Background: Tree tomato (Cyphomandra betacea (Cav.) Sendtn.) is a neglected, fast-growing, promising small fruit crop which provides a rich source of nutrition for human consumption. However, the transcriptome atlas of this important species is still lacking.Results: In this study, RNA samples from a broad diversity of tissues (roots, leaves, stems, flowers and fruits) of tree tomato were sequenced using Pacific Biosciences' long-read single-molecule real-time sequencing technology. A total of

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... 08699 full-length non-chimeric sequences with a mean length of 1005 bp and an N50 length of 1974 bp were obtained from our multi-tissue normalized cDNA libraries. A total of 140327, 104294, 135138, 78300, 53520, 152310 and 53520 transcripts were functionally annotated using Nr, Swiss-Prot, KEGG, KOG, GO, Nt and Pfam databases, respectively. Gene structural characteristics of the full-length transcriptome of tree tomato was subsequently investigated, including the predication of coding sequence and the identification of transcription factor families, long non-coding RNA and simple sequence repeat (SSR) marker. Thirty primers were randomly selected to evaluate the application of SSR markers, 23 of which obtained successfully amplification.Conclusions: This is the first confident characterization of FL transcriptome profiling of tree tomato. The large-scale and high-quality transcriptome atlas and SSR molecular markers provided in the present study will facilitate further genetic studies of this important species.