The next-generation sequencing technologies are able to produce millions of short sequence reads in a high-throughput, cost-effective fashion. The emergence of these technologies has not only facilitated genome sequencing but also started to change the landscape of life sciences. Here, I survey their major applications ranging from whole-genome sequencing and resequencing, single nucleotide polymorphism (SNP) and structural variation discovery, to mRNA and noncoding RNA profiling and protein-nucleic acid interaction assay. These case studies in structural, functional and comparative genomics, metagenomics, and epigenomics are providing a more complete picture of the genome structures and functions. In the near future, we will witness broad impacts of these next-generation sequencing technologies for solving the complex biological problems in food, nutrition and agriculture. In this article, recent patents based information is also included.