Research Topic

Emerging tools for emerging symbioses—using genomics applications to studying endophytes

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About this Research Topic

Endophytes are abundant, diverse and play critical ecological roles across natural and agricultural ecosystems. Plants are typically colonized by hundreds of endophyte species symbiotically without any noticeable disease symptoms. Endophytes have attracted the attention of researchers from all over the world ...

Endophytes are abundant, diverse and play critical ecological roles across natural and agricultural ecosystems. Plants are typically colonized by hundreds of endophyte species symbiotically without any noticeable disease symptoms. Endophytes have attracted the attention of researchers from all over the world due to their various beneficial effects on plants. Several agricultural crops host numerous beneficial host-associated symbiotic bacteria and fungi, and genomic tools will enhance our understanding of the growth and nutritional requirements of the host-symbiont relationship in the crop plants. Understanding the host-endophyte systems is also important for development of biofuels and exploiting various plant–symbiont products.
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


Important Note: All contributions to this Research Topic must be in line with the scope of the specialty and field to which they are submitted, as defined in their mission statements. Manuscripts discovered during any stage of peer review to be outside of the scope may be transferred to a suitable section or field, or withdrawn from review.

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