Next Generation Sequencing Approach and Impact on Bioinformatics: Applications in Agri-Food Field

Author(s): Tiziana Maria Sirangelo, Grazia Calabrò

The advances in omics fields and the growth of high-throughput biological data required the use of bioinformatics tools to elaborate complex data, as well as the development of network resources, such as databases referred to specific biological fields and shared by the scientific community. This work mentions some of the main typologies of software tools used in the standard workflow of the NGS approach, focusing on the main problems associated with their use. Crucial applications in agri-food fields are also described. Particularly, in agricultural area it is highlighted how advanced bioinformatic tools made genome sequencing of key species possible, such as rice, grapevine, corn, tomato, potato, peach, barley, while numerous other sequencing projects are nearing completion. It is also shown how metagenomics approaches and complex software packages were applied to soil microbiome investigation. In the food microbiology area it is underlined how today the metagenomic techniques based on amplicon sequencing as well as on whole genome sequencing are widely used for analysing the microbial composition of products and for studying the microbiome and the mycobiome in the fermentative processes. Finally, some current needs are discussed. Among them relevant ones are those related to the elaboration of big amount of data provided by NGS data analysis, requiring new and more powerful bioinformatics resolutions to handle such large biological collections. Furthermore, specialized software tools and advanced computational resources for data integration are necessary.