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Objectives Cupressaceae is the second largest family of coniferous trees (Coniferopsida) with important economic and ecological values. However, like other conifers, the members of Cupressaceae have extremely large genome (&gt; 8 gigabytes), which limited the researches of these taxa. A high-quality transcriptome is an important resource for gene discovery and annotation for non-model organisms. Data description Juniperus squamata , a tetraploid species which is widely distributed in Asian mountains, represents the largest genus,  Juniperus , in Cupressaceae. Single-molecule real-time sequencing was used to obtain full-length transcriptome of  Juniperus squamata . 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 2839, were obtained. A total of 57,393 simple sequence repeats were identified and 268,854 open reading frames were predicted for  Juniperus squamata . A BLAST alignment against non-redundant protein database was conducted and 10,818 sequences were annotated in Gene Ontology database. InterPro analysis shows that 30,403 sequences have been functionally characterized against its member database. This data presents the first comprehensive transcriptome characterization of  Juniperus  species, and provides an important reference for researches on the genomics and evolutionary history of Cupressaceae plants and conifers in the future.

Building a reference transcriptome for Juniperus squamata (Cupressaceae) based on single-molecule real-time sequencing