About this Research Topic
Recent advances in DNA sequencing technologies and bioinformatic pipelines have allowed analyzing the plant microbiome and host-endophyte interaction more effectively with limited biases. For example, the large-scale gene discovery performed on the grass fungal endophytes Neotyphodium coenophialum, Neotyphodium lolii, and Epichloë festucae led to the identification of molecular genetic markers such as single nucleotide polymorphism and simple sequence repeats. High-throughput transcriptome analyses including microarrays and RNAseq provide tools for analyzing treatment or genome-specific gene expression and facilitate the investigation of the host–symbiont interactions.
Genomic tools have enabled us to study endophyte host-symbiont associations. For example, a genomic analysis of endophytic Klebsiella pneumoniae identified metabolic pathways of plant-derived cellulosic and aromatic compounds and the corresponding transport genes. Comparative genomic analysis with pathogenic Klebsiella pneumoniae revealed critical divergences that influence preferred host ranges and lifestyles between the two strains. Furthermore, various studies have employed and utilized transcriptomic and genomic tools to understand the role of endophytic fungi and their interaction with plant hosts. This Research Topic will discuss and highlight the important developments on endophytes using these tools.
This Research Topic will have the following 5 sections:
1. Using next generation sequencing technologies to investigate plant microbiomes
2. Host-endophyte interaction
3. Endophyte genome and transcriptome analysis
4. Production of biofuels by endophytes
5. Endophytic bioactive compounds
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