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Background  Kiwifruit is a perennial, deciduous and functionally dioecious plant. However, very little is known about the whole-genome molecular mechanisms contributing to distinct sexual phenotypes. To gain a global view of genes differentially expressed between male and female flowers, we analyzed genome-wide gene expression profiles in the flowers of male and female plants using high-throughput RNA sequencing.    Results  A total of 53.5 million reads were generated. Based on the alignments of unigenes to kiwifruit genome predicted genes, a total of 39,040 unique genes with a mean length of 970 bp were identified. There were 2,503 UniGenes differentially expressed between female and male flowers, with 1,793 up-regulated and 710 down-regulated in the female flowers. Moreover, the gene expression pattern of 17 out of 19 unigenes differentially expressed between male and female flowers revealed by RNA-Seq was confirmed by real-time quantitative PCR (qRT-PCR).    Conclusions  Here, we obtained a large number of EST sequences from female and male flowers of kiwifruit. This comparative transcriptome analysis provides an invaluable resource for gene expression, genomics, and functional genomic studies in  A .  chinensis  and its related species. This study also represents a first step toward the investigation of genes involved in kiwifruit sex determination.

Comparative transcript profiling explores differentially expressed genes associated with sexual phenotype in kiwifruit