Recent developments in, and widespread availability of, platforms, technologies, and computer software and hardware have enhanced the use of genetic markers to address major scientific questions in non-model organisms, even by researchers with limited expertise in genomics. However, there are few studies investigating the genomes of non-model insects using these approaches. This review discusses the application of next-generation sequencing (NGS) technologies to the study of genomes of wild organisms. We first introduce currently available NGS-based methods—including restriction site-associated DNA sequencing; multiplexed inter-simple sequence repeat genotyping by sequencing; target capture; and amplicon, transcriptome, and whole genome sequencing—as useful tools for studies of non-model insects. We also provide guidelines for first-time users of NGS systems. In addition to the massive amount of information that it provides, a major advantage of NGS data is the scalability to future research projects. Studies using NGS technology can answer questions related to basic entomology by focusing on the unique nature of non-model insects in wild environments in a way that is not possible for model organisms.
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