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Background   Cupressus gigantea , a rare and endangered tree species with remarkable medicinal value, is endemic to the Tibetan Plateau. Yet, little is known about the underlying genetics of the unique ecological adaptability of this extremely long-lived conifer with a large genome size. Here, we present its first de novo and multi-tissue transcriptome in-depth characterization.    Results  We performed Illumina paired-end sequencing and RNA libraries assembly derived from terminal buds, male and female strobili, biennial leaves, and cambium tissues taken from adult  C. gigantea . In total, large-scale high-quality reads were assembled into 101,092 unigenes, with an average sequence length of 1029 bp, and 6848 unigenes (6.77%) were mapped against the KEGG databases to identify 292 pathways. A core set of 41,373 genes belonging to 2412 orthologous gene families shared between  C. gigantea  and nine other plants was revealed. In addition, we identified 2515 small to larger-size gene families containing in total 9223 genes specific to  C. gigantea , and enriched for gene ontologies relating to biotic interactions. We identified an important terpene synthases gene family expansion with its 121 putative members.    Conclusions  This study presents the first comprehensive transcriptome characterization of  C. gigantea . Our results will facilitate functional genomic studies to support genetic improvement and conservation programs for this endangered conifer.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5584-6) contains supplementary material, which is available to authorized users.

bmc genomics

In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species’ adaptability to environmental cues