Equal amount of RNAs from the vegetative and flower buds were used to constructed cDNA libraries separately, and then sequenced. A total of 35,511,583 and 32,514,423 raw reads were obtained in the flower and vegetative buds, respectively. After removing the short raw reads and quality inspection by fastQC, the RNA-seq produced 35,510,239 and 32,513,288 clean reads for the flower and vegetative buds, respectively (Table 1). All of these reads were employed for further de novo assembly. And 189,300 contigs with an average length of 755 bp were generated using the Trinity software package. These contigs were assembled into 172,959 unigenes (200 to >10,000 bp) with an average length of 698 bp and an N50 (N50 represents weighted median length of all contigs) of 1340 bp (Table 2). Among them, 59,505 (34.4 %) unigenes were more than 500 bp. The size distribution of the assembled unigenes is shown in Additional file 2: Fig. S1. And this transcriptome shotgun assembly project has been deposited at DDBJ/EMBL/GenBank under the accession of GDHD00000000.Table 1Statistical summary of C. faberi transcriptome sequencing dataStatistics of data productionFlower budsVegetative budsRaw reads35,511,58332,514,423Raw bases5,326,737,4504,877,163,450Clean reads35,510,23932,513,288Clean bases5,280,378,5284,841,503,927Clean data rate (%)99.12599.27 Table 2Summary of assembly quality from transcriptome in C. faberi ContigsUnigenesTotal number189,300172,959Average length(bp)755.549698.016Max length(bp)11,79711,797Min length(bp)201201GC percentage (%)42.142.0Length of N50 (bp)14521340