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Zanthoxylum , an ancient economic crop in Asia, has a satisfying aromatic taste and immense medicinal values. A lack of genomic information and genetic markers has limited the evolutionary analysis and genetic improvement of  Zanthoxylum  species and their close relatives. To better understand the evolution, domestication, and divergence of  Zanthoxylum , we present a  de novo  transcriptome analysis of an elite cultivar of  Z. bungeanum  using Illumina sequencing; we then developed simple sequence repeat markers for identification of  Zanthoxylum . In total, we predicted 45,057 unigenes and 22,212 protein coding sequences, approximately 90% of which showed significant similarities to known proteins in databases. Phylogenetic analysis indicated that  Zanthoxylum  is relatively recent and estimated to have diverged from  Citrus ca . 36.5–37.7 million years ago. We also detected a whole-genome duplication event in  Zanthoxylum  that occurred 14 million years ago. We found no protein coding sequences that were significantly under positive selection by  Ka / Ks . Simple sequence repeat analysis divided 31  Zanthoxylum  cultivars and landraces into three major groups. This  Zanthoxylum  reference transcriptome provides crucial information for the evolutionary study of the  Zanthoxylum  genus and the Rutaceae family, and facilitates the establishment of more effective  Zanthoxylum  breeding programs.

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De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development