De novo assembly and transcriptome characterization of spruce dwarf mistletoe Arceuthobium sichuanense uncovers gene expression profiling associated with plant development

BACKGROUND: The parasitic flowering plant dwarf mistletoe (Arceuthobium spp., Viscaceae) is one of the most destructive forest pests, posing a major threat to numerous conifer species worldwide. Arceuthobium sichuanense (spruce dwarf mistletoe, SDM) infects Qinghai spruce (Picea crassifolia) and causes severe damage to spruce forests in Northwest China. SDM is a Chinese native parasitic plant and acquires carbohydrates and mineral nutrition from its hosts. However, underlying molecular basis of the physiological development is largely unknown. Investigations of these physiological traits have been hampered by the lack of genomic resources for this species. RESULTS: In this study, to investigate the transcriptomic processes underlying physiological traits and development in SDM, we used RNA from four major tissues (i.e., shoots, flowers, fruits, and seeds) for de novo assembly and to annotate the transcriptome of this species. We uncovered the annotated transcriptome and performed whole genome expression profiling to uncover transcriptional dynamics during physiological development, and we identified key gene categories involved in the process of sexual development. The assembled SDM transcriptome reported in this work contains 331,347 assembled transcripts; 226,687 unigenes were functionally annotated by Gene Ontology analysis. RNA-Seq analysis using this reference transcriptome identified 22,641 differentially expressed genes from shoots, flowers, fruits, and seeds. These genes are enriched in processes including organic substance metabolism, cellular metabolism, biosynthesis, and cellular component. In addition, genes related to transport, transcription, hormone biosynthesis and signaling, carbohydrate metabolism, and photosynthesis were differentially expressed between tissues. CONCLUSION: This work reveals tissue-specific gene expression patterns and pathways of SDM and implied to a difference between photosynthetic and non-photosynthetic tissues in plants. The data can potentially be used for future investigations on endophytic parasitism and SDM-spruce interaction, and it dramatically increases the available genomic resources for Arceuthobium and dwarf mistletoe communities. This preliminary study of the Arceuthobium transcriptome provides excellent opportunities for characterizing plant parasitic genes with unknown functions. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3127-y) contains supplementary material, which is available to authorized users.