The next generation sequencing (NGS) technology has been changing many fundamental researches in biology. This technology can sequence millions of short DNA or RNA fragments parallelly and then reconstruct their original sequences by computer within few days. Thus, the deluged NGS data can help biologists to study questions in the whole genome scale, but also have many computational problems and challenges needed to be solved. In this talk, I will first give an overview of next generation sequencing, form why sequencing, what the first and second generation sequencing, to what the computational challenges. Then, I will describe what are the memory and speed problems for the current de novo assemblers of short read sequences and why our new developed method, called JR-Assembler, can conquer these two problems. In the last part, I will talk about how we provided a new study of gene duplication profiles in C4 photosynthesis evolution when analyzing the transcriptomic data of maize mesophyll and bundle sheath cells.