## 6 Third-Generation Sequencing Technology for Fungal Genomics  
Advances in technologies for genome sequencing have generated a huge quantity of high-throughput and high-dimensional biological data [101]. Sequencing technology is rapidly evolving, and many options are now available for massively parallel DNA sequencing. By combining them with complementary methods, such as RNA-seq, hybrid sequencing, or ChIP-Seq, a greater insight into the genetic bases of biosynthetic pathways is now possible [12].  
Although the enormous numbers of reads generated by NGS have enabled genome sequencing at an unprecedented speed, this technology is not free from limitations. A drawback of NGS sequencing consists in relatively short reads, making genome assembly more difficult, with a need for the development of novel alignment algorithms [10]. Genomes of many organisms (especially of plant and fungi) are highly complex with many repetitive elements, copy number, and structural variations which are relevant for evolution and adaptation. Many of these elements are so long that they cannot be resolved through short-read paired-end technologies [11]. Therefore, other NGS methods have been developed, out of which the so-called third generation methods could be especially promising for the field of fungal genomics. Third-generation methods allow for the detection of single molecules, but sequencing occurs in real time as an additional common feature [102]. Readsin excess of several kilobases are delivered by such long-read sequencing, which allows for the resolution of these large structural features. These long reads can span repetitive regions with a single continuous read, which eliminates ambiguity in the position or size of genomic elements. Long reads can also be used in transcriptomic research, considering that they can span entire mRNA transcripts, thus allowing to identify the precise connectivity of exons and discern gene isoforms [11].  
Out of the third-generation sequencing technologies, two main types of long-read technologies in particular seem to be most suitable for fungal genomics, that is the single-molecule real-time sequencing approaches delivered by Pacific Biosciences (PacBio) [103] and Oxford Nanopore [104]. The advantages of nanopore sequencing for studying plant genomes, especially in the context of addressing challenges for producing high-quality, highly contiguous plant genome assemblies was recently demonstrated by Oxford Nanopore Technology [105]. Furthermore, there are more and more examples of using the advantages of the third-generation technology in the field of fungal genomics. The accurate long-read sequences obtained through the PacBio Sequel Systems were used to assemble the draft genomes of fungal endophytes isolated from _G. biloba_[83]. The genome of an endophytic strain of _Amphirosellinia nigrospora_ (JS-1675), isolated from _Pteris cretica_, was recently sequenced with the PacBio RS II technology [106]. This strain produces an oxygenated cyclohexanone, which is particularly effective against the agent of bacterial wilt of tomato, _Ralstonia solanacearum_, and various phytopathogenic fungi. Finally, genome sequence of an endophytic strain of _Gaeumannomyces_ sp. (JS-464), producing a new glycosylated anthraquinone and two new C-glycosated dialkylresorcinol derivatives, was generated using both the HiSeq 2000 (Illumina) and PacBio RSII platform [107].