Genome Assembly by a Non-bioinformatician: Case Study of a Small Predatory Natural Enemy Insect, Nesidiocoris tenuis

With advancements in genome sequencing technology and decreasing costs, whole-genome sequencing has become accessible for a wide range of species. Open-source software now enables researchers, including those without bioinformatics expertise, to perform whole-genome analyses on target species. In this chapter, we describe the approach taken by a non-bioinformatician to analyze the genome of Nesidiocoris tenuis, a small predatory insect used as a biological control agent in tomato cultivation in Europe and Asia. Our goal was to decode the entire genome to obtain genomic data to support breeding efforts for this species. We employed a combination of short- and long-read sequencing technologies, along with high-throughput chromosome conformation capture (Hi-C) analysis, to assemble the genome at the chromosomal level. While this protocol reflects our methodology as of 2022, more advanced techniques and software may be available today. Nevertheless, we hope that the core steps we followed and the challenges we encountered will benefit other biologists embarking on whole-genome-sequencing projects.