Abstract
Recent investigations carried out all over the world have disclosed the capacity of a multitude of endophytic fungal species/strains to produce bioactive compounds which are the same or structurally related to those synthesized by their host plants. This intriguing phenomenon has implemented huge research activity aimed at ascertaining the nature of the biological processes underlying this convergence, as well as to characterize the genetic bases of the biosynthetic schemes. Insights on these basic issues may support the biotechnological exploitation of wild strains, and their eventual improvement through genome editing. Aspects concerning the use of next generation sequencing technologies for the comparative elucidation of the biosynthetic pathways operating in endophytic fungi and their host plants are reviewed in this paper in view of applicative perspectives. Our literature search yielded 21 references dealing with at least 26 strains which have been the subject of experimental activities involving massively parallel genome and transcriptome sequencing methods in the last eight years.
Highlights
Endophytic fungi are known to be able to develop inside tissues of healthy plants during their life cycle without inducing obvious disease symptoms
This paper provides an overview of published projects that utilized genome and transcriptome Next-generation sequencing (NGS) technology in endophytic fungi to elucidate biosynthetic pathways underlying bioactive metabolite production
A broad study was conducted on the genome and transcriptome of strain WP1 of Rhodotorula graminis, an endophyte isolated from Populus trichocarpa [77], revealing the absence of genes for the biosynthesis of indole-3-acetic acid (IAA) via indole-3-pyruvate and indole-3-acetate
Summary
Endophytic fungi are known to be able to develop inside tissues of healthy plants during their life cycle without inducing obvious disease symptoms. One of the possible biotechnological applications concerning this component of biodiversity derives from the capacity to synthesize bioactive products originally known as plant secondary metabolites This intriguing aptitude was first reported for Taxomyces andreanae, an endophyte of the Pacific yew tree (Taxus brevifolia) producing taxol in axenic cultures [4]. Based on evidence of physical clustering of genes for specialized plant metabolic pathways provided by an increasing number of reports [38], HGT is thought to be responsible for the transfer of whole gene clusters from host plants, conferring novel biosynthetic abilities to the associated fungi According to this hypothesis, many endophytes have developed the capacity to synthesize bioactive products originally known from their hosts, which has triggered the expectation to exploit endophytes as an alternative and sustainable source of important plant metabolites for relieving our dependence on plants. The development of sequencing and bioinformatics methods, as well as the availability of multiple strategies to comprehensively study genomes and transcriptomes [9,10,11], should allow the elucidation of biosynthetic pathways underlying the synthesis of bioactive secondary metabolites, including those operating in endophytic fungi
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