claro. The most strongly associated locus is intergenic and flanked by genes encoding a predicted effector and a serine type protease, respectively. The center of the locus contained a highly dynamic region consisting of multiple families of TEs. Based on a large global collection of assembled genomes, we show that the virulence locus has undergone substantial recent sequence evolution. Large insertion and deletion events generated length variation between the flanking genes by a factor of seven (5-35 kb). The locus showed also strong signatures of genomic defenses against TEs (i.e. RIP) contributing to the rapid diversification of the locus. Conclusions: In conjunction, our work highlights the power of combining GWAS and population-scale genome analyses to investigate major effect loci in pathogens.

genomics↗

bioRxiv2020

A population-level invasion by transposable elements in a fungal pathogen

AO_SCPLOWBSTRACTC_SCPLOWGenome evolution is driven by the activity of transposable elements (TEs). The spread of TEs can have deleterious effects including the destabilization of genome integrity and expansions. However, the precise triggers of genome expansions remain poorly understood because genome size evolution is typically investigated only among deeply divergent lineages. Here, we use a large population genomics dataset of 284 individuals from populations across the globe of Zymoseptoria tritici, a major fungal wheat pathogen. We built a robust map of genome-wide TE insertions and deletions to track a total of 2,456 polymorphic loci within the species. We show that purifying selection substantially depressed TE frequencies in most populations but some rare TEs have recently risen in frequency and likely confer benefits. We found that specific TE families have undergone a substantial genome-wide expansion from the pathogens center of origin to more recently founded populations. The most dramatic increase in TE insertions occurred between a pair of North American populations collected in the same field at an interval of 25 years. We find that both genome-wide counts of TE insertions and genome size have increased with colonization bottlenecks. Hence, the demographic history likely played a major role in shaping genome evolution within the species. We show that both the activation of specific TEs and relaxed purifying selection underpin this incipient expansion of the genome. Our study establishes a model to recapitulate TE-driven genome evolution over deeper evolutionary timescales.

genomics↗