Applications of High-Throughput Sequencing Chemistries in Decoding Pathogen Genomes

Genome sequencing enables us to determine the complete sequence of DNA in an organism’s genome (Cooper 2000). It has a rich history spanning several decades, with significant advancements in techniques and technologies. Genome sequencing of plant pathogens has been instrumental in understanding their biology, evolution, and mechanism of pathogenicity (Jackson et al. 2011). The first widely used method for genome sequencing was Sanger sequencing, developed by Frederick Sanger and his colleagues in the late 1970s, also known as the chain termination method (Hagemann 2015). Sanger sequencing relies on the incorporation of chain-terminating dideoxynucleotides during DNA synthesis, resulting in the production of DNA fragments of different lengths (Slatko et al. 2018). By separating these fragments based on their size using gel electrophoresis, the DNA sequence can be determined. The field of genome sequencing in plant pathogens started to gain momentum in the later 1990s and early 2000s (Li et al. 2018). During this time, several pioneering studies sequenced the genomes of important plant pathogens, such as bacteria, fungi, and viruses. These initial efforts provided insights into the genetic makeup of plant pathogens and their interactions with host plants. Genome sequencing has progressed from the labor-intensive Sanger sequencing approach to the highly efficient and cost-effective next-generation sequencing technologies (Niedringhaus et al. 2011).