Summary and assessment of the data set

<i>Juniperus squamata</i>, a tetraploid species which is widely distributed in Asian mountains, represents the largest genus, <i>Juniperus</i>, in Cupressaceae. Single-molecule real-time sequencing was used to obtain full-length transcriptome of <i>Juniperus squamata</i>. The full-length transcriptome was corrected with Illumina RNA-seq data from the same individual. A total of 47, 860 non-redundant full-length transcripts, N50 of which was 2, 839, were obtained. Simple sequence repeats for <i>Juniperus squamata</i> were also identified. This data presents the first comprehensive transcriptome characterization of Cupressaceae species, and provides an important reference for researches on the genomic evolutionary history of Cupressaceae plants and even conifers in the future.