Abstract Pepper (Capsicum) is an economically important genus of the Solanaceae family that also includes tomato and potato. Pepper has the same chromosome number as tomato and potato, but there is a huge difference in genome size between pepper and tomato/potato. Pepper genome expansion occurred after the pepper-tomato divergence (~36 Mya), which made it perfect model for genome evolution studies. Developments on research technology have led to the achievements of exciting investigation results in this field in the last decade. Pepper genome expansion, the types of chromosome rearrangements, whole genome duplication, fruit development biology, evolution of genes involved in capsaicin synthesis, and molecular footprints of artificial selection have been elucidated successively. In this paper, we review the research advances in genomics of pepper and make some suggestion for future investigation and provide a resource for genetic improvement and breeding programs.
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