Endophytic fungi are ubiquitously distributed organisms that colonise internal plant tissues conferring several benefits including plant growth promotion and enhanced protection against biotic and abiotic stresses. In recent years, endophytic fungi have gained a lot of attention and advances in high-throughput sequencing technologies have shed light on the complexities of plant-endophyte interactions. However, many of these studies have primarily focused on the host plant, leaving the molecular mechanisms deployed by the fungus relatively unexplored. Colletrotrichum tofieldiae strain 0861 (Ct0861) is an endophytic fungus originally isolated from Arabidopsis thaliana surface-sterilised leaves. Different studies have shown that this fungus is able to colonise the roots of both A. thaliana and other agronomically valuable hosts, providing several fitness advantages to the plants.
In this study, the genome of Ct0861 has been characterised in five different functional categories typically involved in host plant colonisation and interaction: secreted CAZymes, secreted proteases, effectors, transporters and genes involved in secondary metabolite biosynthesis. An RNA-Seq experiment was conducted to obtain transcriptomic data of the fungus interacting with maize at two different timepoints. The results obtained were used to perform a differential gene expression analysis. Functional categories within the differentially expressed genes were examined and functional enrichment analyses using Gene Ontology (GO) terms were performed. The same pipeline was applied to a second host plant, A. thaliana, from previously published raw transcriptomic data, allowing the comparison between the findings obtained in both hosts.
Overall, this study demonstrates that the genome of Ct0861 encodes extensive repertoires of genes across the different functional categories examined. These genes play crucial roles during the interaction with both hosts, as evidenced by the transcriptomic analyses. However, not all of them participate at the same level in the interaction with the plant: some genes, such as those encoding secreted proteases and transporters are highly induced during host colonisation at different timepoints and hosts, while genes involved in secondary metabolite biosynthesis exhibit low expression levels in planta, despite the high biosynthetic capacity of Ct0861.
The comparative analyses of Ct0861 transcriptomes in both host plants and at different timepoints reveal distinct temporal dynamics and functions, suggesting divergent strategies for the colonisation and establishment of trophic interactions with different hosts. The results from the GO enrichment analysis also highlight the relevance of polysaccharides metabolism and transport in the interaction of Ct0861 with the different hosts and across various timepoints. The insights gained with this work pave the way to future research aimed at elucidating the molecular bases of endophytism.
Endophytic fungi are ubiquitously distributed organisms that colonise internal plant tissues conferring several benefits including plant growth promotion and enhanced protection against biotic and abiotic stresses. In recent years, endophytic fungi have gained a lot of attention and advances in high-throughput sequencing technologies have shed light on the complexities of plant-endophyte interactions. However, many of these studies have primarily focused on the host plant, leaving the molecular mechanisms deployed by the fungus relatively unexplored. Colletrotrichum tofieldiae strain 0861 (Ct0861) is an endophytic fungus originally isolated from Arabidopsis thaliana surface-sterilised leaves. Different studies have shown that this fungus is able to colonise the roots of both A. thaliana and other agronomically valuable hosts, providing several fitness advantages to the plants.
In this study, the genome of Ct0861 has been characterised in five different functional categories typically involved in host plant colonisation and interaction: secreted CAZymes, secreted proteases, effectors, transporters and genes involved in secondary metabolite biosynthesis. An RNA-Seq experiment was conducted to obtain transcriptomic data of the fungus interacting with maize at two different timepoints. The results obtained were used to perform a differential gene expression analysis. Functional categories within the differentially expressed genes were examined and functional enrichment analyses using Gene Ontology (GO) terms were performed. The same pipeline was applied to a second host plant, A. thaliana, from previously published raw transcriptomic data, allowing the comparison between the findings obtained in both hosts.
Overall, this study demonstrates that the genome of Ct0861 encodes extensive repertoires of genes across the different functional categories examined. These genes play crucial roles during the interaction with both hosts, as evidenced by the transcriptomic analyses. However, not all of them participate at the same level in the interaction with the plant: some genes, such as those encoding secreted proteases and transporters are highly induced during host colonisation at different timepoints and hosts, while genes involved in secondary metabolite biosynthesis exhibit low expression levels in planta, despite the high biosynthetic capacity of Ct0861.
The comparative analyses of Ct0861 transcriptomes in both host plants and at different timepoints reveal distinct temporal dynamics and functions, suggesting divergent strategies for the colonisation and establishment of trophic interactions with different hosts. The results from the GO enrichment analysis also highlight the relevance of polysaccharides metabolism and transport in the interaction of Ct0861 with the different hosts and across various timepoints. The insights gained with this work pave the way to future research aimed at elucidating the molecular bases of endophytism. Read More
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