## 1 Introduction  
Endophytic fungi are known to be able to develop inside tissues of healthy plants during their life cycle without inducing obvious disease symptoms. After having been almost completely neglected for over a century, in the last decades, the concept of endophysism has been re-evaluated concomitantly to the increasing awareness of the important ecological role played by these microbial symbionts of plants, and of the opportunity to exploit their unique biocenotic aptitudes and biosynthetic properties [1, 2, 3]. 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 _Taxonyces andareane_, an endophyte of the Pacific very tree (_Taxus brewifolia_) producing taxol in axenic cultures [4]. Since, it has been documented for more and more strains recovered from plants from any environment and climatic area [5, 6, 7, 8], which represents an evident indication that, rather than being accidental, it is a common outcome of the intimate interactions established within these symbiotic communities. The possibility of the pharmaceutical industry effectively using endophytic fungal strains for a more economic production of some drugs clearly depends on a more thorough understanding of this biological phenomenon, particularly with insights on the conditions enabling the transfer of biosynthetic capacities between phylogenetically distant organisms. In this respect, genetic aspects have a basic relevance, starting from assessments concerning the share of a common gene base. Next-generation sequencing (NGS) methods enable faster and cheaper nucleotide sequencing than the traditional Sanger method, opening a new era in genomics and molecular biology. Compared to the Sanger capillary electrophoresis sequencing method, NGS technologies provide higher throughput data at lower costs and better support genome research [9]. These new sequencing methods share three major advantages. First, NGS libraries are prepared in a cell-free system instead of requiring bacterial cloning of DNA fragments. Second, they produce thousands to millions of sequencing reactions in parallel. Finally, base interrogation is performed cyclically and in parallel, so that the sequencing output is detected without electrophoresis. As a result, the enormous number of reads generated by NGS enables genome sequencing at an unprecedented speed [10]. During the past decade, NGS technologies have evolved through the incorporation of revolutionary innovations to tackle the complexities of genomes [11]. Short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor, and nanoball sequencing, maximize the number of bases sequenced in a short time, generating a wealth of data that can help understand complex phenotypes. Otherwise, long-read sequencing techniques aim to sequence longer contiguous DNA sectors, which is required to resolve structurally complex regions. Third generation long-read sequencing has the potential to overcome many limitations of the short-read approaches, e.g., the resolution of repeated sequences and large genomic rearrangements [11; 12]. The advancement in genome sequencing technologies has boosted genomics research by enabling many small laboratories to achieve sequencing of entire genomes. In addition, gene expression studies frequently shifted from microarrays to NGS-based methods, enabling the identification and quantification of transcripts without a preliminary knowledge of a particular gene, and providing information on alternative splicing and sequence variation [13]. Currently, efficient and modern NGS technologies are used in studies concerning endophytes due to their precision, sensitivity, and specificity. Hopefully, together with other approaches such as metabolomics, metagenomics, proteomics, and bioinformatics, they will fill a gap in fungal endophyte research.