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Background  The color of berry skin is an important economic trait for grape and is essentially determined by the components and content of anthocyanins. The fruit color of Chinese wild grapes is generally black, and the profile of anthocyanins in Chinese wild grapes is significantly different from that of  Vitis vinifera . However,  V. davidii  is the only species that possesses white berry varieties among Chinese wild grape species. Thus, we performed a transcriptomic analysis to compare the difference of transcriptional level in black and white  V. davidii , in order to find some key genes that are related to anthocyanins accumulation in  V. davidii .    Results  The results of anthocyanins detection revealed that 3,5- O -diglucoside anthocyanins is the predominant anthocyanins in  V. davidii . It showed obvious differences from  V. vinifera  in the profile of the composition of anthocyanins. The transcriptome sequencing by Illumina mRNA-Seq technology generated an average of 57 million 100-base pair clean reads from each sample. Differential gene expression analysis revealed thousands of differential expression genes (DEGs) in the pairwise comparison of different fruit developmental stages between and within black and white  V. davidii . After the analysis of functional category enrichment and differential expression patterns of DEGs, 46 genes were selected as the candidate genes. Some genes have been reported as being related to anthocyanins accumulation, and some genes were newly found in our study as probably being related to anthocyanins accumulation. We inferred that  3AT  (VIT_03s0017g00870) played an important role in anthocyanin acylation,  GST4  (VIT_04s0079g00690) and  AM2  (VIT_16s0050g00910) played important roles in anthocyanins transport in  V. davidii . The expression of some selected DEGs was further confirmed by quantitative real-time PCR (qRT-PCR).    Conclusions  The present study investigated the transcriptomic profiles of berry skin from black and white spine grapes at three fruit developmental stages by Illumina mRNA-Seq technology. It revealed the variety specificity of anthocyanins accumulation in  V. davidi  at the transcriptional level. The data reported here will provide a valuable resource for understanding anthocyanins accumulation in grapes, especially in  V. davidii .    Electronic supplementary material  The online version of this article (doi:10.1186/s41065-016-0021-1) contains supplementary material, which is available to authorized users.

Transcriptome analysis of genes involved in anthocyanins biosynthesis and transport in berries of black and white spine grapes (Vitis davidii)