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Background  Tree peony ( Paeonia  section  Moutan  DC.) is known for its excellent ornamental and medicinal values. In 2011, seeds from  P. ostii  have been identified as novel resource of α-linolenic acid (ALA) for seed oil production and development in China. However, the molecular mechanism on biosynthesis of unsaturated fatty acids in tree peony seeds remains unknown. Therefore, transcriptome data is needed to better understand the underlying mechanisms.    Results  In this study, lipid accumulation contents were measured using GC-MS methods across developing tree peony seeds, which exhibited an extraordinary ALA content (49.3%) in  P. ostii  mature seeds. Transcriptome analysis was performed using Illumina sequencing platform. A total of 144 million 100-bp paired-end reads were generated from six libraries, which identified 175,874 contigs. In the KEGG Orthology enrichment of differentially expressed genes, lipid metabolism pathways were highly represented categories. Using this data we identified 388 unigenes that may be involved in  de novo  fatty acid and triacylglycerol biosynthesis. In particular, three unigenes ( SAD ,  FAD2  and  FAD8 ) encoding fatty acid desaturase with high expression levels in the fast oil accumulation stage compared with the initial stage of seed development were identified.    Conclusions  This study provides the first comprehensive genomic resources characterizing tree peony seeds gene expression at the transcriptional level. These data lay the foundation for further understanding of molecular mechanism responsible for lipid biosynthesis and the high unsaturated fatty acids (especially ALA) accumulation. Meanwhile, it provides theoretical base for potential oilseed application in the respect of n-6 to n-3 ratio for human diets and future regulation of target healthy components of oils.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1429-0) contains supplementary material, which is available to authorized users.

Fatty acid composition of developing tree peony (Paeonia section Moutan DC.) seeds and transcriptome analysis during seed development