Solanaceae, Rosaceae, and Plantaginaceae exhibit the S-RNase-based gametophytic self-incompatibility (GSI) system. This type of GSI is controlled by a single polymorphic locus (S locus) containing the pistil S determinant gene, S-ribonuclease (S-RNase), and the pollen S determinant, the S locus F-box gene (SFB/SLF). In addition to these determinant genes, non-S factors, called modifier genes, are required for the GSI reaction. Here, we conducted large-scale transcriptome analysis of

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... , self-pollinated, and cross-pollinated pistils of Japanese apricot (Prunus mume Sieb. et Zucc. cv. Nanko) to capture all of the molecular events induced by the GSI reaction in Prunus, using next-generation sequencing technologies. We obtained 40,061 unigenes from 77,521,310 reads from pollinated and unpollinated pistils and pollen grains. Among these unigenes, 29,985 and 27,898 unigene sequences showed at least one hit against the NCBI nr and TAIR10 protein databases, respectively, in BLASTX searches using an E-value cutoff of 1e-6. Digital expression analysis showed that 8,907 and 10,190 unigenes were expressed at significantly different levels between unpollinated (UP) and cross-pollinated (CP) pistils and between UP and self-pollinated (SP) pistils, respectively. The expression of 4,348 unigenes in both CP and SP pollination was commonly and significantly different from that in UP, while the expression of 4,559 and 5,842 unigenes in CP and SP, respectively, was specifically and significantly different from UP. The expression of 2,227 unigenes was up-regulated both in CP and SP compared with UP. Genes supposedly involved in S-RNasebased GSI were included among the unigenes up-regulated by pollination, while no unigenes homologous to the solanaceous pistil modifiers HT-B or 120K were included among the unigenes up-regulated by pollination or in the whole unpollinated/pollinated pistil transcriptome. We discuss the distinct molecular mechanism of S-RNase-based GSI in Prunus.